ColSci preprints

Beyond abstract selection coefficients: Protandry impacts the buildup of heterozygote advantage over the lifespan in a color polymorphic moth

evolutionary biology
new results

Population genetic models excel at identifying the conditions for polymorphisms based on balancing selection but typically disregard the ecological processes that yield particular values of selection coefficients. We model a system that combines antagonistic pleiotropy, dominance reversal and heterozygote advantage: the wood tiger moth Arctia plantaginis, where alternative haplotypes at a major-effect locus determine male hindwing coloration. Yellow offers better protection against predators, while white is often associated with better mating success. The effects of mortality and reproductive success overlap in time because protandrous males can mate as long as they are alive, but they need to avoid predation for several days before the bulk of females emerge. We show that protandry aids polymorphism maintenance whenever the second-fittest genotype (after the heterozygote) is the poorly surviving but mating advantaged homozygote, while increased protandry harms polymorphism when the second-best fitness is that of the survival advantaged morph. Ecologically plausible protandry times predict that dominance reversal does not have to be strong for polymorphism to be maintained. Our study highlights the importance of timing traits in maintaining polymorphisms in Lepidoptera and showcases the benefits of deriving fitness explicitly in place of abstract selection coefficients that lack temporal components within the life cycle.

Mar 31, 2026
Selenius, E., Keaney, T., Winters, S., Mappes, J., Kokko, H.
CC BY-NC
https:/www.biorxiv.org/content/early/2026/03/31/2026.03.29.715091.source.xml

Replaying the Tape: Comparative Genomics of Color Pattern in Heliconius

evolutionary biology
new results

Understanding the repeatability of evolution requires disentangling the roles of constraint, contingency, and convergence in shaping phenotypic diversity. Mullerian mimicry in Heliconius butterflies offers a powerful natural experiment, with co-occurring species independently evolving similar wing color patterns under shared selective regimes. Here, we integrate high-throughput image-based phenotyping, genome-wide association studies (GWAS), and comparative pan-genomics to investigate the genetic architecture underlying convergent wing pattern evolution across parallel hybrid zones in Heliconius erato and H. melpomene. Using automated computer vision pipelines, we extracted and quantified color pattern variation from over 650 butterfly specimens. Principal component analysis (PCA) of recolorized, landmark-aligned wing images captured biologically meaningful axes of variation, which were used as phenotypes in GWAS. We identified strong associations at known patterning loci, including ivory:mir193 (previously coretex), optix, WntA, and vvl, as well as novel regions, including a chromosome 2 inversion in H. erato and a gustatory receptor gene (Gr21a) in H. melpomene. Comparative analyses using a Heliconius pan-genome revealed that while significant associations mapped to homologous regulatory regions across species, the specific variants were lineage-specific, consistent with parallel evolution via distinct cis-regulatory changes. These findings demonstrate that repeated adaptive outcomes can arise through different genetic paths within conserved regulatory architectures. More broadly, our study highlights the power of integrating machine learning, high-resolution phenotyping, and comparative genomics to dissect the molecular basis of convergent evolution in natural populations.

Mar 25, 2026
Lawrence, C. G., Rubenstein, D., McMillan, O., Arias, C.
CC BY-ND
https:/www.biorxiv.org/content/early/2026/03/25/2026.03.23.713665.source.xml

Beyond Gloger’s rule: multiple biogeographic drivers of dark and red colouration in ants

ecology
new results

Colour is a key trait involved in camouflage, physiological protection and thermoregulation. Yet environmental drivers of colour variation remain poorly understood at large spatial scales. Gloger’s rule predicts animals should be darker in warmer and wetter climates, and in a complex version, redder in warmer and drier climates. Here, we present the first test of the complex Gloger’s rule in insects using 34,331 images of 10,400 ant species across 586 assemblages worldwide. We decompose species mean colouration into two orthogonal axes, linked to darkness and redness. Assemblages were darker under high UV-B radiation and low dry-season precipitation, consistent with UV protection and desiccation resistance via melanisation. Canopy height increased both axes, suggesting camouflage. In contrast, higher mean temperature of the warmest quarter increased redness, as predicted by the complex Gloger’s rule. Ant colouration cannot be explained by one macroecological rule but reflects environmental drivers acting independently on darkness and redness.

Mar 18, 2026
Klaftenberger, T., Fisher, B. L., Perochon, E., Bertelsmeier, C., Ollier, S.
CC BY
https:/www.biorxiv.org/content/early/2026/03/18/2026.03.16.712184.source.xml

ATPLyzer An advanced ratiometric multi-colour biosensor for long-term monitoring of ATP dynamics

bioengineering
new results

Adenosine triphosphate (ATP) is a central molecule in cellular metabolism, serving as the primary energy currency that links catabolic and anabolic pathways. Monitoring intracellular ATP in vivo is essential for understanding the dynamics of metabolic states, as well as intracellular functions and intercellular interactions in health and disease. We report the design and application of ATPLyzer, a series of genetically encoded, ratiometric biosensors for the monitoring of ATP levels in living cells. The matryoshka design consists of an ATP-binding cassette linked to a circularly permutated GFP coupled with an internal large stokes shift reference fluorophore, allowing for single-wavelength excitation and ratiometric output. This design overcomes limitations of conventional biosensors, reliance on dual excitation wavelengths, and susceptibility to photobleaching. Multi-colour ATPLyzer variants with different dissociation constants were characterized in vitro, exhibiting high specificity for ATP over ADP. Monitoring ATP in Escherichia coli confirmed in vivo utility and revealed growth-phase and carbon-supply-dependent ATP dynamics. The ATPLyzer biosensor offers a robust and tuneable tool for minimally invasive, time-resolved monitoring of intracellular ATP dynamics.

Mar 17, 2026
Papadopoulos, A., Kaiser, C. F., Schlumpberger, P., Esser, J., Reiners, J., Gertzen, C. G. W., Grossmann, G., Smits, S.
CC BY-NC
https:/www.biorxiv.org/content/early/2026/03/17/2026.03.14.711787.source.xml

Mechanistic insights into the color transformation of a non-FRET substrate for RNase activity detection

bioengineering
new results

DNA-templated silver nanoclusters (DNA/AgNCs) have created a new class of non-FRET DNase substrates, termed Subak, that exhibits a color change upon DNase digestion. Although Subak substrates offer advantages such as ratiometric readouts and low manufacturing costs over traditional FRET substrates, the mechanism governing AgNC color switching remains unclear. Here, using a site-specific cleavage strategy, we identify color-switching hotspots and demonstrate that AgNC transformation can be controlled by the cleavage positions within the nucleic acid host. Our data support a cleavage-driven reorganization of the AgNC coordination environment, converting a non-emissive precursor into a red-emitting cluster, rather than direct enzyme-cluster interactions. Leveraging this insight, we engineer rSubak, an RNA-incorporated Subak that displays 95 nm red shift (530 to 625 nm) upon RNase cleavage. In amplification-free CRISPR/Cas13 assays for SARS-CoV-2, influenza A (A/H5N1), and measles viruses (MV) detection, rSubak achieved a limit of detection of 0.3 pM, superior to that of the commercial RNaseAlert (~250 pM). Collectively, our results establish Subak as a generalizable, non-FRET platform for sensitive ratiometric reporting the activities of diverse nucleases.

Mar 13, 2026
Kim, S., Hong, S., Walker, J. N., He, Y., Nguyen, A.-T., Chen, W.-R., Seifi, S., Chen, Y.-I., Kuo, Y.-A., Brodbelt, J. S., Yeh, H.-C.
CC BY-NC
https:/www.biorxiv.org/content/early/2026/03/13/2026.03.11.710959.source.xml

An empirical three-dimensional metric field for color space

neuroscience
new results

A complete empirical characterization of color discrimination in three dimensions has long remained out of reach. Classical studies, beginning with MacAdam’s ellipses, provided local measurements in restricted chromatic planes, but a spatially dense and internally consistent mapping of discrimination structure across full color space has not yet been achieved. Here we present such a systematic three-dimensional measurement of color discrimination in RGB space. Eight observers measured discrimination regions at 35 reference colors distributed on a body-centered cubic lattice within the RGB cube. At each location, color differences were probed along seven orientations, yielding 14 directional extents. These measurements defined centrally symmetric convex regions that were fitted with minimum-volume ellipsoids, providing a compact description of local discrimination structure. Ellipsoids were represented as symmetric positive-definite matrices and analyzed using a Frobenius geometry, enabling normalization across observers and smooth interpolation to arbitrary locations. The resulting metric field is spatially smooth, highly structured, and remarkably consistent across observers up to an individual global scale factor. Grain size increases along the achromatic axis and exhibits systematic chromatic asymmetries. Comparison with CIEDE2000 reveals substantial agreement in overall scale variation but systematic differences in local anisotropy. Together, these data provide a coherent three-dimensional empirical mapping of color discrimination across RGB space and establish an empirical framework for perceptual color metrics.

Mar 11, 2026
Koenderink, J., van Doorn, A., Braun, D. I., Gegenfurtner, K. R.
CC BY
https:/www.biorxiv.org/content/early/2026/03/11/2026.03.09.710376.source.xml

Construction of distinct k-mer color sets via set fingerprinting

bioinformatics
new results

The colored de Bruijn graph model is the currently dominant paradigm for indexing large microbial reference genome datasets. In this model, each reference genome is assigned a unique color, typically an integer id, and each k-mer is associated with a color set, which is the set of colors of the reference genomes that contain that k-mer. This data structure supports a variety of pseudoalignment algorithms, which aim to determine the set of genomes most compatible with a query sequence. In most applications, many distinct k-mers are associated with the same color set. In current indexing algorithms, color sets are typically deduplicated and compressed only at the end of index construction. As a result, the peak memory usage can greatly exceed the size of the final data structure, making index construction a bottleneck in analysis pipelines. In this work, we present a Monte Carlo algorithm that constructs the set of distinct color sets for the k-mers directly in any individually compressed form. The method performs on-the-fly deduplication via incremental fingerprinting. We provide a strong bound on the error probability of the algorithm, even if the input is chosen adversarially, assuming that a source of random bits is available at run time. We show that given an SBWT index of 65,536 S. enterica genomes, we can enumerate and compress the distinct color sets of the genomes to 40 GiB on disk in 7 hours and 17 minutes, using only 14 GiB of RAM and no temporary disk space, with an error probability of at most 2^(-82).

Feb 18, 2026
Alanko, J. N., Puglisi, S. J.
CC BY
.na.character

Robust individual alignment of color qualia structures: toward a structure-based taxonomy of divergent color experiences

neuroscience
new results

Whether qualitative aspects of consciousness, or qualia in short, are equivalent across individuals is a foundational scientific question. Testing this is challenging because one cannot assume a shared mapping between stimuli and private experience (my “red” may be your “green”). Previously, we proposed a structural characterization of qualia and the quantitative assessment of structural correspondences through an unsupervised alignment method, which does not presuppose such correspondence. Using this approach, our previous work focused on identifying optimal mappings between relational structures of color qualia at the group level. Given known perceptual diversities, however, it remained unknown whether any two individuals’ structures could be empirically aligned. Here, we resolve this by collecting 4,371 pairwise similarity ratings for 93 colors from 11 individuals, enabling direct individual-to-individual alignment. We reveal two fundamental, coexisting features. First, we identified two clusters of individuals showing robust within-cluster alignment, corresponding to color-neurotypicals and atypicals. Second, we uncovered a continuous spectrum of diversity: some participants who showed normal color discrimination ability in terms of the Total Error Score (TES) on Farnsworth-Munsell 100 hue test nevertheless failed to align with either cluster, revealing idiosyncratic structures that defy simple categorization. Together, these findings suggest a novel structure-based taxonomy of divergent color qualia that complements conventional performance-based classification. Our method is generalizable to other sensory modalities, and opens a path to the scientific investigation of both shared and idiosyncratic qualitative aspects of consciousness.

Feb 15, 2026
Togashi, Y., Yotsumoto, Y., Hiramatsu, C., Tsuchiya, N., Oizumi, M.
CC BY
.na.character

Urbanization drives parallel shifts in morphology and colouration of Pieris rapae across three cities

ecology
new results

Urbanization is a major driver of global environmental change, yet the evolutionary consequences for natural populations remain poorly understood. The cabbage white butterfly, Pieris rapae, is one of few butterfly species that thrives in cities, offering a unique opportunity to investigate whether urbanization drives parallel phenotypic evolution. In this study, we quantified phenotypic divergence between urban and non-urban populations across three independent metropolitan regions (Cleveland, Philadelphia, and Pittsburgh, U.S.), measuring body size, flight morphology, and wing pigmentation and reflectance in >500 field-caught individuals from 19 sites. Across regions, we found repeated reductions in overall body size and relative thorax mass in urban butterflies of both sexes, along with reduced relative forewing area in urban males, suggesting sex-specific impacts on mobility. Wing pigmentation showed limited urban-associated variation, but we detected novel sexual dimorphism in near-infrared reflectance within urban populations. Together, these results demonstrate repeatable divergence between urban and non-urban butterfly populations across multiple trait axes and suggest that plastic responses to urban stressors previously documented in experimental work manifest as consistent phenotypic shifts in natural populations.

Feb 14, 2026
McManus, C. A., Koski, M. H., Spigler, R. B.
CC BY-NC-ND
.na.character

Tracking Transgenes with Color: RUBY as a Visual Marker in CRISPR-Edited Mutant Plants in Two Triticum Species

plant biology
new results

CRISPR-Cas9 is a powerful tool for precise genome editing in plants, but the presence of foreign DNA, such as T-DNA, raises regulatory concerns and complicates mutant screening and field studies of edited material. Detecting plants with good transgene expression and later removing the T-DNA from edited plants is both time-consuming and costly. To address this, we developed a system that uses the non-destructive RUBY reporter, linked to the CRISPR-Cas9 cassette, and expressed under the ZmUbi1 promoter. To assess the applicability of the system, it was tested on two Triticum species, targeting three genes in either tetraploid or hexaploid wheat. Strong correlations were observed in both T0 and T1 plants between betalain content and Cas9 expression, allowing for the quick identification of plants likely to be edited. Furthermore, the RUBY reporter could be used to select against the transgenic CRISPR-Cas9 cassette in subsequent generations at both the seed and seedling stages, thereby reducing the number of plants that need to be screened to identify edited lines without a T-DNA. This approach, using a nondestructive reporter, enabled rapid distinction between transgene expression in primary transgenics and served as a negative selection in the T1 generation, streamlining selection towards edited and T-DNA-free progeny.

Feb 12, 2026
Kumar, R., Palayur, A., Lunde, C., Krasileva, K., Milner, M. J.
CC0
.na.character

Repeated evolution of convergent iridescence in closely-related species of Morpho butterflies living in sympatry

evolutionary biology
new results

The evolution of visual traits in closely-related species living in sympatry is highly influenced by their ecological interactions: while sexual selection tends to promote the divergence of visual cues involved in mate choice, natural selection via predation may promote the convergence of dissuasive signals between prey species, especially in unpalatable or evasive prey. Here, we investigate the impact of sympatry on the evolution of the blue structural colouration in the wings of two closely-related Morpho butterfly species across several localities throughout Central and South America. Dorsal iridescence might affect mate choice and species recognition, which should promote its local divergence among species. However, the bright flashes and dynamic colour patterns produced by iridescence during flight might also increase survival by confusing predators and favouring escape. Such an effect might in turn lead to convergence in wing iridescence between evasive species occurring in sympatry, a phenomenon dubbed evasive mimicry. To test the effect of these putative antagonistic selective forces on visual cues evolution, we quantified the variation of the structural blue colour displayed at 13 different combinations of illumination/observation angles, on the wings of two closely-related Morpho species. We contrasted 10 sympatric and 11 allopatric locations and specifically compared the phenotypic distances between individuals from different species. Phenotypic distances between heterospecific pairs of individuals were significantly smaller in sympatry, consistent with the hypothesis of a local convergence of iridescence due to evasive mimicry. Interestingly, sexual dimorphism was found between males and females, suggesting that the trade-off between natural and sexual selection on the evolution of iridescence might differ between sexes. Our results suggest that local predation pressures may promote repeated evolutionary convergence of structural colouration between evasive prey species living in sympatry.

Feb 9, 2026
Ledamoisel, J., Debat, V., Llaurens, V.
CC BY
.na.character

Predation and the Evolution of Island Bird Plumage Colouration: Experimental Insights from Island and Mainland Environments

evolutionary biology
new results

Islands serve as natural laboratories for exploring evolutionary processes, often fostering unique species through their isolation and distinct ecological conditions. These environments present opportunities to study how a range of selective pressures shape biodiversity. Bird plumage colouration is one trait that has shown to consistently change in island populations, and predation has been hypothesized to influence these differences. While animals often face a trade-off between signalling to conspecifics and avoiding detection by predators, the role of predation in shaping conspicuousness remains underexplored experimentally. In this study, we asked how predation pressure differs between insular and mainland habitats, and whether predation risk covaries with conspicuousness of male and female birds across environments. In a field experiment, we investigated predation rates using 3D-printed models painted to represent both sexes of 12 bird species from three archipelagos (Madeira, Azores, and Canary Islands) and their closest mainland relatives. These models were deployed in the species’ natural environments to measure hit rates (a proxy for predation risk), accounting for factors that influence prey detectability, such as colour of the models, background contrast, and vegetation. We found that models on the islands experienced less hits compared to those on the mainland, while sexual dichromatic models were more likely to be dislodged on the mainland. In addition, for mainland sites, increased chromatic contrast correlated with a higher probability of dislodgment, suggesting that more conspicuous models were more likely to be hit. These results highlight that while predation constrains conspicuousness, other ecological and evolutionary factors likely drive the reduced plumage colouration observed in island birds. Our research offers experimental insights into how predation interacts with conspicuous traits in shaping plumage colouration in birds.

Feb 3, 2026
Leitao, A. V., Alonso Moya, C. D., Lopes, R. J., Ponti, R., Covas, R., Doutrelant, C.
CC BY
.na.character

Peroxisome dysfunction alters metabolism of photoreceptor outer segments in human retinal pigment epithelium

cell biology
new results

Purpose: Peroxisomes are ubiquitous organelles that compartmentalize metabolic reactions including lipid catabolism and cellular detoxification. Biallelic loss-of-function variants in genes responsible for peroxisome assembly and function cause peroxisome biogenesis disorders (PBDs). Approximately three-quarters of PBDs are due to pathogenic variants in PEX1 or PEX6 and result in multisystem disease, including retinal degeneration and blindness. Despite retinal pigment epithelial (RPE) dysfunction and retinal degeneration occurring frequently in PBDs, precisely how impaired peroxisome activity disrupts retinal function remains to be fully explored. To address this, we differentiated PEX1 knockout (PEX1-/-), PEX6 knockout (PEX6-/-), and wildtype human induced pluripotent stem cells (iPSCs) into RPE to study the consequences of peroxisome dysfunction in this disease-relevant cell type. Methods: CRISPR/Cas9-mediated genome editing was used to generate PEX1-/- and PEX6-/- in human iPSCs. The knockouts and isogenic wildtype iPSCs were differentiated into RPE (iRPE) and characterized by morphology, pigmentation, transepithelial electrical resistance (TEER), and expression of proteins associated with differentiated RPE using immunofluorescence microscopy and flow cytometry. Immunoblot analysis of whole iRPE lysates was used to evaluate the proteolytic processing of peroxisome enzymes, a measure of the integrity of peroxisome matrix protein import. Immunofluorescence detection of peroxisome membrane proteins was used to determine the abundance of peroxisomes across iRPE lines. Targeted lipidomics by gas and liquid chromatography with mass spectrometry were used to quantitatively compare the profiles of wildtype, PEX1-/-, and PEX6-/- iRPE. Accumulation of intracellular neutral lipid, and more specifically lipid droplets, in iRPE was measured using flow cytometry and perilipin-2 immunoblotting, respectively. Phagocytosis of photoreceptor outer segments (POS) by iRPE was evaluated using rhodopsin immunoblotting. Results: PEX1-/-, PEX6-/-, and wildtype iRPE all had comparable hexagonal morphology and integrity of tight junctions, developed pigment, and similarly expressed proteins characteristic of RPE. Immunoblot analysis demonstrated aberrant processing of ACOX1, MFP2, and ACAA1 in PEX1-/- and PEX6-/- iRPE, suggesting impaired peroxisome matrix protein import. Targeted lipid profiling, including total fatty acid (FA) lipid profile analysis, revealed that in comparison to wildtype, PEX1-/- and PEX6-/- iRPE had significantly reduced docosahexaenoic acid (C22:6{omega}3) (p<0.001) and phosphoethanolamine plasmalogens (p<0.0001 for C18:0(plasm)-Total-PE), while very long-chain fatty acids (VLCFA) (p<0.001 for C26:0 and p<0.01 for C26:1{omega}9) and branched-chain FAs (p<0.01 for both pristanic acid and phytanic acid) were significantly elevated. Following a POS challenge, wildtype iRPE had significantly elevated eicosapentaenoic acid (C20:5{omega}3) (p=9.3E-5) and arachidonic acid (C20:4{omega}6) (p=0.013), both retroconversion products from the two most abundant polyunsaturated FAs in POS: C22:6{omega}3 and docosapentaenoic acid (C22:5{omega}6). PEX1-/-and PEX6-/- iRPE accumulated twice the amount of C22:5{omega}6 (p<0.05) relative to wildtype iRPE following a POS challenge, without a significant increase in C20:5{omega}3 or C20:4{omega}6, suggesting impaired {omega}3 and {omega}6 retroconversion pathways. Finally, PEX1-/-and PEX6-/- iRPE demonstrated delayed degradation of internalized POS based on rhodopsin immunoblotting, increased intracellular lipid droplets, and reduced TEER following a POS challenge. Conclusions: Our work has established the first human iRPE models to study the effects of peroxisome dysfunction in the RPE. Impaired peroxisome activity resulted in significant lipid profile changes and defective phagocytosis in iRPE. Dysregulated POS metabolism in the RPE is a potential mechanism driving retinal degeneration in patients with PBDs. Fully understanding the role of peroxisomes in the RPE will facilitate the development of novel therapies for degenerative retinal disorders.

Feb 3, 2026
Mouzaaber, C., Feldman, C. B., Huguenin, S. M., Han, J. Y. S., Trombly, E., Zhang, Q., Rieger, A., Hojjat, H., Huynh, B. C., Misaghi, E., Radziwon, A., Fufa, T. D., Hufnagel, R. B., Miller, J. M. L., Benson, M. D.
CC NO
.na.character

Syntaxin-3 regulates Tight Junction Assembly in Human Retinal Pigment Epithelium

cell biology
contradictory results

The retinal pigment epithelium (RPE) consists of polarized epithelial cells, serving as a support system for photoreceptor maintenance, where the polarity is contributed by the distribution of syntaxins (STX) within the cell. STX3, a known regulator of apical trafficking in epithelial cells, was previously understood to be absent in human RPE cells, with its functions thought to be compensated by STX1A. However, our results on SNARE mRNA expression profile in RPE detected the presence of 2 splice variants of STX3. Further investigation in donor retina, primary hRPE, and ARPE-19 cells revealed detectable levels of STX3 mRNA and protein. STX3 knockdown in ARPE19 resulted in a significant reduction of tight junction (TJ) proteins, compromising TJ assembly, highlighting the critical role of STX3 in maintaining RPE integrity. In addition, immunoprecipitation followed by LC-MS/MS analysis revealed that STX3 and STX1A have a distinct novel protein interactome in RPE. This study identified unique and shared interactants for STX3 and STX1A, suggesting a broader role for RPE beyond its traditional photoreceptor support function. This further emphasises the biological significance of STX1A and STX3 in maintaining retinal homeostasis, which could facilitate the development of novel therapeutic strategies for retinal disorders.

Feb 2, 2026
Ramesh, A., Sivagurunathan, S., Baburajan, N. V., Chidambaram, S.
CC NO
.na.character

A cryptic hybrid zone reveals the genomic basis of flower colour variation in a plant with a large and complex genome

evolutionary biology
new results

Flower colour is known to be an automatic magic trait, undergoing divergent selection pressures exerted by distinct pollinators and involved in reproductive isolation. However, variation at this trait may also results from other eco-evolutionary factors whose interpretation requires throughout context-specific analyses. Here, we investigated the eco-evolutionary causes of pink- and yellow-flowered morphs in Pedicularis comosa where their parapatric ranges form a contact zone: in the East of the Pyrenees Mountains. First, we generated a near-chromosome-scale reference genome assembly for this species. We then used a Genotyping By Sequencing approach to infer patterns of genetic diversity and differentiation between populations and morphs at a total of 158 individuals from 11 localities. We found that neutral genetic structure is primarily consistent with geography rather than with colour. However, admixture analyses and clines suggest the existence of a cryptic hybrid zone between morphs. Outlier detection methods and examination of locus-by-locus cline features, then allowed to pinpoint candidate loci to explain colour variation. To gain insight into the functional aspects of these loci, we finally analysed floral transcriptomes and quantified pigments using Liquid Chromatography coupled with Mass Spectrometry (LC-MS) and confirmed the involvement of key genes in the anthocyanin metabolic pathway (e.g. DFR, FLS) and associated pigments (e.g. cyanidin and delphinidin). Our results show that implementing a highly integrative multi-omic approach can allow unraveling the genetic basis and the eco-evolutionary significance of adaptive traits with even very limited previous knowledge, on species with large and complex genomes.

Feb 2, 2026
Salvado, P., Gibert, A., Chaib, S., Raviglione, D., Bertrand, C., El Baidouri, M., Mariault, L., Llauro, C., Cravero, C., Dufau, I., Marande, W., Carpentier, M.-C., Martin, M., Quelennec, C., Gaultier, P., Lewin, J.-M., Aymerich, P., Hinoux, V., Bertrand, J. A. M.
CC NO
.na.character

Quantitative muscle color as a proxy for structural and functional characteristics during muscle remodeling in Gryllus lineaticeps

physiology
new results

Understanding the cellular and physiological mechanisms underlying muscle remodeling requires model systems that allow rapid, reliable, and quantitative assessment of muscle state. The cricket Gryllus lineaticeps naturally undergoes non-pathological striated muscle breakdown (histolysis), making it a promising system for studying this process. However, current assessments of muscle state are largely qualitative, subjective, and poorly standardized across experiments. Here, we developed and validated a continuous, quantitative muscle color metric to objectively capture histolysis progression and functional changes in muscle. We show that this metric robustly tracks variation in muscle color across remodeling stages, including the challenging fully transparent stage, and strongly predicts protein content, mitochondrial abundance, and iron content in a muscle- and trait-specific manner. The reproducibility of these relationships across independent datasets demonstrates the generality and robustness of this approach. By providing a rapid, objective, and biologically informative proxy of muscle state, this framework not only advances the utility of G. lineaticeps as a model for muscle remodeling but also offers a strategy for exploring the cellular dynamics underlying age-related muscle diseases and disorders, addressing an increasing public health concern in aging populations.

Jan 30, 2026
Laturney, M., Martins, L., Diaz, T., Lo, E., Uen, N., Williams, C. M.
CC BY-NC-ND
.na.character

From Sensory Details to Verbal Codes: Visual Memory Reinstatement of Location and Color Features

neuroscience
new results

Successful episodic memory depends on the reinstatement of encoding content and processes during retrieval. However, it remains unclear how such reinstatement (1) differs for various perceptual features, (2) supports subjective versus objective memory retrieval, and (3) relies on linguistic information. To investigate these three issues, we designed an fMRI study in which participants encoded and recalled the colors and spatial locations of object pictures, and provided subjective vividness and objective precision measures. We used encoding-retrieval similarity (ERS) to identify feature-level reinstatement for location or color features, and trial-specific reinstatement for individual location trials or individual color trials. The study yielded three main findings. First, feature-level reinstatement in frontoparietal and visual regions supported both location and color memory, whereas trial-specific reinstatement in early visual cortex contributed to location memory and feature-level reinstatement in lateral/anterior temporal cortices, to color memory. Second, trial-specific reinstatement in early visual cortex supported both location vividness and precision, while feature-level reinstatement in inferior frontal gyrus contributed to color vividness, and trial-specific reinstatement in posterior inferior temporal gyrus (including the color area), to color precision. Finally, color name richness (the number of names associated with a particular color) enhanced color memory precision and modulated trial-specific color reinstatement in right anterior inferior temporal gyrus. Together, these findings suggest that perceptual and linguistic reinstatement play complementary roles in visual episodic memory: perceptual replay provides fine-grained sensory details, whereas linguistic replay can scaffold and refine these representations, especially for features that are easier to verbalize such as colors.

Jan 30, 2026
Wang, X., Becker, M., Rahman, R. A., Davis, S. W., Cabeza, R.
CC BY-NC
.na.character

Modulation of Avian Iridescence via Malanogenesis

evolutionary biology
new results

The iridescent colors of birds originate in nanoscale feather structures that interact with light. Although the physical principles governing avian iridescence are well-established, the molecular mechanisms assembling these nanostructures into photonic materials remain unknown. Here, we investigate the genetic and developmental basis of iridescence by analyzing mutations from peafowl domestication and color variation in wild birds. We show that melanogenesis governs diverse geometric aspects of feather photonic nanostructures, enabling gains, shifts, and losses in iridescence. Mutations altering melanin composition collapse multilayered photonic systems and yield non-iridescent tissues, while alterations to melanosome abundance, elongation, or deposition timing generate multilayer architectures of variable periodicity and striking color differences. Notably, transitions from non-iridescent to iridescent plumage can arise from single-nucleotide mutations in melanogenic genes, revealing that minimal genetic change can prompt feathers to organize photonic structures. These results demonstrate that the nanoscale order underlying iridescence is developmentally plastic, emerging from physicochemical self-assembly responsive to the biochemical environment rather than from genetically encoded spatial cues. Single-cell transcriptomes from wild species further uncovered extensive melanocyte-centered regulatory rewiring associated with iridescence. Our findings identify melanogenesis as a key pathway for evolving structural coloration and illustrate how genetic programs harness self-organizing processes to generate biological diversity.

Jan 27, 2026
Barbosa, S., Bittner, C., Arbore, R., Araujo, P., Pereira, P., Andrade, P., Fekete, C., Afonso, R., Afonso, S., Amorim, M., Marques, C., Nicolai, M., Carita, J., Brejcha, J., Lopes, R., Alves, J., Cruz, F., Gomez-Garrido, J., Zamarreno, C., Gut, M., Alyoto, T., Ali, M., Hilpert, A., Hech, A., Spiecker, E., Zubiri, B. A., Ito, S., Wakamatsu, K., Andersson, L., Corbo, J., Vogel, N., Carneiro, M.
CC BY-NC-ND
.na.character

A 14-Color Blue-Violet Laser Restricted Full Spectrum Flow Cytometry Panel for Comprehensive Immunophenotyping of Pulmonary Inflammation in Mouse Bronchoalveolar Lavage Fluid

immunology
new results

Here we describe a 16-parameter, 14-color surface staining panel optimized for murine bronchoalveolar lavage cells that enables reproducible identification of major innate and adaptive immune populations relevant to pulmonary infections or other inflammatory conditions of the airways. The panel enables confident identification of neutrophils, eosinophils, B cells, T cells and subtypes, NK cells, and distinguishes between tissue resident and monocyte-derived macrophages populations. The panel was carefully designed for BAL samples that vary in cell number, are rich in debris, and often autofluorescent. Antibody concentrations are optimized to provide reproducible results regardless of sample-variable cell numbers allowing for the preparation of a single antibody cocktail master mix and rapid sample staining time, thereby cutting down on sample preparation and optimizing cell viability of analyzed samples. The panel facilitates robust cross-sectional and longitudinal comparison of airway inflammation across different airway inflammatory conditions, infections by different respiratory pathogens, impact of vaccination or therapeutics on the inflammatory landscape, and more. It facilitates hypothesis generation by revealing recruitment kinetics and remodeling of myeloid compartments, supports downstream sorting for transcriptomic or functional assays, and provides a standardized baseline for labs to adopt or extend for activation or intracellular cytokine analyses. We have successfully utilized this panel to identify differential host responses to different respiratory Mycoplasma pathogens as well as to longitudinally track the progression of inflammatory response to Mycoplasma pneumoniae over a 21-day time course study. This panel provides an economic immunophenotyping option by utilizing only 14 markers and a two laser (Blue and Violet) full spectrum cytometer to provide comprehensive immunophenotyping power of both myeloid and lymphoid cells. Furthered by lacking the requirement for advanced unmixing for sample analysis, the panel can be easily adopted by the community, enabling comparative meta-analyses of host responses across murine respiratory infection models.

Jan 25, 2026
Mara, A. B., Miller, J. M., Ozyck, R. G., Hunte, M. L., Tulman, E. R., Szczepanek, S. M., Geary, S. J.
CC BY-NC-ND
.na.character

Rare shell colours in bivalves reveal multiple evolutionary pathways to blue and green colouration

evolutionary biology
new results

Green and blue are rare colours in bivalve shells. Where such colours occur, it is unclear whether they result from shared pigments across taxa, as similar appearances may arise from different compounds and are not necessarily homologous. Identifying their biochemical basis is therefore crucial to understanding the evolution and possible metabolic costs of these unusual traits. We used Raman spectroscopy to analyse resin-embedded cross-sections of valves from 15 bivalve species with green or blue shells. Species represented diversity in shell colour in terms of both phylogeny and morphological traits, including colour location (organic periostracum, organic layers in the calcareous shell or inorganic calcareous matrix). Green colour consistently occurred in organic layers rather than calcareous shell, while blue colour occurs in both calcareous shell and organic layers. Blue colour appears to be due to carotenoid-based pigments, similar to other pigments observed in bivalve shells. Green colour, however, is due either to novel pigments, not previously identified in mollusc shells, which are only weakly Raman active or nanostructures that produce structural colour in the absence of green pigments. Within bivalves, to date structural colour has been reported only in one genus, underscoring its evolutionary significance.

Jan 23, 2026
Ingram, A. L., Razzell Hollis, J., Williams, S. T.
CC NO
.na.character

Colour preference and constancy in the giant Asian honey bee Apis dorsata

animal behavior and cognition
new results

Tropical pollinators forage in environments where floral resources vary in space and time, requiring flexible strategies to optimise foraging efficiency. One such strategy, floral constancy - the temporary restriction to a single flower type - strongly influences foraging success and plant-pollinator interactions. We aimed to: (1) quantify spontaneous colour preferences and constancy in the Asian giant honeybee Apis dorsata, (2) test whether reward concentration modulates these preferences, (3) evaluate how quickly learned associations override spontaneous biases, (4) determine whether bees can use multiple colour associations simultaneously, and (5) assess whether local floral spectral patterns correlate with bee preferences. Bees trained to a neutral UV-grey stimulus showed a strong spontaneous preference and high constancy to blue, revealing a robust short-wavelength bias. Crucially, the strength of this spontaneous bias depended on reward concentration; Low-reward conditions elicited strong blue constancy, whereas high-reward conditions weakened it, demonstrating that reward expectation shapes spontaneous colour choices. This bias was flexible. When bees learned that yellow was rewarding, they switched their preferences. Bees sequentially trained to both colours visited blue and yellow, showing no overall bias, or effect of the last-trained colour, indicating that recent experiences disrupt colour-specific constancy and generate largely random foraging choices. Bees were capable of learning and retaining two colours simultaneously, effectively suppressing the influence of spontaneous preferences. Finally, analysis of the community floral spectral distribution revealed a strong dominance of short-wavelength flowers, suggesting that long-term selection by the local floral environment may underlie the spontaneous blue preference observed in A. dorsata.

Jan 21, 2026
Sudeep, R., Bhaskar, S., Somanathan, H.
CC NO
.na.character

EEG-Based Decoding of Color and Visual Category Representations Is Reliable Within and Across Sessions

neuroscience
new results

The human visual system represents stimuli in a rich and detailed manner. Traditional methods of studying visual representations in humans, such as event-related potentials (ERP), revealed numerous distinctions between the brain activity elicited by different categories of stimuli. However, these methods miss the information embedded in the spatial distributions of brain activity, or patterns, and are not always sensitive to study visual representations of different stimuli at the single participant or single trial level. Time-resolved multivariate pattern classification analysis (MVPA), or Decoding, efficiently extracts the visual representations of stimuli from the EEG topography without a-priori assumptions about the location of the effect in time and space at the single participant level. The rich information this method provides has increased its popularity dramatically in recent years. Yet, different participants show variable quality of decoding performance, and it is unclear if the accuracy of decoding is maintained within participants across multiple sessions, tasks, attentional conditions and visual features. In the current study, participants performed three visual tasks, over two sessions (1-7 days apart). We examined the correlation of decoding accuracy: within the cross-validation set, between sessions, between features (color and category) and to different measurements of the ERP signal and behavioral performance. We also examined how models generalized to different tasks and different attention conditions. We found that decoding accuracies varied substantially across participants, and that decoding accuracy was reliable within participant, over sessions, attention condition and task. This suggests the decodability behaves like an individual trait. Moreover, the spatial patterns underlying the decoding (classification weights) generalized across different tasks, attentional conditions and sessions. This suggests minimal representational drift at the resolution allowed by the EEG. We conclude that EEG decoding is a reliable method, and that visual representations are stable.

Jan 21, 2026
Frenkel, C., Deouell, L. Y.
CC BY
.na.character

An Adenine-Based Molecular Rotor as a Universal Fluorescent Nucleobase with High Brightness

biophysics
new results

Chemically modified nucleic acids have become a powerful platform for basic research and applied technologies. Universal nucleobases are used in PCR,sequencing, and the design of nanodevices and aptamers. Fluorescent universal nucleobases have an even wider range of applications, including the development of nucleic acid-based sensors, switches, and relay logic gates. However, few such nucleobases have been proposed to date, and most of them have suboptimal optical properties. Here, we propose an adenine-based molecular rotor, 7,8-dihydro-8-oxo-6-(3-methylbenzo[d]thiazol-2(3H)-ylidene)adenine (oxo-AdeBZT), as a new, remarkably bright and potent fluorescent universal nucleobase. Its brightness in both oligodeoxyribonucleotides (ODNs) and DNA duplexes (4200 - 10000 M-1 * cm-1) originates from a high molar extinction coefficient (averaged 37000 M-1 * cm-1), provided by the appended 3-methylbenzo[d]thiazolyl moiety, and a relatively high quantum yield (0.11 - 0.27). Melting temperature variations observed upon the incorporation of oxo-AdeBZT opposite native nucleobases in a duplex context did not exceed 10%. The basis of these universal hybridizing properties was unveiled using computational methods. According to molecular dynamics simulations, oxo-AdeBZT pushes the opposite nucleobase out of the DNA double helix and forms multiple hydrophobic contacts with the flanking base pairs. At the same time, the rotational mobility of the bonds between the oxo-AdeBZT-constituting heterobicycles decreases, and oxo-AdeBZT adopts a planar conformation in both ODNs and their duplexes, resulting in the light-up effect. These properties make oxo-AdeBZT a promising molecular tool for analytical, biophysical and biochemical studies.

Jan 18, 2026
Pushkarevskaya, A. A., Kamzeeva, P. N., Belyaev, E. S., Brylev, V. A., Lomzov, A. A., Aralov, A. V.
CC BY-NC
.na.character

Behavior evolves as a correlated response to selection on cuticle color in Drosophila melanogaster and D. simulans

evolutionary biology
new results

Understanding whether traits evolve independently or as integrated units is central to predicting adaptive evolution. Correlated trait evolution can reflect genetic covariation, such that selection on one trait can constrain or redirect evolutionary responses in others. Here, we used artificial selection on cuticle color in Drosophila melanogaster and D. simulans to investigate whether color and behavior evolve in tandem. We selected for light and dark thoracic colors across 16 generations in two populations per species and measured correlated responses in a suite of behavioral traits, including aggression, basal activity, total activity, sleep, and geotaxis. Dark selected individuals generally showed higher aggression and basal activity than light selected or control flies across both species and sexes, pointing to a modest but repeatable correlated response that must be interpreted in light of low and variable aggression in our assay. In contrast, patterns for geotaxis, sleep, and total activity evolved unpredictably, often varying across species and populations, and showed no clear or uniform association with color. Taken together, our results suggest that some behaviors may share a predictable relationship with color, whereas others behave largely independently under the conditions we examined. The persistence of correlated responses in aggression and basal activity in response to selection on color is consistent with a conserved genetic basis, such as pleiotropy or tight linkage, although our data do not, by themselves, distinguish among these mechanisms. Future work that identifies the loci underlying variation in both color and behavior and tests their effects experimentally will be important for clarifying how multivariate genetic covariance shapes the direction and pace of adaptive evolution.

Jan 14, 2026
Ruckman, S. N., Duffy, A. G., Mendez, P. M., McCaffery, K. D., Miller, S., Crews, A., Tan, N., Campbell, L. A., March, A., Brown, E. B., Houle, D.
CC BY-NC-ND
.na.character

Differential effectiveness of bee and beetle pollinators creates flower colour polymorphism

animal behavior and cognition
new results

Floral diversity is the hallmark of Angiosperms and is often shaped by pollinator-mediated selection, which drives floral divergence as plants evolve traits that attract specific pollinator groups. Mediterranean red, bowl-shaped flowers are specialized on pollination by glaphyrid beetles in areas with beetles and bees but evolved different colours and specialize on bees as pollinators when beetles are absent. What explains this geographic variation in specialization and concomitant flower colour differences? We assessed pollination effectiveness of honeybees and glaphyrids for the colour-polymorphic Anemone pavonina in its natural habitat. We recorded the duration and number of flower visits and quantified single-visit seed set. Per-visit effectiveness (relative seed set) was threefold higher for Pygopleurus (36.3%) than for honeybees (9.5%). Flower visitation lasted substantially longer for beetles (56.3 sec. on average) than for honeybees (2.3 sec.). For beetles, pollinator importance (single-visit seed set x visitation frequency) was highest at low elevations but declined with increasing elevation, whereas for bees pollinator importance remained low yet constant across the elevational gradient. The high pollinator effectiveness of beetles indicates that floral specialization for this pollinator group is advantageous, even to the point that excluding low-quality bee pollinators - by producing inconspicuous flower colours - is beneficial. Non-red flowers may only be beneficial at higher elevations, where bee pollinator importance exceeds that of beetles.

Jan 13, 2026
Heinze, J., van der Kooi, C. J., Spaethe, J.
CC BY-NC
.na.character

The cuticle lamellae responsible for structural coloration in red algae display common features with the metazoan extracellular matrix

biochemistry
new results

Structural coloration is a physical phenomenon observed in many living organisms, including seaweeds, via the formation of highly organized nanostructures. Although a widespread system is characterized by the deposition of multilayer thin-film in the extracellular matrix (ECM), enabling light interference, to date such lamellae have only been described in the cuticle of red algae belonging to the Gigartinaceae family within macroalgae. Here, we determine the composition of the multilayered cuticle components in the model species Chondrus crispus (Rhodophyta), using genomic, transcriptomic, proteomic, metabolomic and analytical profiling of carbohydrates. The complex structural assembly revealed common features with the ECM of animals. The carbohydrate fraction consists of a complex mixture of ECM carrageenans and glycosaminoglycan-like structures. A major von Willerbrand factor A domain (VWA) protein plays a critical role for the adhesion of macromolecules, including protein-protein interactions and to sulfated polysaccharides. We propose the name of Lamellae Cohesive Protein (LCP) regarding the alternate distribution of chemically distinct constituents within the cuticle. For the first time, we identified major proteins of the algal cuticle, providing a framework for addressing the evolutionary origins of the algal cuticle biosynthesis and raise important questions regarding its role, particularly across the life cycle marked by major structural ECM modifications.

Jan 12, 2026
Philippe, G., Godfroy, O., Beisson, F., Gautier, A., Jouanneau, D., Le Panse, S., Com, E., Delage, L., Czjzek, M., Ficko-Blean, E., Collen, J.
CC BY-NC-ND
.na.character

Lysosome-Related Organelles Orchestrate Guanine Crystal Formation in Pigment Cells

developmental biology
new results

Iridosomes, the guanine crystal-forming organelles of pigment-producing iridophores, are among the most versatile, visually striking yet mechanistically uncharacterized organelles in vertebrate biology. Lysosome-related organelles (LROs) support cell type-specific functions by adapting endolysosomal pathways for specialized roles. Here, we show that iridosomes represent a previously unrecognized subtype of LROs. Using transcriptomic profiling of zebrafish iridophores, CRISPR-Cas9-mediated gene disruption, and cryogenic transmission electron microscopy, we define the molecular program underlying iridosome biogenesis. Iridosomes have evolved unique adaptations for crystal growth while retaining core features of other LROs. Key regulators, including RAB32a, AP3M2, and HPS5, are essential for crystal formation, with gene knockouts causing reduced crystal number, altered morphology, and distinct maturation defects. We further identify hallmark LRO features in iridosomes, including intraluminal vesicles and pH-regulated developmental transitions. Cross-species transcriptomic analysis confirms that iridosomes share an LRO signature across vertebrates, including teleost fish and reptiles, suggesting ancient evolutionary origins. These findings establish iridosomes as crystalline LROs and as a model for investigating how cells construct structurally specialized organelles through coordinated trafficking, acid-base regulation, and crystallization, with implications for LRO evolution and human disease.

Jan 5, 2026
Gorelick-Ashkenazi, A., Barzilay, Y., Lerer-Goldshtein, T., Olender, T., Eyal, Z., Glaser, M., Broder, Y., Mishol, N., Deis, R., Kedmi, M., Gur, D.
CC BY-NC-ND
.na.character

Environmental Variation Promotes Convergent Evolution and Rapid Diversification of Wing Shape and Color in Skipper Butterflies

evolutionary biology
new results

Predation is a key driver of speciation and phenotypic diversification, yet how antipredator traits evolve and persist over evolutionary time remains poorly understood. We generated target sequence capture and whole-genome sequencing data for the skipper butterfly subfamily Eudaminae (Hesperiidae) to test whether antipredator defenses, in interaction with environmental variation, promote diversification. We focus on two antipredation wing traits: hindwing tails, which deflect predator attacks, and blue-green coloration, which may enhance motion dazzle and be used as warning coloration. Applying phylogenomics, morphometrics, and comparative methods, we model trait evolution in relation to diel activity and geographic distribution and find that hindwing tails repeatedly evolved at least seven times and blue-green coloration at least fifteen times. Both traits are associated with elevated speciation rates, but evolutionary transitions toward tailless wings and non-iridescent coloration occurred more frequently than trait gains, indicating high evolutionary lability of these antipredator defenses. Trait loss, particularly pronounced in tropical diurnal species, may reflect trade-offs in flight performance, shifts in predation guilds, or the evolution of alternative defensive traits. Our findings highlight rampant convergent evolution of wing traits that are under strong predator-mediated selection. By identifying how antipredator defenses and environmental contexts influence phenotypic and species diversification, this study provides new insights into the ecological and evolutionary processes underlying insect diversity.

Dec 27, 2025
Matos-Maravi, P., Linke, D., Ribeiro, P., Lamas, G., Freitas, A. V., Nunez, R., Kawahara, A. Y., Toussaint, E. F., Bacon, C. D., Wahlberg, N., Antonelli, A.
CC BY-ND
.na.character

Two-colour Imaging Fluorescence Correlation Spectroscopy (ImFCS) probes the influence of the juxta-membrane actin-cortex

biophysics
new results

Here we extend Imaging Fluorescence Correlation Spectroscopy (ImFCS), together with bright, photostable fluorophores, to quantify how the juxta-membranous actin cortex influences plasma membrane dynamics. This problem is technically challenging because the membrane is only a few nanometres thick, whereas the axial resolution of live-cell fluorescence imaging is on the order of 100 nm. We address this by engineering a membrane-anchored actin reporter that combines a weakly interacting actin-binding domain with bright, photostable fluorophores optimized for two-colour ImFCS. This design enables the generation of simultaneous, co-registered diffusion maps where the mobility of the reporter serves as a dynamic sensor for the local density of the cortical actin network. The actin-binding reporter displays diffusion coefficients spanning more than two orders of magnitude, in stark contrast to an otherwise similar reporter that cannot bind actin, which diffuses much faster and within a much narrower range. Thus, the mobility of the reporter becomes a sensitive spatial readout of actin-mediated constraints. By comparing, on a pixel-by-pixel basis, the diffusion of the actin-binding reporter with that of the non-binding mutant, we construct an actin-occupancy map that quantifies the fraction of the membrane functionally influenced by cortical actin. Using this approach, we find that the juxta-membrane actin cortex modulates transport over more than 80% of the cell surface. Our two-channel ImFCS strategy establishes diffusion-based comparison as a general methodology to map the functional footprint of the cortical cytoskeleton on live cell membranes.

Dec 25, 2025
Talluri, S., Krishna, P. S., Wohland, T., Mayor, S.
CC BY-NC-ND
.na.character

Museum genomics links MC1R alleles to adaptive winter coat color polymorphism in the long-tailed weasel

evolutionary biology
new results

Understanding the architecture of biological adaptations is a major endeavor of evolutionary biology. Using Natural History collections, we study the genetic basis and evolution of white/brown winter coat color variation in the long-tailed weasel (Neogale frenata), a crucial phenological adaptation for camouflage in habitats with seasonal snow. We produced whole-genome sequencing data for museum specimens, along two winter color morph transition areas in North America, at the West and East coasts. Genome-wide association scans identified a single genomic region linked to color variation polymorphism with approximately 300kb and 200kb in the West and East regions, respectively, which included the pigmentation gene MC1R. We identified three MC1R alleles, two of which with deletions of nine or eight amino acids, alternatively associated with the winter brown morphs in the West and East, respectively. These deletions affect the second transmembrane domain, and in one case also the first extracellular loop, which in silico analyses predicted to impact the protein’s function. Our findings show alternative intraspecific evolutionary solutions for environmental adaptation in long-tailed weasels, building on the evidence that major genes of the melanin production pathway are hotspots for recurrent and independent evolution of winter camouflage adaptation.

Dec 19, 2025
Pimenta, J., Miranda, I., Farelo, L., Alvarenga, M., Mills, L. S., Melo-Ferreira, J.
CC BY-NC-ND
.na.character

Temperature and Ultraviolet Radiation Drive Divergent Visible and Near-Infrared Reflectance Patterns in Butterflies

ecology
new results
  1. Climate change poses extreme risks to biodiversity, threatening the ecosystems upon which humanity depends. Understanding the traits that mediate how organisms respond to climatic gradients in space and time will enable better predictions of the taxa and ecological communities most at risk from warming. 2. In insects, colouration influences thermoregulation, but warming responses must be traded off against other selective pressures. We hypothesise that butterfly wing reflectance in visible and near-infrared (NIR) spectra respond differently to temperature and ultraviolet radiation over space and time. We combined existing reflectance data of 97 butterfly species in both NIR and visible wavelengths, with long-term abundance monitoring data of 120 butterfly communities sampled across 1650 m altitude gradients from May to August in two time periods (2004/5 and 2017). 3. The visible and NIR reflectances of butterfly communities showed a non-linear relationship with altitude, with the lowest reflectance (darkest butterflies) at the coolest, highest sites. In contrast, community visible reflectance decreased through the year as temperatures warmed over spring-summer, whereas community NIR reflectance remained constant, revealing divergent responses of reflectance types to seasonal changes. Temperature had opposing effects on visible and NIR reflectance of butterfly communities, where increasing temperature reduced community visible reflectance strongly while increasing community NIR reflectance slightly. 4. Considering the effects on reflectance of shared evolutionary history in a Bayesian hierarchical model for individual species, lighter-coloured (more reflective) species were associated with warmer temperatures - flying later in spring-summer or at lower altitudes. However, instead of decreasing in reflectance through the year and across temperature gradients, species instead became lighter, we expect as a result of a Simpson’s paradox. 5. These results emphasise how visible and NIR reflectance wavelength bands mediate butterflies’ responses to environmental gradients in distinct ways, despite being highly correlated across species. We also show that incorporating phylogeny into trait-environment models is essential; relying on traits alone would lead to incorrect inferences and predictions of taxa most at risk from warming climates.
Dec 18, 2025
Kou, C. Z. E., Kang, C., Brindle, M., Maclean, I., Bridle, J., Pigot, A. L., Wilson, R. J., Williamson, J.
CC NO
.na.character

Systematic comparison of color representations between humans and deep neural networks: towards predicting human color perception in a vast color space

neuroscience
new results

The representational structure of human color perception, particularly within vast color spaces, remains incompletely understood. While representational structures for dozens of colors have been studied, exploring structures spanning hundreds or thousands of colors has been infeasible due to the time costs of psychophysical experiments. Given these constraints, deep neural networks (DNNs) have attracted attention as a promising tool for providing proxies or predictions of human perception beyond the scope of psychophysical experiments. However, it remains unclear which DNN models possess internal representations that geometrically align with human color perception. Furthermore, it is unclear which learning paradigm enables DNNs to acquire a color representation that is geometrically aligned with that of humans. Here, we systematically investigate which learning paradigm enables DNNs to produce a color representation that is structurally congruent with that of humans, with a focus on three types: self-supervised learning (SSL) that trains on images alone, supervised learning (SL) that trains on images with category labels, and contrastive language-image pre-training (CLIP) that trains on image-text pairs. We compared internal representations of DNNs with the human similarity judgments of 93 colors using a rigorous unsupervised method termed Gromov-Wasserstein Optimal Transport (GWOT), which reveals whether the representational structures of humans and models align at the fine-item level. Our results show that only the CLIP paradigm acquires color representations that strongly align with human data at the fine-item level. Furthermore, when we leveraged a key advantage of DNNs and investigated a substantial representational structure of 4096 colors, the human-aligned CLIP models consistently converged on a non-trivial distorted ring-like structure, which presents a plausible prediction for the large-scale human color representation. Our work demonstrates an approach for exploring unknown territories of human perception through the use of computational models validated in a limited empirical space, and provides predictions for future large-scale psychophysical experiments.

Dec 13, 2025
Wickramanayaka, N. R., Oizumi, M.
CC BY
.na.character

Equiluminant Border Ownership Cells as a Missing Link in Color Form Perception

neuroscience
new results

We propose the existence of a sub-population of border ownership neurons that signal figure side along equiluminant borders, those defined purely by color contrast. We postulate that these neurons, similar to primate equiluminant V1 [26] and V4 [5] cells, are strongly activated by equiluminant contrast on their preferred side, with diminished response for strictly luminance contrast. To test this hypothesis, we propose a hierarchical and mechanistic model that explains how equiluminant border ownership signals can be achieved in the ventral stream. Our simulation results suggest that model equiluminant neurons are highly color-selective while exhibiting similar orientation and border ownership selectivity as their luminance counterparts. Additionally, our model equiluminant cells indeed exhibited the above postulated pattern of responses. We suggest that these neurons are the missing links in the equiluminance channels in the ventral stream that transform equiluminant oriented edge signals in V1 to equiluminant object-centered shape representations in V4. Our findings point to the importance of re-examining the border ownership neuron population to further detail their role in equiluminant channels in the ventral stream.

Dec 10, 2025
Mehrani, P., Tsotsos, J. K.
CC BY-NC
.na.character

Graded BMP signals modulate yellow and red color in fishes impacting adult pigment pattern and behavior

developmental biology
new results

Among the most interesting adult traits are those with roles in animal communication. Yet developmental mechanisms by which genes drive cell behaviors in building the final forms of such traits are rarely known. In this context, pigmentation is useful because colors and patterns often provide signals in mate choice, predation avoidance and other behaviors and pigmentation is unusually accessible to observation and manipulation. Here we focus on some of the most prominent signaling colors–red, orange and yellow–and show how BMP signaling at the cellular level allows for a very different kind of signal at the organismal level. Using pearl danio, Danio albolineatus, we find that spatially and temporally graded BMP signals promote development of yellow/orange xanthophores over red erythrophores in the fin of this species and a distantly related minnow, Tanichthys albonubes, and that conserved mechanisms, involving BMP co-receptor Rgmb, regulate differentiation of other pigment cell types in corresponding locations of zebrafish, D. rerio. We further use mutants of D. albolineatus with more red or more yellow cells than wild-type to demonstrate female responsiveness to carotenoid-based color differences between males in shoaling preference assays, and we show the existence of polygenic standing variation for this pigmentary trait. Our findings illustrate a chain of function spanning hierarchical levels and provide a deeper understanding of pigmentary form and function and its evolution.

Dec 9, 2025
Huang, D., de Mello, P. L. H., Liu, T., Liu, Y., Kapadia, E., Liang, Y., Lu, J., Corbo, J. C., Parichy, D. M.
CC BY-NC
.na.character

Damselflies Overcome Color Saturation Barriers of Photonic Glasses via Structural Dispersion and Pigment Loading

animal behavior and cognition
new results

Biology’s strategies for manipulating light offer rich inspiration for the design of sustainable replacements to conventional pigments in paints, coatings, and displays. For these applications, where angle-independent color is required, photonic glasses, composed of random arrangements of dielectric spheres, offer a promising solution. However, their intrinsic disorder, particularly from particle polydispersity, fundamentally limits their color saturation and practical utility. In contrast, insects like damselflies and dragonflies exhibit surprisingly vivid, non-iridescent structural colors, despite relying on disordered photonic structures. Here, we show how damselflies combine compositional and structural dispersion to overcome color saturation limits of photonic glasses. Firstly, doping transparent particles with yellow pigments dramatically enhances blue-green structural resonances by the coupled effects of narrowband absorption and refractive index (material) dispersion. Secondly, the refractive index of the nanospheres varies with their size and crystallinity. This gives rise to a ‘structural dispersion’ which maintains consistent optical path lengths in polydisperse assemblies, preserving high color purity. Finally, we show how damselflies tune their structural colors during maturation by precisely modulating the size of the nanospheres. Remarkably, the tuning of particle size, refractive index and pigment loading, arises naturally during the development of the pigment cells - where the pteridine nanospheres undergo a process of densification, crystallization and metabolic maturation.

Dec 2, 2025
Lemcoff, T., Alus, L., Batushansky, A., Fishman, Y., Theodor, N., Shavit, K., Hyitner, L., Kelber, A., Haataja, J., Oron, D., Palmer, B. A.
CC BY-NC-ND
.na.character

Egg colour mimicry in the common cuckoo results from coevolutionary alternation, not coevolutionary arms races

evolutionary biology
new results

The exquisite eggshell mimicry found in many cuckoo-host systems has been the textbook example of a coevolutionary arms race [1]. In this system, cuckoos lay their eggs in their hosts’ nests leaving these foster parents to rear their young [2]. In defence, most of these hosts have evolved the ability to recognize cuckoo eggs. It is long-assumed that these interactions select for ever-improving eggshell mimicry in cuckoo host-races laying distinct eggs that specifically mimic their host’s eggshell, regardless of its particular colour [3,4]. We challenge this paradigm and demonstrate that coevolutionary arms races and egg colour mimicry are the exception to the rule. Here, using eggshell reflectance spectra from 39 host species and the specific cuckoo eggs found in their nests, we show that eggshell colour mimicry is very uncommon even among frequent hosts. Although cuckoo eggs display considerable variation in eggshell colour, their hosts’ eggshell colours occupy 6 times their colour volume. As a result, mimicry is only achieved for a small subset of the egg colour gamut. Furthermore, cuckoo host-races rarely lay eggs that match their hosts’ eggs better than those of other potential hosts or that are distinct from those laid by other cuckoo host-races. These patterns are inconsistent with the long-held assumption of coevolutionary arms races, but consistent with coevolutionary alternation that is defined by a process of continual host-switching. These findings open new avenues for research in a system that has long served as a model for studying coevolutionary processes.

Dec 2, 2025
Hanley, D., Kepplinger, D., Nasir, A., Samas, P., Villa, J., de Alcantara Viana, J. V.
CC BY-NC-ND
.na.character

Spectral tuning and signaling of diverse and most red sensitive visual rhodopsins that drive high colour discrimination in Mantis Shrimp eyes

biophysics
new results

Of all visual systems shaped over billions of years, stomatopod crustaceans or mantis shrimps possess arguably one of the most extraordinary eyes, with unmatched potential for broad colour detection (T. W. Cronin & Marshall, 1989; J. Marshall & Oberwinkler, 1999; J. Marshall et al., 2007). Yet how their unusual diversity of visual opsins (Porter et al., 2020) maps onto functional spectral sensitivities (Streets et al., 2022; T. W. Cronin et al., 2022) has remained unresolved. Here, we uncover the molecular rhodopsin-based physiological mechanisms of spectral tuning and show that seventeen opsins, mostly from the colour-sensing midband of the Neogonodactylus oerstedii eye, exhibit distinct spectral absorption ranges and couple to Gq- or Gi-proteins. Two mid-wavelength opsins (NOMs) preferentially absorb blue light, while twelve long-wavelength opsins (NOLs) absorb in the green range. In addition, three NOLs are red-sensitive beyond 600 nm, representing the most far-red-sensitive opsins functionally characterized in animals. Several opsins exhibit photoreversibility with inverse blue-red spectral shifts, revealing an unrecognised layer of photochemical flexibility in stomatopod photoreception. Combined with ommatidial carotenoid filters, our mechanistic model shows how individually tuned rhodopsins shape row-specific spectral sensitivity across the eye, promoting far-red sensitivity in tier 3P in relation to other spectral wavelengths. These specialised rhodopsin-filter combinations collectively enable robust colour vision along a broad light spectrum and across dim and bright conditions, offering new insights into the evolution of one of Natures most sophisticated visual systems.

Nov 28, 2025
Brouillon, C., Pushkarev, A., Lienard, M. A., Hwang, S., Munhoven, A., McDowell, R. J., Lucas, R. J. J., Porter, M., Sun, H., Hegemann, P.
CC BY-NC
.na.character

charisma: An R package to perform reproducible color characterization of digital images for biological studies

evolutionary biology
new results
  1. Advances in digital imaging and software tools have provided increasingly accessible datasets and methods for analyzing color evolution. Despite the variety of computational packages available, most rely on color classification before running analyses. Previous methods limit the ability to analyze large-scale image databases, decreases the accuracy of downstream analyses, and is not always representative of biologically relevant color classes. 2. Here, we present charisma, an R package designed to characterize the distribution of distinct color classes in images suitable for large-scale studies of biological organisms. Here, we demonstrate the utility of our package through an analysis of color evolution in a sample of diverse and charismatic birds, tanagers, in the subfamily Thraupinae. 3. We show that charisma can quickly and accurately classify every pixel in an image and validate these results using pre-identified, canonical color swatches. We find that charisma color classifications are consistent with those made by color-pattern experts in the field. Applying charisma to tanager color evolution, we find that charisma outputs seamlessly integrate with downstream evolutionary analyses. 4. Our results demonstrate that using charisma to manually curate and characterize colors in images provides a standardized, reliable, and reproducible framework for high-throughput color classification.
Nov 27, 2025
Schwartz, S. T., Tsai, W. L. E., Karan, E. A., Juhn, M. S., Shultz, A. J., McCormack, J. E., Smith, T. B., Alfaro, M. E.
CC BY-NC
.na.character

Distinct NIR Reflectance Spectra Associated with Foliar Symptoms of Beech Leaf Disease

plant biology
new results

Beech leaf disease (BLD) is an epidemic spreading among American beech (Fagus grandifolia) populations, with characteristic symptoms including dark green, yellow, or brown bands of thickened leaf tissue between secondary veins. Whereas near infrared (NIR) light is reflected by leaf tissue structure, here we used multispectral NIR imaging to distinguish symptomatic from asymptomatic leaf reflectance, as well as to distinguish between different expressions of symptoms (dark green, yellow, and brown bands) within symptomatic leaves. Key findings include significantly higher NIR reflectance in dark green bands of symptomatic tissue compared to asymptomatic tissue ({lambda} = 840, 860, 900, 940, and 980 nm; [~]26.2%, 25.9%, 35.0%, 35.3%, and 32.5% increase respectively). A partial least squares regression model predicted 97% of variation in symptomatic vs. asymptomatic NIR reflectance was attributed primarily to the increase in spongy mesophyll thickness and overall leaf thickness in symptomatic tissue. Water infiltration of the intercellular airspaces in symptomatic and asymptomatic leaves removed differences in NIR reflectance, supporting a mechanistic link between increased NIR reflectance and the foliar symptoms of BLD. Our results highlight the interaction of leaf internal architecture with NIR wavelengths, and informs the development of targeted remote sensing tools, with implications for detecting even early-stage symptoms of BLD.

Nov 25, 2025
Moore, E. G., Dabydeen, L. C., Salha, R., Bichler, J., Borsuk, A. M.
CC BY-NC-ND
.na.character

Chemogenetic modulation of luciferase emission color for imaging and sensing

cell biology
new results

Bioluminescent luciferases have emerged as powerful tools for bioimaging, enabling to image biological systems without external excitation light, reducing thus phototoxicity and eliminating background autofluorescence. Advanced imaging requires luciferases that deliver high photon output for enhanced sensitivity, tunable emission colors for multicolor imaging, and red-shifted emission for effective deep tissue imaging. Here, we introduce LumiFAST, a small tunable luciferase engineered by fusing the bright blue-light emitting NanoLuc with the tunable chemogenetic fluorescent reporter pFAST. pFAST binds and stabilizes the fluorescent state of a variety of synthetic fluorogenic chromophores (also called fluorogens). Its proximity with NanoLuc leads to efficient bioluminescence resonance energy transfer (BRET), enabling customizable red-shifted emission. Thanks to the small size of pFAST, LumiFAST maintains a compact structure, while its modular design allows emission color to be tuned from cyan to green, yellow, orange and red simply by changing the fluorogen. Systematic optimization of the fusion topology and linker length yielded an optimal variant with apparent BRET efficiencies reaching up to 90 %. The red-shifted emission of LumiFAST enables dual-color microscopy imaging when used alongside NanoLuc and allows imaging through thick scattering media. Beyond imaging, our insights into the structural factors governing efficient BRET allowed us to engineer biosensors based on NanoLuc and pFAST for the visualization of protease activity and protein-protein interactions in live cells.

Nov 24, 2025
Manirakiza, H., Shpinov, Y., Gontier, A., El Hajji, L., Jullien, L., Gautier, A.
CC BY-NC-ND
.na.character

Peculiar Pigment Pattern and Population Profile of a Poisonous Pufferfish

evolutionary biology
new results

Pufferfish are well-known for their toxicity, yet they also exhibit a remarkable diversity of pigment patterns. Mushifugu (Takifugu exascurus) is a pufferfish endemic to Japan’s coastal waters and is characterized by conspicuous labyrinthine patterns. Despite being recorded along both the Sea of Japan and the Pacific coasts, it has a limited distribution and is infrequently observed. Aside from its unique body pattern, mushifugu shows little to no morphological differences from other Takifugu species, often leading to speculation that it may be an interspecific hybrid. In addition, previous theoretical and empirical studies have shown that complex camouflage-like labyrinthine patterns can emerge through the ‘pattern blending’ caused by hybridization between spotted species, providing support for this possibility. Here, we investigate the phylogenetic origin of mushifugu and its distinctive pattern through population structure analysis and demographic inference in comparison with its closest spotted relative, komonfugu (T. flavipterus). Mitochondrial DNA (mtDNA) analysis revealed two regional haplogroups within mushifugu–one in the Sea of Japan (SJ) and the other in the Pacific Ocean (PO). In the haplotype network, the SJ haplogroup formed a distinct cluster, whereas the PO haplogroup appeared as its own cluster connected to the komonfugu haplogroup. By contrast, genome-wide SNP analyses indicated limited structure between the SJ and PO mushifugu populations, while clearly separating mushifugu from komonfugu. Coalescent-based demographic inference suggested that the two species diverged following a bottleneck event in the early Pleistocene. These results confirm that mushifugu is a distinct species rather than a recent interspecific hybrid. Nevertheless, evidence of introgression was detected in both mitochondrial and nuclear genomes, suggesting multiple episodes of past hybridization between mushifugu and komonfugu, highlighting the potentially complex evolutionary processes shaping Takifugu species and their pigment patterns.

Nov 20, 2025
Miyazawa, S., Doi, H., Takahashi, H., Nishiyama, T., Shigenobu, S., Misawa, K., Kikuchi, K., Sakai, H.
CC BY
.na.character

MicroRNA166-HD-ZIP III module impacts tuber shape, color and productivity in potato

plant biology
new results

MicroRNA165/166 is a highly conserved and abundant microRNA family in plants that targets class III homeodomain leucine zipper (HD-ZIP III) transcription factors. Their essential roles in plant development, organ polarity, meristem maintenance, and vascular differentiation have been well established. However, their role in storage organ development, particularly in potato tuberization remains unknown. Here, we demonstrate the pleiotropic effects of miR166 on potato (Solanum tuberosum spp. Andigena) growth and development. Suppression of miR166 via target mimicry (MIM166) resulted in reduced plant height, altered vascular patterning, diminished leaf curvature, and impaired root development. Remarkably, MIM166 lines produced elongated, pigmented tubers with reduced yield under short-day conditions. Transcriptomic analyses of swollen head versus stalk of tuberizing stolons revealed altered expression of auxin-, cytokinin-, and gibberellin-related genes, consistent with hormone quantification data, suggesting the key role of phytohormones in governing tuber shape. Anthocyanin profiling indicated elevated accumulation of cyanidin 3-glucoside, pelargonidin 3-glucoside, and delphinidin 3-glucoside in MIM166 tuber peels, correlating with the upregulation of anthocyanin biosynthetic genes. Tuber productivity in these lines was reduced possibly due to the decreased expression of SWEET11b and distorted vascular structures in the MIM166 lines. Further, StREVOLUTA, a direct miR166 target, exhibited dynamic expression during stolon differentiation and could modulate the expression of auxin biosynthesis genes. Collectively, our results demonstrate that the miR166-HD-ZIP III module is functional in potato, plays conserved roles in regulating key developmental traits, and is active through early stolon-to-tuber transition stages, affecting tuber shape, color and productivity.

Nov 20, 2025
Patil, N. S., Vasav, A., Kumari, J., Arora, G., Natarajan, B., Banerjee, A. K.
CC NO
.na.character

Predictive Networks Generate Motion-Induced Color Illusions

neuroscience
new results

Subjective color (SC) refers to chromatic perception induced by achromatic stimuli, as classically demonstrated using Benham's top. Despite nearly two centuries of investigation, the underlying neural mechanisms remain unclear. We developed artificial neural network (ANN) models trained on natural videos using predictive learning to investigate SC generation. These models successfully reproduced artificial subjective color (ASC) despite the absence of explicit color information in the training stimuli. Critically, ASC characteristics were systematically influenced by the colors of moving objects in the training videos. Using progressively simplified stimuli, ranging from natural scenes to 3D computer graphics to 2D animations, we demonstrated that the colors of moving objects are the primary determinant of ASC properties. We propose that predictive learning establishes color associations with motion patterns, causing the arcs on Benham's top to be perceived as moving objects with their corresponding colors. These findings suggest that cortical predictive mechanisms may complement retinal processes in generating subjective color phenomena.

Nov 14, 2025
Ueda, K., Sinapayen, L., Watanabe, E.
CC BY-NC
.na.character

Insertion of an invading retrovirus regulates a novel color trait in swordtail fish

evolutionary biology
new results

For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable within and between species and can serve as an important window into the mechanisms of adaptation. Here, we map the genetic basis of a newly described iridescence trait in swordtail fish to a single locus. Individuals with this trait appear to sparkle as they move through the water. We find that the trait is driven by the recent endogenization of a retrovirus that inserted near the gene alkal2a. This insertion is associated with changes in the chromatin landscape, upregulation of alkal2a, and accumulation of iridescent cells that adhere to the scales. Rather than causing diseases, our results demonstrate that invading endogenous retroviruses can also regulate novel trait variation in the host. Moreover, we find that this coloration trait may act as an important signal in interactions between fish and their predators in the natural environment.

Nov 11, 2025
Haghani, N., Dodge, T. O., Baczenas, J. J., Gunn, T., He, Q., Pangburn, W., Sood, R., Du, K., Fascinetto-Zago, P., Kaatmann, A., Ou, Z., Dougan, S., Olmos-Santiago, N. S., Preising, G. A., Payne, C. Y., Haase Cox, S. K., Hunnicutt, K. E., Madrzyk, M., Moran, B. M., Stigloher, C., Powell, D. L., Schartl, M., Gifford, C., Han, G. z., Schumer, M.
CC BY
.na.character

Anthropogenic factors explain wing colour variation in Colias (Lepidoptera: Pieridae) across the Toronto urbanization gradient

evolutionary biology
new results

Hybridization, or interbreeding between two previously diverged populations, is increasing due to human influences on the environment. Rates of hybridization might be increasing particularly quickly among urban species, especially those that are known to be sensitive to environmental disturbances. Butterflies are one such taxa, as some species are commonly found in urban areas, despite being sensitive indicators. For example, Colias philodice and C. eurytheme (Lepidoptera: Pieridae) hybridize when their ranges are in contact or overlap and are commonly found in large cities throughout North America. However, it is an open question how variation in urbanization might affect variation in hybridization. Using wild Colias across a gradient of urbanization in Toronto, Ontario, we tested how the variation in Colias colour, as an indicator of hybridization, relates to human disturbance and urbanization. We created an objective numeric classification for both C. eurytheme and C. philodice, against which we categorized Colias samples. We found that some of the urbanization metrics, including distance to road, Julian date, and number of pedestrians affect the variation in Colias colour, suggesting that urbanization affects Colias colouration, and potentially rates of hybridization, in Toronto. This means that human disturbance of the environment could be affecting Colias rates of hybridization.

Nov 7, 2025
Sabatino, A., Jahner, J. P., McFarlane, S. E.
CC BY
.na.character

Estimating resource acquisition and water-use traits in wine grapes using reflectance spectroscopy

plant biology
new results

In agroecosystems, the variable expression of crop functional traits is expected to play a role in key processes, including plant nutrient cycling and water acquisition, that confer ecosystem resistance and/ or resilience to environmental change. The ability to estimate crop trait data is therefore critical to predict crop responses to environmental change, enabling more informed diagnosis of crop performance and on-farm management strategies. Yet, many traditional methods for quantifying plant traits are time-consuming and resource-intensive, limiting sample sizes and study durations. In response, high-throughput phenotyping–specifically reflectance spectroscopy– has emerged as a key element of plant trait research, capable of estimating plant traits more rapidly. However, little is known about whether or not reflectance spectroscopy can detect within-species variation in resource acquisition and plant-water traits. Using wine grapes (V. vinifera subsp. vinifera) as a focal crop, this study aimed to assess the ability of reflectance spectroscopy and the subsequent partial least squares regression modelling approach to quantify intraspecific variation in 12 functional traits across 12 different cultivars. Results showed significant differences in traits, especially in the photosynthetic and hydraulic traits, among closely related cultivars, falling along a resource-conservative to resource-acquisitive axis of variation. We also found that reflectance differentiated this fine-scale trait variation, specifically in leaf chemical and morphological traits, contributing to higher accuracy, and indicating that this HTP approach is viable for detailed trait estimation in diverse agroecosystems.

Nov 3, 2025
Mariani, R. O., Isaac, M. E., Cathline, K., Robertson, G., Martin, A. R.
CC BY
.na.character

A 37-color spectral flow cytometry panel to characterize phenotype and cytokine expression in human intestinal T cells

immunology
new results

We developed a 37-color spectral flow cytometry panel to characterize T cell function, with a focus CD4+ T helper (Th) cells, in the human intestine. The panel includes lineage-defining transcription factors, markers for memory status, tissue residency and T cell activation, and 11 cytokines representing multiple Th cell lineages. The panel is currently being used to investigate CD4+ Th cell function in intestinal and peripheral blood samples of inflammatory bowel disease (IBD) patients. The panel could however be applied to investigate both peripheral and tissue-resident T cell function in a range of immune-mediated diseases.

Oct 31, 2025
Lindelauf, C., Jiang, Q., Koning, F., van der Meulen-de Jong, A. E., van Unen, V., Pascutti, M. F.
CC NO
.na.character

Sensory receptor expansion and neural accommodation in butterfly color vision

developmental biology
new results

The evolution of more complex brains required existing neurons and neural circuits to accommodate new inputs. The genetic and developmental mechanisms that enable such integration are largely unknown. Butterflies evolved more complex retinal mosaics through the addition of a second R7 color photoreceptor per ommatidium (unit eye). In Drosophila, the unique R7 makes a stochastic choice to express one of two opsin genes. In butterflies, the two R7s make two independent stochastic cell fate choices in each ommatidium, producing three ommatidial types instead of the two in flies. Here, we investigate the developmental basis of this change and how the butterfly brain accommodates an expansion in sensory receptor input. We first identified the developmental mechanisms that specify the second R7 cell. We then modified Drosophila retinas to have butterfly-like transcription factor expression, causing recruitment of an additional R7. The two R7s make independent stochastic choices, like butterflies, leading to three stochastically distributed ommatidial types instead of two. In Drosophila, each of the two subtypes of R7s connects to one of two types of Dm8 neurons. Dm8 neurons of both types are born in excess, with Dm8s that are not connected to their cognate R7s undergoing apoptosis. In the presence of extra R7s in butterfly-like retinas, additional Dm8s are retained, leading to two Dm8s per medulla column. We propose a model in which population-level variation in the ratio of R7 subtypes produced in the retina maintains an excess pool of two types of potentially interacting partners in the brain, thus providing developmental flexibility which allows brains to accommodate additional inputs. We demonstrate how excess neurons that are eliminated in normal development facilitated the expansion of color vision in butterflies, and similar cooption events may represent a general mechanism of neural evolution.

Oct 31, 2025
Gao, K., Ainsworth, J., Donati, A., Zhao, Y., Ragsac, M. F., Genduso, C., Andre, Z., Tomlinson, A., Perry, M. W.
CC BY
.na.character

Opposing seasonal dynamics in phylogenetic and flower color diversity of co-flowering wildflower assemblages

ecology
new results

Flower color is a key trait mediating plant-pollinator interactions, yet the ecological rules governing its distribution across co-flowering assemblages remain poorly understood. We examined spatiotemporal patterns of flower color and phylogenetic diversity in Eastern North American wildflowers to test for non-random community structure, seasonal shifts, and associations between flower color similarity and phylogenetic relatedness. Using occurrence, phenology, and color data from community science datasets, we reconstructed communities of co-flowering assemblages and calculated standardized effect sizes of mean pairwise distances for both flower color and phylogenetic relatedness. We analyzed seasonal trends using mixed models and assessed whether closely related species co-flowered non-randomly with respect to color similarity using bootstrap correlations. We found that, on average, co-flowering assemblages were overdispersed for both flower color and phylogeny. However, flower color dispersion significantly decreased over the growing season, while phylogenetic dispersion significantly increased, reflecting a pattern in which co-flowering assemblages shifted to more distantly related but similarly colored assemblages. Finally, color and phylogenetic dispersion were negatively correlated across communities, indicating that communities composed of more closely related species tended to exhibit more dissimilar flowers. Together, our results suggest that wildflower assemblages in Eastern North America show detectable, non-random structure across space and time with respect to color and relatedness at the broad scale, and that mechanisms underlying the structure of co-flowering groups may shift throughout the growing season.

Oct 22, 2025
Talbot, C. A., Weber, M. G.
CC BY
.na.character

Genomic and genetic insights into speciation and pigment pattern diversification in Danio fishes

genomics
new results

The Danioninae subfamily of teleost fishes boasts up to four hundred distinct species that have evolved to display a stunning diversity of morphological forms. Here we use newly assembled genome sequences of four laboratory and wild zebrafish strains as well as eleven species of the Danio and Danionella genera to explore their phylogenetic history and the genetic basis of pigment pattern diversification. Phylogenomic analyses uncover extensive introgression and incomplete lineage sorting that have obscured phylogenetic relationships within Danio and corroborate an ancient hybrid origin of zebrafish. Whereas D. rerio inherited ancestral horizontal stripes, relatives repeatedly evolved spots and vertical bars. Interspecific complementation tests reveal functional divergence of the adhesion molecule gene igsf11 and the gap junction gene gja5b between the striped zebrafish and Danio species with divergent patterns. Comparative genomic and transcriptomic analyses suggest that protein and regulatory evolution have accompanied pigment pattern diversification. Our analyses elucidate complex genetic changes underlying the phylogenetic history and morphological diversification in the Danio genus. Resolved phylogenetic relationships, available genome assemblies, transcriptomes, and genetic tractability establish Danio fish species as excellent models for biomedical research in vertebrates.

Oct 18, 2025
Lu, J., Podobnik, M., Huang, J., McCluskey, B. M., McCarthy, S. A., Wood, J., Collins, J., Torrance, J., Sims, Y., Gao, D., Huang, J., Liu, J., Fang, W., Huang, P., Ma, C., Parichy, D. M., Irion, U., Liu, J., Howe, K., Postlethwait, J. H.
CC BY
.na.character

Perceiving surface colour requires attention

neuroscience
new results

Colour constancy refers to our ability to distinguish changes in surface properties from changes in the properties of light illuminating the scene. The apparent ease with which we can tell that objects do not change colour, for example, when moving from sunlight to the shade, belies the complexity of solving this ill-constrained problem. Although there is a substantial body of work testing which image cues might be used to accomplish this, there is surprisingly little known of how the brain performs this computation. Here, we tested a fundamental aspect of this perceptual process: whether it requires attention. We measured visual search times for both surface colour (requiring separation of surface and illuminant properties) and ‘raw’, colorimetric colour (which does not). We found a clear difference between the two: visual search for colorimetric colour was fast and near-parallel, while search for surface colour was slow and consistent with the serial deployment of attention. That is, search times suggest that the perceptual separation of surface and illuminant properties in colour constancy may require an attention-based process analogous to perceiving conjunctions of simple features in ‘feature binding’. Colour discrimination thresholds suggested that while colorimetric colour detection is fast and parallel, once attention was directed to these stimuli and perceptual scission occurs, colorimetric colour information was discarded by the visual system. These results offer important new insights into the sequence of processes the brain uses to accomplish colour constancy.

Oct 16, 2025
Goddard, E., Paul Remician, K.
CC BY-NC-ND
.na.character

Color, size, shape: The drivers of floral variation in Hesperis matronalis (Dames Rocket)

evolutionary biology
new results

Evolutionary biologists have long been intrigued by the factors that sustain genetic and phenotypic variation within and among natural populations. Polymorphisms underlying components of floral display – such as floral color, size, and shape – are uniquely of interest since variation in these traits impact pollinator attraction, rates of visitation, and pollinator efficiency, which ultimately influence patterns of plant reproduction and therefore fitness. We leverage existing floral variation present within and among populations of Hesperis matronalis (Dames Rocket) to disentangle the relative influence of natural selection and genetic drift in shaping floral trait variation. We employ a multi-tiered approach: we determine if variation in floral traits (color, size, and petal shape) is influenced by geography or environmental variables such as temperature and precipitation, we evaluate whether selection underlies trait variation by comparing phenotypic divergence (PST) with neutral genetic structure (FST), and we perform a Lande-Arnold selection analysis to explore the relationship between fitness and floral trait variation within natural populations. We find that selection underlies the divergence of floral color, floral size, and petal width among H. matronalis populations, with PST > FST for each trait. We find no indication, however, that variation in size in this species is influenced by the environment, but some evidence that variation in floral color and petal shape may be influenced by temperature. Finally, selection analyses of contemporary populations indicate divergent selection affecting combinations of color, petal shape, and plant size. These results suggest that the variation in floral shape in this species may be maintained due to environmental pressures, whereas floral color is influenced by pollinator visibility and the presence of different pollinator groups.

Oct 16, 2025
Johnson, S. E., Rifkin, J. L., Wright, S., Baucom, R. S.
CC NO
.na.character

Effects of color-enhancing filters on color salience in normal trichromats

neuroscience
new results

Notch filters can alter color contrasts by selectively filtering different spectral bands of the stimulus and have been developed to enhance reddish-greenish contrasts for color-deficient observers with anomalous trichromacy. We examined the effects of such filters on color salience for normal trichromats, using a visual search paradigm where the task was to locate a color target superimposed on a variegated chromatic background, similar to foraging for fruits among foliage. Background colors varied along a bluish-yellowish or purplish to yellow-green (short-wave cone isolating) axis, roughly spanning the range of dominant color variations in arid or lush environments. Target colors sampled a wide range of hue angles and contrasts. Testing was conducted on a computer monitor, with the filter effects simulated by calculating corresponding chromaticities with or without the filter for naturalistic (Munsell) reflectances. The filter evaluated (Enchroma SuperX glasses) was designed to increase color contrast along a magenta-green axis. Consistent with this, search times for targets on the blue-yellow background were significantly faster for the filter condition, because the filter increased the target-background color difference. Alternatively, overall differences in search times were not observed for the S-cone background. The differences on the two backgrounds could be qualitatively accounted for by the relative salience of the stimuli predicted by a perceptual color space (CIELAB). Our results demonstrate the efficacy of the filters for enhancing visual performance for normal trichromats and naturalistic tasks, and illustrate how these effects depend on the potential color characteristics of the environment.

Oct 15, 2025
Webster, M., Knoblauch, K., Simoncelli, C., McPherson, D.
CC BY-NC-ND
.na.character

The hallmark of colour in EEG signal

neuroscience
new results

Our perception of the world is inherently colourful, and colour provides well-documented benefits for vision: it helps us see things quicker and remember them better. We hypothesised that colour is not only central to perception but also a rich and decodable source of information in electroencephalography (EEG) signal recorded non-invasively from the scalp. Previous work has shown that brain activity carries colour information for uniform patches, but it remains unclear whether this extends to natural, complex images where colour is not explicitly cued. To investigate this, we analysed the THINGS EEG dataset, comprising 64-channel recordings from participants viewing 1,800 distinct objects (16,740 images) for 100 ms each, totalling over 82,000 trials. We established a perceptual colour ground truth through a psychophysical experiment in which participants viewed each image for 100 ms and selected perceived colours from a 13-option palette. An artificial neural network trained to predict these scene-level colour distributions directly from EEG signals showed that colour information was robustly decodable (average F-score of 0.5). We next modelled the interaction between colour and object perception in neuroimaging decoding. Images were segmented using the Segment Anything Model (SAM), each object was assigned a representative colour, and features were extracted from these colour-augmented images using CLIP vision encoders. We trained an EEG encoder, CUBE (ColoUr and oBjEct decoding), to align features in both object and colour spaces. Across EEG and MEG datasets in a 200-class recognition task, incorporating colour improved decoding accuracy by about 5%. Together, these findings demonstrate that EEG signal recorded during natural vision carries substantial colour information that interacts with object perception. Modelling this mutual interaction enhances neural decoding performance.

Oct 7, 2025
Akbarinia, A.
CC BY-NC
.na.character

Modeling MEK-inhibitor Associated Retinopathy in vitro using human induced-1 pluripotent stem cell-derived retinal pigment epithelial cells

molecular biology
new results

Pharmacologic inhibitors of MEK are important anti-cancer drugs but can result in MEK-inhibitor Associated Retinopathy (MEKAR) in which vision is lost due to serous retinal detachments that form via an unknown mechanism. We hypothesized that the cause of this side effect is drug-induced dysfunction of retinal pigment epithelial (RPE) cells. To test this hypothesis, we used human induced pluripotent stem cell-derived RPE cells. We treated mature, hiPSC-derived RPE cells with selumetinib and measured impacts on RPE-specific function, structure, and gene expression. Selumetinib increases the ability of hiPSC-derived RPE to internalize bovine rod outer segments (1.9 vs 3.0, p=0.0024). It also decreases expression of aquaporin 1 during the first 10 days of treatment (2.7 vs 1.1, p=0.0015). It has no effect on the ability of hiPSC-derived RPE to maintain membrane integrity. Selumetinib alters gene expression of hiPSC-derived RPE, with significant changes in genes involved in transport of ions and small molecules regulating cell volume and lysosomal acidification. Selumetinib may lead to subretinal fluid accumulation by both increasing secretions into this space and decreasing outflow.

Oct 4, 2025
Lozano, L. P., Jennisch, M., Jensen, R., Ratcliff, J. A., Wiley, L. A., Harman, B., Riker, M. J., Wright, A. T., Erickson, B. A., Boldt, H. C., Boyce, T. M., Mullins, R., Binkley, E. M., Tucker, B. A.
CC NO
.na.character

Aposematic color patterns are the dominant axis of phenotypic diversification in Nymphalid butterflies

evolutionary biology
new results

Butterfly wing patterns serve diverse roles in visual communication, from aposematic signaling and mimicry to mate attraction and camouflage. In brush-footed butterflies (Nymphalidae), this diversity can be traced to the wing pattern “ground plan” that generates phenotypes deterministic in origin yet highly multidimensional in form. Quantifying such complexity at scale has long been a challenge, limiting our understanding of how visual signals interact, constrain one another, and evolve. Here, we used computer vision to extract high-dimensional traits from standardized museum specimens and assembled the largest comparative dataset of wing color patterns to date, spanning over one third of all known Nymphalid species. We first tested whether chemically defended species occupy a distinct region in morphospace and then derived a quantitative score for aposematism from the principal color patterns associated with defense. Using this score, we examined whether aposematic signals are expressed consistently across wing surfaces and sexes, and whether their origins are linked to shifts in evolutionary rate. We found that the dominant axis of morphospace is defined by chromatic and achromatic contrast, along which defended and undefended species cluster. Validation with an expert-labeled moth dataset confirmed that this axis separates aposematic from non-aposematic phenotypes across Lepidoptera. Consistent with theory, strongly aposematic species showed greater visual similarity between dorsal and ventral surfaces, between sexes, and among individuals. Rate analyses further indicated that aposematic patterns evolved repeatedly and were associated with non-linear shifts in evolutionary tempo. Together, these results identify aposematism as the dominant organizing axis of wing color pattern evolution in Nymphalidae.

Oct 1, 2025
Luerig, M. D., Shirai, L. T., Mota, L., Willmott, K. R., Freitas, A. V. L., Porto, A.
CC BY-NC
.na.character

A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection

genomics
new results

The sequencing-by-synthesis technology by Illumina, Inc. enables efficient and scalable readouts of mutations from genomic data. To enhance sequencing speed and efficiency, Illumina has shifted from the four-color base calling chemistry of the HiSeq series to a two-color fluorescent dye chemistry in the NovaSeq series. Benchmarking sequencing artifacts due to biases in the newer chemistry is important to evaluate the quality of identified mutations. We re-analyzed a series of whole-genome sequencing experiments in which the same samples were sequenced on the NovaSeq 6000 (two-color) and HiSeq X10 (four-color) platforms by independent groups. In several samples, we observed a higher frequency of T-to-G and A-to-C substitutions (“T>G”) at the read level for NovaSeq 6000 versus HiSeq X10. As the per-base error rate is still low, the artifactual substitutions have a negligible effect in identifying germline or high variant allele frequency (VAF) somatic mutations. However, such errors can confound the detection of low-VAF somatic variants in high-depth sequencing samples, particularly in studies of mosaic mutations in normal tissues, where variants have low read support and are called without a matched normal. The artifactual T>G variant calls disproportionately occur at NT[TG] trinucleotides, and we leveraged this observation to bioinformatically reduce the T>G excess in somatic mutation callsets. We identified a recurrent artifact specific to the Illumina two-color chemistry platform on the NovaSeq 6000 with the potential to contaminate low-VAF somatic mutation calls. Thus, an unexpected enrichment of T>G mutations in mosaicism studies warrants caution.

Sep 29, 2025
Fu, B. J., Viswanadham, V. V., Maziec, D., Jin, H., Park, P. J.
CC BY-NC
.na.character

Structural basis for color tuning and passive ion conductance in red-shifted pump-fold channelrhodopsin ChR024

biophysics
new results

ChR024 is a cation-conducting channelrhodopsin with a red-shifted absorption spectrum, recently discovered from a previously unidentified clade through machine-learning-guided gene mining. Due to its unique position in the phylogenetic tree and distinctive spectral properties, it serves as an important model for elucidating rhodopsin evolution and for engineering optogenetic tools with enhanced performance, but its structure and function remain poorly understood. Here, we present cryo-electron microscopy structures of ChR024 in detergent micelles and lipid nanodiscs at resolutions of 3.2 and 2.5 [A], respectively. The structures reveal an architecture strikingly similar to that of ion-pumping rhodopsins, even more so than other pump-like channelrhodopsins such as ChRmine. Structural, theoretical, and spectroscopic analyses uncover a unique color-tuning mechanism, in which charged residues close and distant from the retinal chromophore cooperatively modulate the pKa of the Schiff base counterion and thereby determine the absorption maximum wavelength. Finally, comparative structural analysis of channel- and pump-type rhodopsins, combined with electrophysiology, provides insights into the molecular boundary between these two functional classes and demonstrates the conversion of an outward proton pump into a light-gated channel. Together, these findings illuminate diverse mechanisms of color tuning and functional specification within the rhodopsin family, paving the way for the rational engineering of next-generation optogenetic tools.

Sep 17, 2025
Takeno, Y., Tajima, S., Kim, S., Tsujimura, M., Ito, Y., Sugiura, M., Yamashita, Y., Kishi, K. E., Fukuda, M., Nakamura, S., Watanabe, M., Ikeda, H., Katayama, K., Furutani, Y., Kandori, H., Ishikita, H., Inoue, K., Kato, H. E.
CC BY-NC-ND
.na.character

Discrimination of Annonaceae using herbarium leaf reflectance spectra under limited sample size conditions

plant biology
new results

Herbarium collections offer an unparalleled archive of plant biodiversity, but their use for species identification through spectral data remains constrained by uncertain effects of preservation histories. This study assesses whether a single herbarium specimen can reliably represent its species based on its leaf reflectance spectrum, despite variations in age, geographic origin, or conservation method. We scanned herbarium specimens of different ages and geographic distribution of 14 species of the pantropical Annonaceae. In addition, we used a second dataset of 9 species where some specimens were conserved in alcohol prior to drying and some not. We used five supervised classification models frequently used for high-dimensional data such as spectroscopy. All models achieved high accuracy (>80%) when trained on multiple specimens per species. However, when using only one specimen per species, accuracy varied substantially depending on the taxon. Alcohol preservation prior to drying had little impact on classification success. Our findings demonstrate that herbarium specimens often retain a strong taxonomic signal in their spectra, however, inter-individual variability affects accuracy in some taxa. These findings confirm the usefulness of herbarium spectroscopy as a non-destructive tool for species identification and offer a promising avenue for digitizing historical biodiversity data into high-dimensional trait space.

Sep 5, 2025
Boughalmi, K., Santacruz Endara, P. G., Bennett, L. A., Ecarnot, M., Bazan, S., Bastianelli, D., Bonnal, L., Couvreur, T. L. P.
CC BY-NC-ND
.na.character

The ecology and adaptive function of clownfish color patterns

ecology
new results

Anti-predator coloration strategies vary widely from conspicuous to cryptic, and everything between. Coloration serves multiple functions, and determining the selective pressures that drive this diversity is a long-standing mystery. Clownfishes display enormous inter- and intra-specific variation in coloration without the influence of sexual selection, providing an excellent system in which to explore these drivers in closely related and sympatric species. Across clownfishes, three color-pattern phenotypes have evolved convergently with host anemone use, implying adaptive functions linked to the host’s physical and chemical properties. Here we conducted a comprehensive study to infer the ultimate functions of clownfish color patterns. By integrating multiple levels of biological organization, including behavior, visual ecology, dietary niche, and microbiome, our data overwhelmingly indicate that specialist and generalist clownfish color patterns have different underlying ecologies and adaptive functions. Specialist clownfishes background match their anemones, remain near hosts, and have specialized diets and microbiomes. Generalists are highly contrasting with their anemones, remain far from hosts, and have variable diets and microbiomes. Taken together, specialist color patterns align with functional expectations of camouflage while generalists align with aposematic or disruptive coloration. Our study provides novel insights into how ecological conditions shape the evolution of multiple anti-predator coloration strategies.

Sep 1, 2025
Froehlich, C. Y. M., Caves, E., Troscianko, J., Gibson, M., Chiodo, T., De Jode, A., Brown, K., Luckas, N., Titus, B. M.
CC BY-NC-ND
.na.character

Combined multi-color immunofluorescence staining and spatial in situ mRNA expression analysis identifies potential fibrosis drivers in acute lymphoblastic leukemia

cell biology
new results

Acute lymphoblastic leukemia (ALL) is the most prevalent childhood cancer. Bone marrow (BM) fibrosis in ALL has been associated with adverse outcomes, however, little is known about the mechanisms that cause fibrosis in ALL. Therefore, we established a novel and advanced analysis method by combining multi-color immunofluorescence staining with in-situ RNA expression analysis (RNAscope) investigate the spatial expression of putative fibrotic drivers in ALL bone marrows. We analyzed standard BM biopsies from pediatric ALL patients. Sequential 5-color immunofluorescence (IF) staining with CD45, CD271, CD31, CD34 and DAPI was used to identify different BM cell types. Combined RNAscope and IF staining was established for spatial mRNA expression analysis of transforming growth factor beta 1 (TGFB1) and platelet-derived growth factor alpha 1 (PDGFA1), which are known to play major roles in primary myelofibrosis (PMF). PMF and normal BM samples served as controls. As expected, ALL bone marrows showed high cellularities and prominent populations of blast cells. CD271+ MSC density was increased in ALL and was associated with fibrosis in a similar manner as observed for PMF. TGFB1 and PDGFA1 expression was considerably increased in ALL megakaryocytes (MKs) compared to PMF patients and normal controls. Furthermore, MK TGFB1 and PDGFA1 expression intensities in fibrotic ALL correlated with fibrosis grade. TGFB1 and PDGFA1 were also expressed in leukemic blasts, however at lower intensities compared to ALL MKs. Taken together, advanced in-situ RNA and IF staining not only revealed increased expression of TGFB1 and PDGFA1 in fibrotic pediatric ALL, but also identified ALL blasts and MKs as their cellular origin at the single cell level. These novel data strongly suggest a role of these cytokines as potential fibrosis drivers in ALL. More broadly, our findings demonstrate that combined RNA and surface marker analysis is a powerful tool to provide new and valuable insights into bone marrow pathophysiology.

Aug 31, 2025
Braunig, S., Dencker, C., Vo, D. N., Fan, R., Sierras, A. L., Enoksson, J., Hultquist, A., Li, H., Scheding, S.
CC NO
.na.character

RPEGENE-Net: A Multi-Resolution Deep Learning Framework for Predicting Gene Expression from Microscopy Images of Retinal Pigment Epithelium (RPE) Cells

bioengineering
new results

Abstract Purpose: To develop a deep learning framework, RPEGENE-Net, capable of predicting gene expression profiles of retinal pigment epithelium (RPE) cells using live-cell microscopy images. Methods: A dataset of live-cell images of RPE cells, treated with various drug regimens and captured at magnifications of 40x, 100x, 200x, and 400x, was used. Gene expression of six key genes involved in epithelial-mesenchymal transition or EMT (including -SMA, ZEB1, TGF-{beta}, CD90, {beta}-catenin, Snail) and treatment classes (Aflibercept, Bevacizumab, Dexamethasone, Aflibercept + Dexamethasone, and untreated control) were analyzed. After preprocessing the image data and gene expression values, we trained and evaluated twelve state-of-the-art deep learning architectures, including three variants of DenseNet, five variants of ResNet, EfficientNet_b5, Inception_v3, RegNet_y_400mf, and a vision transformer model (Swin_b). A two-stage pipeline was implemented, combining autoencoder-based pretraining to extract meaningful features with fine-tuning specifically optimized for gene expression regression and treatment type classification tasks. Features extracted from the second stage across four magnifications were concatenated to generate the final prediction, leveraging multi-scale morphological information for improved accuracy.

Aug 31, 2025
Nowroozzadeh, M. H., Taghinezhad, N., Mahmoudi, T., Sanie-Jahromi, F.
CC BY
.na.character

Sigma-2 Receptor Modulators Alter Low-density Lipoprotein Receptor-mediated Lipid Uptake in Retinal Pigment Epithelial Cells

cell biology
new results

Lipid and photoreceptor outer segment (POS) trafficking and digestion are important homeostatic functions of retinal pigment epithelial (RPE) cells, the primary cell type that degenerates in late-stage dry AMD preceded by extracellular drusen deposits of lipids and proteins. The sigma-2 receptor (S2R, TMEM97) interacts with proteins involved in lipid trafficking, such as low-density lipoprotein receptor (LDLR), which is the primary receptor for LDL-cholesterol uptake in the retina. Preclinical studies demonstrate the necessity of S2R in protecting the retina and other nervous system tissues, and loss of either S2R or LDLR has been shown to exacerbate RPE cell death and visual dysfunction. Targeting the regulatory receptors of lipid and protein trafficking functions in RPE cells represents a tractable therapeutic strategy for dry AMD. We previously demonstrated that small molecule modulators of S2R can rescue RPE POS trafficking deficits induced by exogenous stressors. Given that disruption in lipid homeostasis is a key factor in dry AMD pathogenesis and S2R interacts with LDLR, we hypothesized that LDLR-mediated lipid trafficking in RPE could be altered using S2R-targeting small molecules. In this study, RPE cells treated with S2R modulators increased LDL uptake, assessed using fluorescently-labeled LDL, compared to vehicle-treatment. Lentiviral shRNAs to reduce TMEM97 or LDLR expression, or a neutralizing blocking antibody against LDLR, reduced S2R modulator-mediated LDL uptake, confirming the requirement of TMEM97 and LDLR for S2R modulator effects. Together, these data elaborate on a potential mechanism that may underlie the favorable reduction in geographic atrophy lesion size found in participants treated with the S2R modulator zervimensine in the Ph2 clinical trial MAGNIFY in patients with geographic atrophy (COG2201, NCT05893537).

Aug 27, 2025
Lizama, B. N., Reaver, A., Look, G., Caggiano, A. O., Hamby, M. E.
CC BY-NC-ND
.na.character

Cell-cell communication as underlying principle governing color pattern formation in fishes

developmental biology
new results

The diverse pigmentation patterns of animals are crucial for predation avoidance and behavioral display, yet mechanisms underlying this diversity remain poorly understood. In zebrafish, Turing models have been proposed to explain stripe patterns, but it is unclear if they apply to other fishes. In anemonefish (Amphiprion ocellaris), we identified gja5b, a gene orthologous to zebrafish leopard and encoding a connexin involved in pigment cell communication, as responsible for the Snowflake phenotype. Using CRISPR/Cas9 and transgenesis, we recapitulate the Snowflake phenotype and show expression of gja5b in iridophores. A matching allele was recovered in zebrafish, revealing complementary requirements in both species. Our findings highlight conserved roles of gap junction mediated communication in pigment patterning across divergent teleosts.

Aug 25, 2025
Klann, M., Miura, S., Lee, S.-H., Vianello, S. D., Ross, R., Watanabe, M., Gairin, E., Liang, Y., Hutto, H. W., McCluskey, B. M., Herrera, M., Solnica-Krezel, L., Besseau, L., Pigolotti, S., Parichy, D. M., Kinoshita, M., Laudet, V.
CC BY-NC-ND
.na.character

Anti-vitronectin single-chain variable fragment targeting the hemopexin-like domain decreases age-related macular degeneration indicators in ex vivo models of the retinal pigment epithelium

cell biology
new results

Vitronectin is a prominent constituent of the extracelluar matrix (ECM) that plays a key role in inflammation by regulating cell adhesion, migration, and complement activation. Together with other inflammatory biomarkers, lipids, and hydroxyapatite, an ECM component, vitronectin, accumulates in abnormal deposits and drusen associated with age-related macular degeneration (AMD). Using an engineered polypeptide (VnHX) containing the hexmopexin-like domain (HX) of vitronectin, we found that the HX domain directly promotes hydroxyapatite (HAP) accumulation. Next, we screened humanized single-chain variable fragments (scFvs) against vitronectin that inhibit the interaction between VnHX and HAP, leveraging the binding of VnHX to HAP. We then tested these scFvs for their ability to block Vn-containg deposits secreted by stem cell-derived retinal pigment epithelium (RPE). In this in vitro drusen model, treatment with the anti-vitronectin antibodies decreased vitronectin accumulation. Furthermore, the antibody treatment led to decreased accumulation of C5b-9 and clusterin, indicating alterations in the complement pathway and cellular stress. These results support that vitronectin has a functional role drusen accumulation and possibly in AMD progression. Vitronectin would be a novel, promising therapeutic target for AMD.

Aug 22, 2025
Kim, J. W., Meyer, S., Lopez, B., Faynus, M., Johnson, L. V., Hemmati, H., Clegg, D. O., Min, H.
CC NO
.na.character

Sex-specific doublesex regulation targeting the color-patterning gene h underlies the evolution of wing sexual dimorphism in the harlequin ladybug Harmonia axyridis

evolutionary biology
new results

Organisms on Earth show various forms of sexual dimorphism, including ornaments, weapon traits, and pheromone glands, which has been acquired through sexual selection during evolution. Although the genetic basis of sexual trait has been investigated in diverse species, its evolutionary origin, evolutionary mode, and evolvability remain poorly understood. To address these issues, we investigated the strain-specific sexual dimorphism in elytral color patterns of the harlequin ladybug, Harmonia axyridis, a species with over 200 color morphs. The most basal Red-nSpots type color morph exhibits sexual dimorphism, whereas other derived color morphs have lost it. To investigate how this loss of sexual dimorphism is associated with the emergence of novel color morphs, we investigated the genetic basis of sexual dimorphism by focusing on the master sex differentiation gene, doublesex (dsx). We show that dsx regulates color pattern dimorphism by negatively modulating black spot size in males. This modulation is primarily mediated by the transcriptional regulation of the color patterning gene, h (Drosophila pannier ortholog). Intraspecific comparative ATAC-seq analysis of the pupal wings revealed that, at the h locus, not the absolute number of Dsx-binding motifs but the proportion of open chromatin regions containing Dsx-binding motifs relative to those lacking such motifs was reduced in strains that had lost sexual dimorphism and acquired novel color patterns, implying that sexual dimorphism evolves based on the balance between novel CREs and Dsx-binding motif density. The present study provides a fundamental molecular framework for understanding how a secondary sexual trait evolves within H. axyridis.

Aug 7, 2025
Yeki, S., Kato, K., Morita, S., Shimomura, K., Niimi, T., Hinomoto, N., Daimon, T., ANDO, T.
CC NO
.na.character

Two mutations in the same MYC-bHLH transcription factor cause segregation of purple coloration of stolons and seed heads in Zoysia japonica x Zoysia matrella F2 and F1 populations

genetics
new results

Anthocyanins play diverse roles in plants, including attracting pollinators and protecting cells from oxidative damage. In zoysiagrass, a warm season turfgrass, their accumulation in seed heads and stolons can decrease the aesthetic appeal. In this study, a high-density genetic map with ~8000 single nucleotide polymorphism (SNP) markers organized into 20 linkage groups was generated in a Zoysia japonica acc. Meyer x Zoysia matrella acc. PI 231146 F2 population. Using this genetic map, a large-effect quantitative trait locus (QTL) for anthocyanin variation in stolons and seed heads was mapped to chromosome 12 (PP locus). Variant analysis of a candidate gene for PP, Zjn_sc00004.1.g07010.1.sm.mk, which encodes a MYC-bHLH transcription factor that regulates anthocyanin biosynthesis, revealed a SNP at an exon-intron boundary in Meyer that led to intron retention. Interestingly, an F1 population derived from the same parents segregated for seed head color but uniformly displayed purple stolons. Seed head color in the F1 population co-mapped with the PP locus which, combined with genotypic and yeast two-hybrid analyses, revealed that a SNP in PI 231146 leading to an Ala163Ser substitution in the MYB-interacting N-terminal domain of the same MYC-bHLH transcription factor was likely causal. The Ala163Ser substitution affected interaction of MYC-bHLH with MYB in a MYB-dependent manner. The identified mutations can be exploited to develop cultivars with green seed heads and stolons. The high-marker-density interspecific Z. japonica x Z. matrella F2 genetic map also provides a robust tool for identifying genomic regions and genes of agronomic interest that differentiate the two species.

Aug 5, 2025
Pradhan, S., Zhao, J., Spiekerman, J. J., Bennetzen, E., Khanal, S., Yu, X., Milla-Lewis, S., Conner, J., Schwartz, B., Devos, K. M.
CC BY-NC
.na.character

Colour and shape evolution reflect ecological specialisation in Pomacentridae

evolutionary biology
new results

How ecological pressures shape phenotypic traits such as colouration and morphology is a fundamental question in evolutionary biology. Colouration often mediates functions such as communication, camouflage, and species recognition, while morphological traits influence locomotion, feeding, and habitat use. In reef fishes, both traits exhibit striking diversity, frequently shaped by ecological interactions. The damselfish family (Pomacentridae) exemplifies this variation, displaying a wide range of colouration, morphology, and ecological strategies, including dietary specialisation, mutualistic behaviours, and freshwater tolerance. In this study, we examined 342 Pomacentridae species using an integrative framework that combined colouration and morphometric analyses, ancestral state reconstructions of habitat, diet, and symbiosis, and Phylogenetic Comparative Methods (PCMs). Our goal was to assess how ecological factors have influenced the evolution of phenotypic traits and to identify patterns of convergence linked to ecological specialisation. We found repeated convergent evolution in both colouration and body shape, often associated with similar ecological pressures. Species with specialised diets exhibited consistent morphological adaptations, underscoring the role of trophic ecology in shaping body form. Additionally, we observed a strong association between habitat type and dominant colouration patterns, consistent with a camouflage function. These findings clarify the evolutionary processes driving phenotypic diversity in damselfishes and highlight the importance of ecological adaptation in shaping both morphology and colouration. Our work contributes to a broader understanding of how form and function evolve in response to ecological pressures in coral reef ecosystems.

Aug 5, 2025
Jimenez, A. G., Salamin, N., Gaboriau, T.
CC BY
.na.character

Retinal pigment epithelium-derived PD-L1 reprograms microglial cells and protects against retinal degeneration in mouse models of experimental AMD and genetic retinitis pigmentosa

genetics
new results

Retinal degeneration is a leading cause of blindness and a significant health burden during aging worldwide. Because of its complex pathogenic mechanisms, however, effective interventions applicable to multiple retinal degenerations remain limited. Excessive microglia-mediated inflammation is a common pathological feature of different retinal degenerative diseases, and inhibiting these overactive inflammatory responses by reprogramming microglia may provide a therapeutic strategy with broad-spectrum potential. Here, we uncover a novel retinal pigment epithelium (RPE) homeostatic signal, PD-L1, that drives the reprogramming of activated microglial toward a retinal-protective phenotype. Using multiple analyses, including gene expression profiling bioinformatics, adeno-associated virus-mediated RPE-specific gene overexpression, pharmacological, and genetic manipulations, we show that RPE cells upregulate the expression of PD-L1 to modulate microglia for protection against retinal degeneration in an experimental dry AMD mouse model. Bioinformatics enrichment analysis of the high-expression gene signatures of subretinal microglia in AMD patients, combined with pharmacological blocking of NF-{kappa}B activity or using Nlrp3 knockout mice, show that PD-L1/PD-1 signaling suppresses NF-{kappa}B activation in microglia, thereby inhibiting NLRP3 inflammasome priming and attenuating microglia-mediated excessive inflammation. Furthermore, the overexpression of PD-L1 by the AAV8 virus exerts similar microglial reprogramming and retinal protective effects to alleviate retinal degeneration in a preclinical model of retinitis pigmentosa. These findings reveal that RPE-derived PD-L1 suppresses inflammatory reprogramming of subretinal microglia and mitigates retinal degeneration, highlighting a promising proof of concept for PD-L1 as a potential therapeutic target for the broad treatment of retinal degenerative diseases.

Jul 31, 2025
Su, Z., Wang, J., Lai, Q., Wang, Z., Liu, P., Tang, Z., Yu, H., Chen, Y., Ma, X., HOU, L.
CC NO
.na.character

A comparative GWAS of eye colour in light and dark eye genetic backgrounds defined by HERC2 rs12913832 polymorphism

genetics
new results

rs12913832, a polymorphism located in an enhancer within the HERC2 gene, which is known to regulate OCA2 transcription, is heavily relied upon as a predictor of light versus dark eyes. Individuals with the GG genotype are projected to have blue eyes, while individuals with the AA or AG genotypes are projected to have darker eye colours (primarily brown). However, eye colour is a polygenic trait, and previous studies have revealed that a significant proportion of individuals self-report an eye colour that is not concordant with their genotype at rs12913832. Herein, we address the question: What common markers are influencing eye colour in individuals whose self-reported phenotype does not correspond to the expected phenotype based on their rs12913832 genotype. Building upon our prior investigation of iris pigmentation genetics in individuals with an expected “blue eye” background (rs12913832:GG genotype) in a sample of the Canadian Partnership for Tomorrows Health (CanPath) cohort, this study extends the analysis to include individuals with an expected “brown eye” background (rs12913832:AA+AG). We identified variants in SLC45A2, TYRP1, TYR, SLC24A4 and TSPAN10, which may influence eye colour presentation in individuals with the rs12913832:GG genotype and variants in IRF4, TYRP1 and OCA2, which may influence eye colour presentation in individuals with the rs12913832:AA+AG genotype. These markers include well-known pigmentation-associated single nucleotide polymorphisms, such as rs16891982 (SLC45A2), rs1126809 (TYR), rs12203592 (IRF4), rs1800407 (OCA2) and rs6420484 (TSPAN10). Several of these loci were replicated using independent quantitative eye colour measures, including heterochromia and CIELAB colour dimensions. This research highlights the importance of gene-gene interactions and the polygenic nature of pigmentation traits, emphasizing modifying effects that can sometimes counteract the dominant influence of rs12913832, contributing to advancements in pigmentation genetics and forensic applications.

Jul 24, 2025
Abbatangelo, C., Lona Durazo, F., Edwards, M., Parra, E. J.
CC BY
.na.character

FLEXTAG: A Small and Self-renewable Protein Labeling System for Anti-fading Multi-color Super-resolution Imaging

bioengineering
new results

Super-resolution fluorescence imaging enables visualization of subcellular structures and molecular interactions at the nanoscale, but its broader application has been hindered by long-standing limitations in current protein tagging systems, including rapid photobleaching, tag-induced artifacts, poor post-fixation labeling efficiency, and restricted multiplexing capability. Here, we present FLEXTAG (Fluorescent Labeling for Exchangeable, X-resilient Tagging in Advanced Generic Nanoscopy), a comprehensive protein labeling system comprising three orthogonal, ultrasmall (12-18 kDa), and self-renewable protein tags that collectively overcome these major limitations of existing tagging systems, enabling optimized multi-color super-resolution imaging. Through continuous exchange of organic fluorophores, FLEXTAG supports unprecedented durations of high-resolution imaging in both live and fixed cells with minimal photobleaching. It is compatible with major super-resolution modalities, such as SIM, STED, STORM, and PAINT, and is applicable to a wide range of subcellar targets. To further address fixation-induced labeling inefficiency and background fluorescence, we developed a novel protection-based fixation method and chemical blocking strategies that significantly preserve tag accessibility and enhance signal-to-noise ratio, improvements that are broadly applicable to other protein tagging systems. Altogether, FLEXTAG enables long-term tracking of dynamic behaviors and interactions of subcellular targets, as well as mapping of nanoscale protein organizations and cellular architecture, advancing both basic research and translational applications in cell biology.

Jul 23, 2025
Zhang, H., Yao, Y., Wang, X., Tao, Y., Yang, H., Wang, Y., Liu, M., Feric, M., Zhou, R.
CC BY-NC-ND
.na.character

The Zika Virus Persistently Infects Retinal Pigment Epithelial Cells, Eliciting Limited Cytopathic Effects and Loss of Epithelial Characteristics Consistent with Epithelial-Mesenchymal Transition.

cell biology
new results

The Zika virus (ZIKV), a pathogenic member of the orthoflavivirus family, is raising serious health concerns worldwide. Like Dengue (DENV) and Chikungunya (CHIKV) viruses, it is one of the arboviruses that poses an emerging threat to areas where its main vectors, Aedes mosquitoes, proliferate, well beyond tropical and subtropical regions. Although often asymptomatic or mild, ZIKV infection has been responsible for a worrying increase in serious congenital syndromes, including microcephaly. The ability of ZIKV to be transmitted sexually and its long persistence in body fluids suggests its incomplete clearance in particular tissues, linked to recurrent infection. Among its clinical presentations, ZIKV infection has been associated with ocular complications, including maculopathy, retinopathy, uveitis, and optic neuropathy, which can lead to lasting visual impairment. The blood-retinal barrier (BRB), primarily composed of retinal pigment epithelium (RPE) and endothelial cells, plays a crucial role in shielding the retina from pathogens. Its disruption has been linked to viral retinal infections. In vitro monitoring of infection on hTERT RPE-1 cells revealed an ability of ZIKV to persist for up to 30 days in nearly 10% of the cells. This prolonged infection was marked by low cytopathic effects but notable morphological changes throughout the cell layer, suggestive of an epithelial-mesenchymal transition (EMT). Long-lasting viral replication and production was associated with reduced expression of epithelial genes and increased expression of certain mesenchymal genes, suggesting that integrity of the RPE layer may be compromised. These results indicate that viral persistence and phenotypical transition observed in vitro in RPE cells could provide clues to understanding the late onset of ocular pathophysiological manifestations in Zika virus-related diseases.

Jul 21, 2025
EL SAFADI, D., MOKHTARI, A., LEBEAU, G., VIRANAICKEN, W., KREJBICH-TROTOT, P.
CC NO
.na.character

Comprehensive characterization of human color discrimination thresholds

neuroscience
new results

Discrimination thresholds reveal the limits of human perception; scientists have studied them since the time of Fechner in the 1800s. Forced-choice psychophysical methods combined with the method of constant stimuli or parametric adaptive trial-placement procedures are well-suited for measuring one-dimensional psychometric functions. However, extending these methods to characterize psychometric fields in higher-dimensional stimulus spaces, such as three-dimensional color space, poses a significant challenge. Here, we introduce a novel Wishart Process Psychophysical Model (WPPM) that leverages the smooth variation of threshold across stimulus space. We demonstrate the use of the WPPM in conjunction with a non-parametric adaptive trial-placement procedure by characterizing the full psychophysical field for color discrimination in the isoluminant plane. Each participant (N = 8) completed between 6,000 and 6,466 three-alternative forced-choice (3AFC) oddity color discrimination trials. The WPPM was fit to these trials. Importantly, once fit, the WPPM allows readout of discrimination performance between any pair of stimuli, providing a comprehensive characterization of the psychometric field. In addition, the WPPM readouts were validated for each participant by comparison with 25 probe psychometric functions. These were measured with an additional 6,000 trials per participant that were held out from the WPPM fit. The dataset offers a foundational resource for developing perceptual color metrics and for benchmarking mechanistic models of color processing. This approach is broadly generalizable to other perceptual domains beyond color.

Jul 21, 2025
Hong, F., Bouhassira, R., Chow, J., Sanders, C., Shvartsman, M., Guan, P., Williams, A. H., Brainard, D. H.
CC BY-NC-ND
.na.character

mScarlet3-H with low brightness and fluorescence lifetime has potential for cellular lifetime-unmixing and lifetime-based pH-sensing applications

cell biology
contradictory results

An independent evaluation of the spectroscopic properties, cellular performance, merits and pitfalls of the red fluorescent protein mScarlet3-H as compared to mScarlet3 is reported. mScarlet3-H was generated from mScarlet3 by a single M163H mutation. Purified mScarlet3-H is characterized by a molar coefficient of 79,040 M-1cm-1, a fluorescence quantum yield of 17.8%, molecular brightness of 14.1 and a heterogeneous multiexponential decay with an average fluorescence lifetime of 1 ns. Evaluation in living mammalian cells revealed a comparable maturation speed and efficiency of mScarlet3 and mScarlet3-H, but the overall cellular brightness of mScarlet3-H was 5-fold lower than that of mScarlet3. Photobleaching analysis in live cells revealed identical photobleaching kinetics of mScarlet3-H and mScarlet-H. The fluorescence intensity, fluorescence spectra and fluorescence lifetime of mScarlet3-H were found to be strongly pH-dependent between pH 4-8. The fluorescence lifetime increased from 1 ns to 3 ns in lowering the pH from 8 to 4 with a pK of ~6. The much lower lifetime of mScarlet3-H (~1 ns) as compared to mScarlet3 (~4 ns) allows dual fluorescence lifetime unmixing applications in single channel FLIM recordings in compartments with neutral to slightly alkaline pH. Furthermore, the strongly pH-dependent fluorescence lifetime of mScarlet3-H enables fluorescence lifetime-based pH sensing in a pH region between pH 5 to 7. Using this property, a pH of 6.5 was measured in the lumen of the Golgi system in living cells and motile endomembrane vesicles revealed pH values between 5.5 and 6. Also autophagy of the cytoplasm can be visualized by the pH-dependent fluorescence lifetime with mScarlet3-H accumulation in lysosomes. Potential useful applications and pitfalls regarding the special properties of mScarlet3-H are discussed.

Jul 16, 2025
Gadella, T. W. J., van Weeren, L.
CC NO
.na.character

Volitional Attention to Color: Breaking Willed Attention out of the Spatial Domain

neuroscience
new results

Attention can be guided by either voluntary (top-down) or involuntary (bottom-up) influences. In real-world vision, voluntary attention can be directed by a wide range of influences such as reward, priming, meaning, experience, selection history, and volition. Laboratory studies of voluntary attention have commonly used attention-directing cues to induce or instruct human subjects to attend one class of stimuli while ignoring others. In recent years, free choice conditions of attention have been introduced, where self-generated volitional shifts of attention (willed attention) are possible (for a review, see Nadra & Mangun, 2023). Prior willed attention studies have focused on mechanisms of covert spatial attention, investigating the neurophysiological correlates of willed attention related to both post-decision processing, and the pre-decision brain activity patterns that predict participants’ free choices about where to attend. Much less work, however, has been done on willed non-spatial attention. In this study, in a fashion similar to prior willed spatial attention studies, we investigated willed attention to stimulus color. In a trial-by-trial cueing design, subjects were either cued what color to attend or were allowed to freely choose what color to attend, in order to subsequently discriminate visual features of the cued or willfully chosen target. Behavioral measures showed that the subjects were selectively attending the cued or willed color. Using support vector machine decoding on EEG alpha (8-12 Hz) signals, we found significant post-decision differences in alpha-band power and broadband EEG voltage when participants chose to attend to orange versus purple. However, in contrast to the findings in prior work on willed spatial attention, no pre-decision EEG signals could be identified that predicted which color participants would choose to attend to.

Jul 16, 2025
Nadra, J. G., Sullivan, G., Mangun, G. R.
CC NO
.na.character

A common mechanism and multiple advantages of pigment loss underlie the convergent evolution of albinism in cave animals

evolutionary biology
new results

The loss of pigmentation is a hallmark adaptation of cave-dwelling animals but the underlying mechanisms are poorly understood. This study investigates the cellular and biochemical basis of albinism, the loss of melanin pigment, which convergently evolved across a wide range of cave animals. Is albinism caused by the interruption of pigment synthesis or elimination of the pigment cell lineage? The results suggest that albinism evolved by a common mechanism, a block in the first step of the melanin biosynthesis pathway, the conversion of L-tyrosine to L-DOPA, in diverse albino cave animals ranging from annelids and mollusks to vertebrates. Pigment cells are conserved in all tested albino cave species and distributed in patterns resembling pigmentation in their close surface relatives. The cells capable of melanin synthesis when provided with L-DOPA substrate were detected at the sites of injuries in a cave annelid, cave mollusk, and cave teleost, suggesting roles in innate immunity during tissue repair, which may explain why pigment cells are conserved despite the loss of pigment production. Next, we focused on the longstanding issue of the evolutionary forces involved in the regression of pigmentation in cave animals and explored hypotheses of why losing pigmentation might be adaptive in cave environments. First, we tested the hypothesis that pigment regression may conserve energy, which is important for survival in the food-limited cave environment. Our results indicate that melanin synthesis has a marked energetic cost in the cavefish, Astyanax mexicanus. Lastly, we show that the disruption of melanin synthesis at its first biosynthetic step is correlated with increased dopamine levels in multiple depigmented cavefish populations, including populations that evolved albinism independently. This result supports a widespread tradeoff between the melanin and catecholamine synthesis pathways in A. mexicanus. We conclude that the interruption of the conversion of L-tyrosine to L-DOPA in the synthesis of melanin confers multiple advantages that could serve as targets of natural selection, supporting an adaptive hypothesis for the evolution of albinism in cave animals.

Jul 14, 2025
Bilandzija, H., Renner, K. J., Cetkovic, H., Jeffery, W. R.
CC BY-NC
.na.character

Generalizability of machine learning models for plant traits using hyperspectral reflectance data: The case of maize

plant biology
new results

Hyperspectral reflectance provides rapid and precise phenotyping of plants in a non-destructive manner both in field and well-controlled settings. The resulting data have been used to devise machine learning (ML) models for paired measurements of different traits in diverse plants and crops. Yet, despite advances in using of hyperspectral data to reliably predict crop traits of interest, there are pressing issues concerning the training of ML models, the aggregation of data from crop field trials, and the generalizability of the models in different prediction settings. We collected hyperspectral reflectance data along with 25 anatomical, gas exchange, and chlorophyll fluorescence traits from 320 recombinant inbred lines of a maize Multi-Parent Advanced Generation Inter-Cross population grown across three consecutive seasons. We use these data to systematically: (1) compare the performance of representative ML models for different traits, including slow fluorescence kinetics whose predictability by hyperspectral data has not yet been investigated, (2) evaluate the ML model performance in prediction scenarios concerning unseen genotypes, unseen seasons, and the combination thereof, (3) investigate the effects of data aggregation of ML model performance. These problems are addressed in a rigorous nested cross-validation setting that provides a template for adequate assessment of performance of ML models for diverse crop traits considering the particularities of the experimental design.

Jul 6, 2025
Xu, R., Ferguson, J. N., Kromdijk, J., Nikoloski, Z.
CC BY-NC
.na.character

Purification and pigment analysis of diadinoxanthin-binding PSI-LHCI supercomplexes from Euglena gracilis strain Z

plant biology
new results

Euglena gracilis, a phototrophic flagellate, possesses light-harvesting complexes (LHCs) with a pigment composition distinct from that of land plants and green algae, despite notable similarities in LHC polypeptide sequences to green algae. Here, we purified photosystem I-LHCI (PSI-LHCI) supercomplexes from E. gracilis strain Z and characterized their biochemical and spectroscopic properties. The purified complex exhibited a unique pigment profile, notably including diadinoxanthin that is typically found in red-lineage organisms, setting E. gracilis apart from green-lineage organisms. The absorption spectrum displayed the Qy band of chlorophyll a at 675nm, while the 77-K fluorescence-emission spectrum revealed a prominent peak at 732nm, closely resembling those in land plants. These features suggest that long-wavelength chlorophylls bound to LHCI may be evolutionarily conserved. Nevertheless, the absence of neoxanthin, lutein, and violaxanthin further differentiates the Euglena LHCIs from other oxyphototrophs. Together, these results illuminate the evolutionary diversification of PSI-LHCI supercomplexes and offer insights into the unique pigment-binding features of the Euglena light-harvesting system.

Jul 1, 2025
Sakamoto, R., Kato, K., Nakajima, Y., Shen, J.-R., Nagao, R.
CC BY
.na.character

Association of iridescence and tails with flight proxies suggests that predation drives convergence in skipper butterflies

evolutionary biology
new results

Phenotypic evolution is shaped by phylogenetic, ecological and biomechanical constraints. Butterfly wings offer an ideal system to explore these constraints as their evolution is strongly influenced by natural and sexual selection affecting colour patterns and wing shape in relation to visual signalling and flight performance. We focus on Eudamina skippers, butterflies with large-scale phenotypic convergences involving wing shape and colour pattern. Using a comprehensive morphometric dataset encompassing 176 species, we assess their morphological evolution in a phylogenetic framework. We show that hindwing tails and dorsal iridescence, proposed to signal high escape ability, have repeatedly evolved in tropical species. Hindwing tails are associated with intermediate body size, low wing loading and a forewing shape that facilitates manoeuvrability; iridescence is more common in large species with significantly high wing loading and aspect ratio, indicating high flight speed and manoeuvrability. The evolution of all tested morphometric traits is best described by Ornstein-Uhlenbeck models, indicating stabilising selection around fitness optima in Eudamina. Models testing for random drift or early burst dynamics were rejected in all cases. We reveal a clear co-evolution between the fore- and hindwing shapes, despite both wings having different functional constraints. Hindwing tails have a significant recurrent effect on forewing shape in lineages evolving them independently, suggesting the existence of evolutionary trade-offs between flight performance and antipredator defences. Our study shows that the convergent morphologies across Eudamina have likely arisen not by neutral evolution but by ecological selection influenced by biomechanical constraints.

Jun 27, 2025
Linke, D., Debat, V., Matos-Maravi, P.
CC BY-NC
.na.character

Monitoring Forest Foliar Moisture Using Sentinel-2 Reflectance and Radiative Transfer Model Inversion

ecology
new results

Foliar moisture content (FMC) of forests canopies is important for understanding biodiversity, including animal habitat quality for forest-dependent fauna and forest fire risk. In this study, we modelled spatiotemporal variation in FMC using optical remote sensing. We inverted the PROSPECT and GEOSAIL Radiative Transfer Models (RTM) on Sentinel-2 satellite reflectance data of 20 m ground resolution to retrieve FMC, and then predicted FMC at sub-continental scales using a random forest (RF) regression emulation of the RTM model. An RTM look-up-table, from earlier work, was filtered by ecological criteria from 24 sites sampled along precipitation and canopy cover gradients and was inverted by using the spectral angle, as a merit function. The RF emulator allowed efficient computation and presentation of an extensive and fine-scale forest FMC data cube of interest in animal, fire and plant ecology. Our RTM-based, predictions of forest and woodland FMC had a root mean square error (RMSE) of 19.9% of dry matter content and explained more than 60% of variance (r2 = 0.62). This represents an improvement over previous models using reflectance data of coarser spatial resolution, particularly in terms of explained variance (r2=0.17 and RMSE=32%). The emulator model achieved similar performance to the RTM with slightly larger error (RMSE = 21.77%) and smaller explained variance (r2 = 0.54). Overall, both models performed best in forests, and woodlands of moderate to high canopy density (> ~0.75 LAI). This study demonstrates that FMC can be monitored at spatial resolutions that allow intra- or inter-landscape patterns to be resolved surpassing previous capabilities.

Jun 27, 2025
Kotzur, I., Boer, M., Yebra, M., Moore, B. D.
CC NO
.na.character

Bird species with color polymorphism have greater ecological success

ecology
new results

The explanation of the variation in ecological success of species is one of the key challenges in ecology, evolutionary biology and conservation biology. Here, we discuss the function of polymorphism in body color which is one of the most conspicuous features of organisms strongly affecting the performance of species. We applied a phylogenetic comparative approach to assess whether body color polymorphisms contribute to species success in birds, reflected in distributional ranges, extinction risk, and current population trends. We compiled and analyzed a comprehensive global dataset that included the distribution, phylogeny, ecology and morphological traits of all extant bird species. Species with body color polymorphism showed larger distributional ranges, larger environmental ranges, lower risk of extinction, and more stable population trends. Our analyses suggest that the presence of color polymorphism contributes to avian species success at the global scale, especially reflected in lower extinction likelihood and better population trends.

Jun 25, 2025
Kazuya, H., Sato, E., Sekercioglu, C. H., Noriyuki, S., Takahashi, Y.
CC BY
.na.character

Hawkmoths learn best without negative reinforcement in a differential colour association task

animal behavior and cognition
new results

Visual learning in insects can be strongly influenced by the underlying context and conditions. Improved colour learning has been demonstrated using differential conditioning with reward-aversion paradigms in insects like wasps, bumblebees, and honeybees, where substances that induce strong aversion, such as quinine, enable more accurate discrimination. Although learning outcomes of differential conditioning are closely tied to the perceived reward and aversion, few studies have compared the role of negative reinforcements in shaping associations, and their relevance across insect groups. In our study, we compare the role of aversive substances for differential in the hummingbird hawkmoth, Macroglossum stellatarum, a diurnal moth that relies on vision for foraging. Tying to previous learning studies in insects, we paired a sugar-rewarded target with a distractor that was paired with either quinine, salt, citric acid, water, or was presented with no aversive substance. Learning outcomes were compared by inverting a strong colour preference between perceptually close or distant colour pairs, to provide tasks with disparate challenges. Contrary to results from other insect species, we found that moths trained with quinine were worse at switching preferences between similar colours compared to training with citric acid and appetitive-only differential conditioning. We also show that quinine interferes with sucrose perception, potentially impairing target acquisition during training. Additionally, we link differences in learning arising from the negative reinforcements to their impact on exploration during foraging. Our results highlight the role of experience in modulating behaviour and discuss the importance of interpreting learning outcomes based on an animal’s sensory ecology and foraging dynamics.

Jun 24, 2025
Manel, A. N., Foster, J. J., Stöckl, A.
CC BY-NC
.na.character

Mechanism of PMC (2,2,5,7,8-pentamethyl-6-chromanol), a sterically hindered phenol antioxidant, in rescuing oxidized low-density lipoprotein-induced cytotoxicity in human retinal pigment epithelial cells

molecular biology
confirmatory results

Geographic atrophy or late stage dry age-related macular degeneration (AMD) is characterized by drusen deposition and progressive retinal pigment epithelium (RPE) degeneration, leading to irreversible vision loss. The formation of drusen leads to dyshomeostasis, oxidative stress and irreversible damage to RPE. In this study, we used an in vitro model of oxidized-low density lipoproteins (ox-LDL) induced human RPE damage/death model to investigate the mechanism whereby a sterically hindered phenol antioxidant compound, PMC (2,2,5,7,8-pentamethyl-6-chromanol) protects RPE against ox-LDL-induced damage. We show that PMC exerts its protective effect by preventing the upregulation of stress-responsive heme oxygenase-1 (HMOX1/HO-1) and NAD(P)H:quinone oxidoreductase (NQO1) at mRNA and protein levels. This effect was due to PMC mediated blockade of ROS generation, which in turn blocked nuclear translocation of the Nuclear factor erythroid 2-related factor 2 (Nrf2) transcription factor, ultimately preventing the upregulation of antioxidant response elements (ARE), including HMOX1 and NQO1. A key role for HO-1 was demonstrated when the protective effect of PMC was inhibited by the knockdown of HMOX1. Additionally, treatment of PMC under different experimental conditions and time points revealed that the continuous presence of PMC is required for optimal protection against ox-LDL-induced cytotoxicity, defining the cellular pharmacokinetics of the molecule. Our data demonstrate the involvement of a key antioxidant pathway through which PMC mitigates oxidative stress induced by ox-LDL and provides a potential therapeutic strategy to suppress RPE degeneration/damage during AMD progression.

Jun 22, 2025
Chaudhary, S., Moon, J., Hu, Z., Kriukov, E., Pestun, S., Baranov, P. Y., Ng, Y.-S. E., Damore, P. A.
CC NO
.na.character

Sustained Lysosomal Delivery of Enhanced Cy3-Labeled Acid Nanoparticles Restores Lysosomal pH in Retinal Pigment Epithelial Cells and Astrocytes

cell biology
new results

Lysosomal pH is frequently elevated in age-dependent neurodegenerations like Age-related Macular Degeneration (AMD), Alzheimer’s Disease (AD), and Parkinson’s Disease (PD). Tools that restore lysosomal pH to an optimal acidic range could enhance enzymatic degradation and reduce waste accumulation. Acidic nanoparticles offer a promising strategy for restoring lysosomal function, but accurate tracking of organelle delivery and long-term retention is needed to optimize dosage. To improve detection and enhance delivery, nanoparticles were synthesized from Poly(D,L-lactide-co-glycolide) (PLGA) polymers covalently linked to the fluorescent Cyanine3 amine (Cy3) probe. Nanoparticle concentration and loading times were optimized to achieve >90% delivery to lysosomes in cultured induced pluripotent stem cell-derived retinal pigment epithelial (iPS-RPE) cells. Uptake was heterogeneous, varying between adjacent cells. Once loaded into lysosomes, the nanoparticles were stably retained, with no detectable changes in concentration, distribution, or size for at least 28 days. iPS-RPE cells internalized more nanoparticles than the ARPE-19 cell line or mouse optic nerve head astrocyte cultures. Functionally, PLGA nanoparticles restored an acidic pH and cathepsin D levels in compromised lysosomes. In summary, Cy3-PLGA nanoparticles enabled improved tracking and long-term delivery to lysosomes, supporting future in vivo applications to restore lysosomal pH in aging and degenerating tissues.

Jun 17, 2025
Li, J., Wang, T., Lu, W., Jishkariani, D., Tsourkas, A., Kaja, S., Nair, R., Dunaief, J., Mitchell, C. H.
CC BY-NC-ND
.na.character

ttc39bl, one of the two duplicated paralogs of the tetratricopeptide repeat domain 39B gene, is essential for carotenoid coloration in medaka (Oryzias latipes) and is the gene responsible for the r locus.

zoology
new results

Body color plays key roles in fitness, communication with others, and hiding. In poikilothermal vertebrates, the body color is mainly determined by types and distributions of chromatophores. Among them, carotenoid color of xanthophores/erythrophores is important for interspecific diversity and colorful males as sexual dimorphism. Most vertebrates cannot synthesize carotenoids in their bodies and must ingest them from food. However, the genes involved in the uptake process are not fully understood. Therefore, we tried to identify the causal gene of the carotenoid color mutant of medaka. The HdrR-II1 strain used in the genome project has orange body color in males and white body color in females. The orange and white body color was known to be controlled by the sex-linked R locus, but the causal gene of this was unknown. In this study, we identified that the causal gene of the R locus is tetratricopeptide repeat domain 39b like (ttc39bl). In the HdrR-II1, the ttc39bl on the Y chromosome is normal, but the ttc39bl on the X chromosome has an 821 bases insertion in exon 3 and is broken. This insertion is also present on both the X and Y chromosomes of commercially available white medaka.

Jun 17, 2025
Kimura, T., Inoue, I.
CC BY-NC-ND
.na.character

Quantifying Misuse of Color in Biological Research

scientific communication and education
new results

Colors are widely used to report biological research data. Effective interpretation of colors relies on accurate, intuitive, and accessible colormaps that are properly labeled. Misuse of colormaps, such as using rainbow, mismatched, and other inaccessible colormaps, hinders reader interpretation. Despite their ubiquitous use to represent biological data, the prevalence of colormap misuse has not been quantified. Using established guidelines, we analyzed over 6,000 articles in 10 high-impact biological journals spanning 2020-2024 to quantify the prevalence of colormap use and misuse. Over 67% of articles contain at least one colormap, of which 81% contain some form of misuse. Among the over 11,000 acquired colormap-associated figures, 60% contain some form of misuse. Heatmaps, scatter plots, images, and image overlays are the most commonly used figures with colormaps. These statistics vary by journal but remain constant over time, demonstrating the urgent need to increase awareness and education about color-based data reporting guidelines.

Jun 15, 2025
Lin, T.-J., Hillman, K., Kim, L., Garg, M., Duong, M., Landry, M. P.
CC NO
.na.character

Take it or leaf it: bees learn leaf shape as a cue when flower color is easily learned

animal behavior and cognition
new results

Over a century of research has demonstrated that pollinators, such as bees, associatively learn diverse flower cues, including tactile, visual, and olfactory cues, to find food rewards. However, floral cues are not always reliable, as flowers of different plant species often differ in terms of the qualities of their food rewards, even when flower types resemble each other. At the same time, some non-floral traits, such as leaf shape, differ reliably among plant species and might be associatively learned by bees to improve foraging success. In this laboratory study, we tested whether generalist bees (Bombus impatiens) can (1) associatively learn differences in leaf shape to discriminate rewarding from unrewarding flowers and (2) rely more on differences in leaf shape when a flower color cue is harder to discriminate. We therefore assigned bees to either of two treatments: in one treatment, rewarding and unrewarding artificial targets (“flowers”) differed greatly in petal color, and in the other treatment, they differed little; each treatment’s targets differed in leaf shape in the same way. As expected, bees learned significantly faster when flower petal colors were more dissimilar and thus relatively easier to discriminate. These bees also learned and recalled the correct combination of petal color and leaf shape. Yet when petal colors differed relatively little, bees had a much harder time learning petal color and did not show evidence of having remembered leaf shape. Our results demonstrate that leaf shape is a cue that foraging bees can learn to associate with a pollen food reward. However, leaf shape may be learned secondarily to, or only in combination with floral cues (such as petal color). We discuss evidence of compound learning and overshadowing and implications of our results for pollinator-mediated selection on non-floral plant traits.

Jun 15, 2025
Castagna, A. M. T., Burrow, J. K., Stewart, C. G., Russell, A. L.
CC BY-NC-ND
.na.character

Pupil size correlates with near-threshold detection performance irrespective of stimulus colour, eccentricity, or retinal adaptation-state

neuroscience
new results

In near-threshold detection tasks, larger pre-stimulus pupil size is associated with improved accuracy. However, previous studies have used black and white peripherally presented stimuli, leaving open the question of whether the relationship persists when targets differ in their colour or eccentricity. Across three experiments (in years 2022-2024), we tested a total of 124 participants while systematically varying the lighting conditions and target properties in a near-threshold detection task. Light conditions ranged from dark to dim to bright, with the dark condition including a period of dark-adaptation. Possible target colours were blue and red on a black background (dark condition), blue and red on a grey background (dim condition), or yellow and cyan on a white background (bright condition). Possible target eccentricities ranged from parafoveal to peripheral, in a continuous manner (experiment 3) or as two predefined near and far eccentricities (experiments 1 & 2). Across all experiments we show that larger pre-stimulus pupil size is associated with improved performance. This large-pupil advantage is not modulated by the colour or eccentricity of the targets, the illumination of the testing room, or retinal adaptation-state. We conclude that the phenomenon is robust, indicating that pupil size affects vision in a behaviourally relevant manner, regardless of the exact conditions.

Jun 6, 2025
Ruuskanen, V., Mathot, S.
CC BY-NC
.na.character

Redesigning petal shape, size, and color in soybean reveals unexpected phenotypes for floral organ development

plant biology
new results

Soybean (Glycine max) has not yet benefited from large-scale hybrid breeding efforts due to its small, self-fertilizing flowers that are difficult to emasculate and limited attractiveness to pollinators. This study explores targeted floral trait engineering to enhance pollinator attraction, aiming to overcome barriers to soybean hybridization. We generated a high-resolution floral organ expression atlas and H3K4 trimethylation ChIP-Seq dataset to identify candidate genes involved in petal development, nectar sugar content, and petal pigmentation. Using CRISPR-based activation and repression systems, we modified the expression of AINTEGUMENTA (GmANT), BIGPETAL (GmBPE), and SUCROSE TRANSPORTER2 (GmSUC2). Contrary to expectations based on Arabidopsis homologs, transcriptional activation of GmANT_B and repression of GmBPE led to reduced, rather than increased, petal size, highlighting divergent regulatory mechanisms in soybean. Complementation of the W1 gene that controls petal pigmentation successfully converted white petals to purple, with preliminary evidence indicating that this color conversion may increase pollinator visitation. These results underscore the complexity of floral development in soybean and provide foundational tools and resources for future efforts to engineer reproductive traits for hybrid seed production.

Jun 6, 2025
Szeluga, N., AlBader, N., Pelletier, S., Weis, K., Johnson, A., Fahlgren, N., Neequaye, M., Vogt, G., DelPercio, R., Baldrich, P., Byers, K. J. R. P., Meyers, B. C., Frank, M.
CC BY-NC-ND
.na.character

The role of secondary pollinators in the evolution of complex colour signals in a bimodal pollination system

evolutionary biology
new results

Flower colour is recognized as a key trait influencing pollinator visitation and behaviour, evolved to match the sensory system of a particular pollinator group. However, some flowers combine colours associated with different pollinators, suggesting bimodal adaptation. The perennial herb Cyrtanthus obliquus produces red corollas with yellow tips and is pollinated by birds, but also by bees. To assess the role of the two pollinator categories in shaping selection on the bi-coloured corollas, we examined bee choices in arrays in which the colour signals of plants had been manipulated, and we quantified total as well as bird-mediated phenotypic selection on flower colour using both bird and bee visual models. Bees preferred flowers with a yellow signal over all-red flowers. The analysis of phenotypic selection indicated that both birds and bees influence net selection on flower colour, resulting in conflicting selection on the colour contrast between corolla and corolla tip. Our findings show that the optimal phenotype should depend on the relative importance of the two categories of pollinators in a given population, and are consistent with bimodal adaptation. This study fills an important gap by showing that secondary pollinators can contribute to selection on complex colour signals in angiosperm flowers.

Jun 3, 2025
Khoury, K. L., Agren, J., Peter, C., Sletvold, N., Newman, E. L.
CC NO
.na.character

A Standardized Method for Insect Color Analyses using Open Source Software: AInsectID Version 1.1 Color Merge

zoology
new results

The accurate representation of color is important in applications involving species identification. Environmental variations introduce inconsistencies in color perception, affecting the reliability of automated image processing algorithms. In previous work, we developed a hybrid algorithm, AInsectID Version 1.1 Color Merge, to overcome challenges posed by over-segmentation and under-segmentation in insect wing color clustering. We achieved this by using color differences between superpixels to measure homogeneity during the superpixels segmentation process. Nevertheless, our algorithm remains sensitive to environmental effects, affecting its performance and accuracy in color analyses. Here, we introduce a standard imaging method for insect species, as a pre-requisite to analysis in AInsectID Version 1.1 Color Merge. We systematically examine the effects of varying lighting conditions, angle of observation, and working distance in a controlled environment to assess their impact on the performance of the algorithm. We find that by meticulously controlling lighting, working distance, and lighting angle, we develop an evidence-based standard approach to imaging colors that is robust and repeatable. By following our standardized procedure, consistent color analyses are possible under varying environmental conditions. The method was tested using the Delta E2000 ({Delta}E) color difference metric with a threshold of 1, demonstrating that our standard approach maintains perceptual accuracy within the Just Noticeable Difference (JND) range, while improving the reliability of color analyses of insect wings in diverse environments. Finally, to validate the robustness of our standardization method, we evaluated the certainty of our results at different levels of confidence.

Jun 1, 2025
Sadia, H., Muttaqin, S. S., Alam, P.
CC BY
.na.character

Movi Color: fast and accurate long-read classification with the move structure

bioinformatics
new results

The number of reference genomes is rapidly increasing, thanks to advances in long-read sequencing and assembly. While these collections can improve the sensitivity and specificity of classification methods, this requires highly efficient compressed indexes. K-mer-based approaches like Kraken 2 are efficient but limit the analysis to a fixed k-mer length. This is hard for the user to set ahead of time, and suboptimal settings can harm sensitivity and specificity. Methods that use compressed full-text indexes like SPUMONI2 and Cliffy lift this constraint, but are less efficient than k-mer-based tools. Further, these methods either cannot report a full listing of genomes where a match occurs, or cannot scale to large reference databases. We propose new methods and algorithms that use compressed full-text indexes to enable multi class and taxonomic classification. Unlike past compressed-indexing methods for classification, ours uses the move structure, which is extremely fast thanks to its locality of reference. Our method, called Movi Color, augments the main table of the Movi index. Specifically, Movi Color assigns a “color” to each run of the Burrows-Wheeler Transform according to the subset of genomes from which the run suffixes originated. When the reference is highly repetitive, as is typical when indexing pangenomes or reference databases, only certain colors occur, creating opportunities to compress the index. For species-level classification, Movi Color achieves over 1.6x higher precision and 2x higher recall than Kraken 2 and Metabuli. At the genus level, it achieves 70% higher precision and 80% higher recall. Movi Color’s read processing time is 7-20x faster than Metabuli and is comparable to Kraken 2. Although Movi Color uses more memory than both Kraken 2 and Metabuli,its speed-accuracy trade-off makes it well-suited for real-time or high-throughput scenarios.

May 27, 2025
Tan, S., Majidian, S., Langmead, B., Zakeri, M.
CC BY
.na.character

High-throughput iNaturalist image analysis reveals flower color divergence in Monarda fistulosa

evolutionary biology
new results

Characterizing patterns of trait variation across widespread species is a fundamental goal of natural history. Here we create a pipeline to analyze a large community science dataset and test hypothesized flower color divergence across the range of a widespread wildflower. Monarda fistulosa is a North American perennial that produces showy lavender inflorescences. Although previous literature suggests that the flowers of western M. fistulosa might display a deeper purple color than the eastern varieties, this divergence has not been assessed at scale. We process over 40,000 community science photographs of M. fistulosa to identify flowers and extract color. We demonstrate that the flowers of the montane western variety have lower lightness and higher chroma, corresponding to a deeper violet color, than those of eastern M. fistulosa. Our approach and validation provides a scalable framework for phenotyping community science images and enables analysis of geographic color variation in other widespread species.

May 26, 2025
McKenzie, P. F., Church, S. H., Hopkins, R.
CC BY
.na.character

A Spectral Image Scanning Microscope for Multi-Color High-Resolution Imaging

biophysics
new results

Fluorescence confocal microscopy is a fundamental and widely used tool for biological, medical, and chemical research. It enables color-coded visualization of sample components, enhancing our understanding of life’s building blocks and their interactions. The recent realization of image scanning microscopy (ISM) using confocal spinning disks (CSD) enhanced the spatial resolution of fluorescence microscopy to twice the diffraction limit with minimal sample perturbation and fast acquisition rates. However, capturing multi-color images using ISM is still time-consuming and introduces temporal artifacts as different colors are not acquired simultaneously. Here, we present a spectral CSD-ISM system designed for concurrent high-resolution and simultaneous multi-color acquisition. By integrating a custom linear Amici prism into the CSD-ISM optical detection path, we achieve multi-color, super-resolution images at a fraction of the acquisition time and with a flexible color palette selection. A digital signal processor (DSP) is employed together with accompanying software as a cost-effective alternative to Field-Programmable Gate Arrays (FPGAs) used in previous studies. We provide an accompanying GPU-compatible, python-based image processing pipeline to decompose spectral signatures into multi-color channel-based images, preserving the optical resolution. System characterization using three color fluorescent beads demonstrated 1.74-fold resolution improvement over the diffraction limit and accurate color classification with three times faster acquisition compared to standard CSD-ISM. Application to neuron cells expressing a Parkinson’s disease-associated mutation, showcased improved resolution and contrast of four distinctly labeled cellular components. This spectral CSD-ISM system provides a valuable tool for biological imaging, enabling the simultaneous acquisition of high-resolution spatial information and multi-color spectral data.

May 18, 2025
Bram, L., Tal-Friedman, O., Fibeesh, N., Bar-Sinai, Y., Flaxer, E., Roichman, Y., Ebenstein, Y., Jeffet, J.
CC BY-NC-ND
.na.character

Lrrns define a visual circuit underlying brightness and contrast perception

neuroscience
new results

Brightness and contrast are fundamental features of vision, crucial for object detection, environmental navigation, and feeding. Here, we identify a brightness- and contrast-processing circuit in the zebrafish visual system and uncover the role of Leucine-rich repeat neuronal (Lrrn) cell adhesion molecules (CAMs) in regulating its assembly. Deep-projecting retinal ganglion cells (RGCs) serve as the first synaptic relay to the brain requiring Lrrn2 and Lrrn3a for precise axonal targeting and connectivity within the optic tectum. Genetic targeting of these CAMs leads to circuit disorganization and impairments in contrast sensitivity, leading to deficits in visually guided behaviors. Additionally, ultrastructural circuit reconstruction and functional imaging analysis revealed their critical role in luminance processing. These studies define a fundamental visual processing pathway and establish Lrrn CAMs as essential molecular drivers of its assembly.

May 10, 2025
Putti, E., Faini, G., Dang, J. T.-M., Eggeler, F., Savaliya, J. H., Duroure, K., Vougny, J., Bahl, A., Lichtman, J. W., Engert, F., Boulanger-Weill, J., Del Bene, F., Albadri, S.
CC NO
.na.character

Random and non-random variation in flower color along an urban-rural gradient in the introduced mustard Hesperis matronalis

evolutionary biology
new results

PremiseUrbanization can alter the interplay of stochastic genetic drift and natural selection but these effects will depend on the biology and history of a species. To explore the influences of drift and selection we investigated patterns of flower color variation among populations of the introduced ornamental mustard, Hesperis matronalis, along an urban-rural gradient in eastern Ontario Canada.

MethodsWe surveyed 136 naturalized stands of H. matronalis over three generations, and for each stand estimated the diversity of the three color morphs (white, pink, purple), the number of reproductive plants, and the degree of urbanization based on night sky brightness.

Key ResultsFlower color morph diversity increased with both stand size and urbanization which is consistent with effects of genetic drift during colonization combined with multiple introductions of this horticultural plant in urban areas. However, the frequency and fixation of the purple morph systematically increased towards the rural end of the gradient. Although lifetime seed production did not vary among morphs, pre-dispersal seed predation by a recently adventive weevil was higher in the purple morph, particularly in rural areas. Estimated seed production in the absence of predation suggests a previous fitness advantage for the purple and pink morphs in rural areas and for the white morph in urban areas.

ConclusionsRandom variation in flower color diversity may be influenced by stochastic processes and colonization history, while systematic variation in color morph frequencies may reflect past fitness differences among morphs that have been recently erased by seed predation.

Apr 29, 2025
Maunder, K. G., Dawson, K., Joslin, L., Eckert, L., Kraml, M. M., Dean-Moore, C., Eckert, C. G.
CC BY
.na.character

Microneedle delivery of stem cell derived retinal pigment epithelial cells

cell biology
new results

Retinal pigment epithelium (RPE) transplantation surgery has shown potential benefits in animal models and early clinical trials. However, current implantation techniques are limited by the need for large retinotomies when cell bearing scaffolds are used or cellular reflux in the case of cell suspension transplantation with micro-cannulae. Here we demonstrate that it is feasible to pass primary and stem cell derived RPE cells through microneedles with a bore as small as 30m. In vitro, there is no immediate loss of cell viability and this remains true throughout 14 days of live cell viability monitoring. Further, when the RPE cells are cultured over 14 days, they attach within 24 hours and become confluent, with normal morphological appearances. The formation of tight junctions is unimpeded with the typical polygonal pattern observed. The effects of shear stress due to passage of the cells through a small lumen were not evident in cultured cells labelled for the cytoskeletal protein F-actin. RPE cell VEGF secretion is unaffected by microneedle size in primary RPE and iPSC RPE cells. Ex vivo surgical implantation demonstrates that the technique is feasible, RPE cells engraft in the outer retina and we show that vitrectomy is not required to successfully transplant cells. Herein, we provide the first evidence of surgical microneedle cell delivery, which may have future applications more broadly within ophthalmic microsurgery and minimally invasive delivery strategies.

Apr 29, 2025
Ching, J., Hinako, I., Kitahata, S., Morrow, L., Kadonosono, K.
CC BY-NC
.na.character

Illuminating the Unconscious: Physical and Perceived Brightness in Cognitive Processing

biochemistry
new results

This study investigated how physical luminance and perceived brightness affect breakthrough time (BT) under continuous flash suppression (CFS). Experiment 1 examined whether the glare illusion, which increases subjective brightness without altering actual luminance, would shorten BT compared to physically identical controls. The results revealed no difference, suggesting that subjective brightness alone does not expedite emergence into awareness. Experiment 2 assessed whether the partial suppression of the illusion’s inducers influenced detection speed and revealed that subjective brightness stimuli gained a BT advantage. Experiment 3 tested participants’ ability to discriminate real versus illusory brightness while stimuli remained suppressed; performance above chance for both conditions indicated that physical and perceived brightness cues were processed unconsciously. Together, these findings suggest that contextual brightness illusions are not simply lost below awareness, they can be discriminated in unconscious vision.

Apr 24, 2025
Martinsen, M. M., Senda, H., Tamura, H., Nakauchi, S., Minami, T.
CC BY-NC-ND
.na.character

Face-, color-, and word-specific patches in the human orbitofrontal cortex

neuroscience
new results

The human ventral occipitotemporal cortex (VOTC) contains multiple category-specific areas, organized along posterior-to-anterior and medial-to-lateral axes. However, the role of regions beyond the VOTC in category-specific processing remains less explored. Here, we report the presence of face-, color- and word-specific patches in the human orbitofrontal cortex (OFC) and systematically describe their location, activity amplitude, category selectivity, representational content, and functional connectivity. We compare these features with those of corresponding VOTC category-specific patches. Our findings reveal that face- and color-specific patches in the OFC follow a similar medial-lateral organization to those in the VOTC and form continuous functional gradients with VOTC patches. These results suggest that the OFC contains a topographic organization similar to, but at a higher hierarchical level than, the VOTC object categorization system.

Apr 23, 2025
Liu, J., Cohen, L., Zhan, M., Bartolomeo, P.
CC BY-NC
.na.character

Sexual signal reliability in male zebra finches: Food intake explains the impact of immune activation on carotenoid-based coloration

evolutionary biology
new results

Theory predicts that traits evolving as animal signals must transmit reliable information about the bearer’s quality. Two hypotheses are often invoked to explain how carotenoid-based colorations function as reliable individual quality signals. The first hypothesis suggests that carotenoid allocation trade-offs between signaling and survival-related functions maintain signal reliability. Only high-quality individuals could resolve these trade-offs without incurring a fitness loss. Such signals are plastic, and the signaler can strategically manage their expression level to increase fitness returns. The second hypothesis posits that certain carotenoid-based signals are strongly constrained in their expression, not allowing strategic manipulations or cheating. We challenged captive male zebra finches (Taeniopygia guttata) with simulated infections by injecting lipopolysaccharides (LPS) derived from Escherichia coli and assessed organ masses, body temperature, and carotenoid levels in several tissues. Compared to controls, LPS-treated birds reduced the bill redness, a sexual signal. However, this reduction was largely explained by decreased food intake caused by LPS. The bill redness was negatively correlated with body temperature and spleen mass but positively correlated with blood, spleen and subcutaneous fat carotenoid levels. Overall, our findings suggest that carotenoid-based bill coloration predominantly reflects the recent physiological condition of individuals and resource allocation trade-offs rather than directly signaling individual quality.

Apr 14, 2025
Cantarero, A., Mateo, R., Camarero, P., Andrade, P., Carneiro, M., Alonso-Alvarez, C.
CC BY-NC-ND
.na.character

Plant silicon defence disrupts cryptic colouration in an insect herbivore by restricting carotenoid sequestration into the haemolymph

ecology
new results

Cryptic colouration is a primary anti-predation strategy in herbivorous insects. Achieving crypsis often requires acquiring dietary carotenoids–tetraterpene pigments vital for plant colouration and photoprotection. Silicon (Si) accumulation in plants makes tissues tougher and less digestible for insects, but its effect on plant pigment levels remains unclear. It is also unknown whether feeding on silicified plants impairs insects’ ability to sequester carotenoids and achieve crypsis. Using the model grass Brachypodium distachyon, we demonstrate that the cotton bollworm (Helicoverpa armigera) larvae exhibited stunted growth and reduced carotenoid sequestration, particularly lutein, into their hemolymph when feeding on Si-supplemented (+Si) plants. This reduction led to distinct body-colour morphs: larvae feeding on +Si plants developed brown colouration, contrasting sharply with the green leaves, whereas larvae feeding on Si-free (-Si) plants exhibited green cryptic colouration that blended seamlessly with the foliage. Plant leaves contained various carotenoids (neoxanthin, violaxanthin, {beta}-carotene and lutein) and chlorophylls (a and b), but larvae only sequestered {beta}-carotene and lutein into their haemolymph while excreting substantial amounts of pigments, regardless of plant Si status. Under insect-free conditions, +Si plants had lower carotenoid and chlorophyll contents than -Si plants. However, following insect herbivory, pigment levels in -Si and +Si plants equalised. Insect herbivory also increased Si accumulation in +Si plants. Our findings provide novel evidence that plant Si defences can disrupt cryptic colouration in insect herbivores by restricting carotenoid sequestration from host plant tissues. This disruption could increase insect visibility to predators, potentially elevating their risk of predation.

Apr 8, 2025
Islam, T., Anwar, S., Cazzonelli, C. I., Moore, B. D., Johnson, S. N.
CC NO
.na.character

Theoretical physical color gamuts define luminosity and naturalness perceptual limits in natural scenes

neuroscience
new results

Realism in augmented reality (AR) hinges on the seamless blending of virtual elements into real-world environments. One possible factor influencing this realism may be the physical gamut: an internal representation of all perceivable colors within a natural scene. Previous studies on luminosity thresholds suggest that this gamut, rooted in optimal colors theory, constrains perceptual judgments. While promising, such findings were based on abstract and two-dimensional stimuli only. Before extending this framework to more realistic AR scenarios, an essential next step is to assess whether the physical gamut theory also applies to naturalistic stimuli. This study addresses that gap. Our results reveal that the physical gamut remains a valid construct for natural objects viewed in realistic scenes. Moreover, observers’ judgments of luminosity thresholds appear guided not only by a criterion of self-luminosity, but also by an implicit sense of naturalness. These insights pave the way for exploring AR realism through the lens of physical gamut theory.

Apr 5, 2025
Duay, K., Nagai, T.
CC BY-NC-ND
.na.character

A modular multi-color fluorescence microscope for simultaneous tracking of cellular activity and behavior

animal behavior and cognition
new results

We present a modular epifluorescence tracking microscope which enables ratiometric imaging of muscles, neurons, and other structures in moving animals. The microscope is assembled entirely from commercial parts within 3 hours, making the system broadly accessible. Leveraging the improved brightness and bleaching characteristics of recent genetically-encoded indicators and fluorophores, the simple microscope is even suitable for simultaneous calcium imaging of neurons and behavior as we demonstrate in C. elegans. We also show how muscle dynamics in D. melanogaster larvae can be analyzed and how dual color fluorescence tracking elucidates inter-species interactions by visualizing both predatory nematodes and their prey. Finally, we showcase a configuration for bright-field imaging, by tracking tardigrade gait as an example of utility for non-model species. The affordability of the hardware and ease of use of the accompanying software make this a suitable tool for education in addition to its use in research.

Apr 1, 2025
Ramahefarivo, E., Böger, L., Saichol, T., Shomali, B., Scholz, M.
CC BY
.na.character

Revisiting Color Efficient Coding through Material Perception

neuroscience
new results

An essential objective of early visual processing is to handle the redundant inputs from natural environments efficiently. For instance, cone signals from natural environments are highly correlated across cone types, indicating channel redundancy. Early visual processing transforms the signals into color and luminance information, such as principle component analysis, and thus achieves efficient and decorrelated representations of natural scenes. Building on these findings, previous research has investigated the effect of color on visual tasks such as object recognition using grayscale conversion, which separates luminance from color. However, recent work suggests that when focusing on object materials, color and luminance remain highly redundant due to complex optical properties. Although this finding indicates that there may be a more efficient decomposition of signals, the specific algorithms remain unknown. This study derives that a classic computer graphics algorithm, the median cut, offers a novel approach to enhance visual processing efficiency while capturing diagnostic features to separate material from object geometry information. Human behavioral experiments show that color reduction based on the algorithm disturbs material classification while preserving object recognition. These findings suggest that object geometric structures are available only from low-bit information. Finally, considering material information can be estimated from summary statistics of image sub-spaces, this study suggests an efficient decomposition of input color images.

Mar 25, 2025
Sawayama, M.
CC BY
.na.character

Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate pathogenic variants in age-related macular degeneration

genomics
new results

Age-related macular degeneration (AMD) is a leading cause of vision loss worldwide. Genome-wide association studies (GWAS) of AMD have identified dozens of risk loci that may house disease targets. However, variants at these loci are largely noncoding, making it difficult to assess their function and whether they are causal. Here, we present a single-cell gene expression and chromatin accessibility atlas of human retinal pigment epithelium (RPE) and choroid to systematically analyze both coding and noncoding variants implicated in AMD. We employ HiChIP and Activity-by-Contact modeling to map enhancers in these tissues and predict cell and gene targets of risk variants. We further perform allele-specific self-transcribing active regulatory region sequencing (STARR-seq) to functionally test variant activity in RPE cells, including in the context of complement activation. Our work nominates new pathogenic variants and mechanisms in AMD and offers a rich and accessible resource for studying diseases of the RPE and choroid.

Mar 25, 2025
Wang, S. K., Li, J., Nair, S., Kosaraju, R., Chen, Y., Zhang, Y., Kundaje, A., Liu, Y., Wang, N., Chang, H. Y.
CC BY
.na.character

Genetic analysis of pigment production in the fungus Exophiala dermatitidis

genetics
new results

Exophiala dermatitidis is a polyextremotolerant black yeast species. E. dermatitidis produces 1,8 dihydroxynaphthalene (DHN) melanin via the Polyketide Synthase 1 (PKS1) pathway enabling it to survive harmful conditions. This study focused on random mutagenesis to obtain albino (alb) and hyper-pigmented (hyp) mutants. Notably, all 17 alb mutants possessed mutations in PKS1 whereas the 133 hyper-pigmented (hyp) mutants harbored mutations impacting a range of functions. Cell morphology and phenotypic assays showed additional differences between the alb and hyp mutants. Strikingly, three of the albino mutants (alb1, alb2, and alb3) were conditional in that despite the presence of mutations inPKS1 they were able to produce melanin upon exposure to different carbon sources. These mutants otherwise shared similar cell morphology and growth patterns with the obligate albinos. No additional shared mutations were found among the conditional albinos. Temperature and UV irradiation assays demonstrated reduced growth of albino mutants at higher temperatures (i.e., 42oC) and a greater sensitivity to higher doses of UV. Single nucleotide variant (SNVs) calling showed that hyper-pigmented mutants had a greater number of SNVs compared to albino strains. To date this is the first study to generate and characterize conditional albino mutants in E. dermatitidis with the ability to recover melanin production.

Mar 20, 2025
Harris, S. D., Chhoker, K., Hausner, G.
CC BY-NC-ND
.na.character

High-Density Multi-Distance fNIRS Enhances Detection of Brain Activity during a Word-Color Stroop Task

bioengineering
new results

Significance: Functional Near-Infrared Spectroscopy (fNIRS) enables neuroimaging in scenarios where other modalities are less suitable, such as during motion tasks or in low-resource environments. Sparse fNIRS arrays with 30mm channel spacing are widely used but have limited spatial resolution. High-density (HD) arrays with overlapping, multi-distance channels improve sensitivity and localization but increase costs and setup times. A statistical comparison of HD and sparse arrays is needed for evaluating the benefits and trade-offs of HD arrays. Aim: This study provides a statistical comparison of HD and sparse fNIRS performance to inform array selection in future research. Approach: We measured prefrontal cortex (PFC) activation during congruent and incongruent Word-Color Stroop (WCS) tasks using both Sparse and HD arrays for 17 healthy adult participants, comparing dorsolateral PFC channel and image results at the group level. Results: While both arrays detected activation in channel space during incongruent WCS, channel and image space results demonstrated superior localization and sensitivity with the HD array for all WCS. Conclusions: Sparse channel data may suitably detect activation from cognitively demanding tasks, like incongruent WCS. However, the HD array outperformed Sparse in detecting and localizing brain activity in image space, particularly during lower cognitive load tasks, making them more suitable for neuroimaging applications.

Mar 14, 2025
Anderson, J. E., Carlton, L., Kura, S., O’Brien, W. J., Rogers, D., Hajirahimi, P., Farzam, P., Zaman, M. H., Boas, D. A., Yucel, M. A.
CC BY
.na.character

Accurate spatiotemporal retinal responses require a color intensity balance fine-tuned to natural conditions

neuroscience
new results

Color vision is vital for animal survival, essential for foraging and predator detection. In mice, as in other mammals, color vision originates in the retina, where photoreceptor signals are processed by neural circuits. However, retinal responses to stimuli involving multiple colors are still not well understood. One possible explanation of this knowledge gap is that previous studies have not thoroughly examined how neuronal activity adapts to a 30 seconds to a few minutes timescale when exposed to multiple color sources. To address this, we systematically varied the UV-to-green light balance with a custom-built stimulator targeting mice opsins spectra while recording retinal ganglion cell responses in the ventral retina using multielectrode arrays. Responses to full-field chirp and checkerboard stimulations with alternating UV and green light revealed that more than one order of magnitude of intensity difference favoring green M-opsin over UV S-opsin is needed for a balanced reliability in retinal ganglion cell responses. An incorrect balance, with slightly increased UV light, silenced responses to green illumination. To determine if these values are consistent with natural conditions, we analyzed isomerisation rates in the mouse retina across different times of the day. We found that the M- to S-opsin activation ratio remains constant through the mesopic-photopic range, and our empirically determined values align well with these natural conditions, lying far from a simple equalization of M- and S-opsin isomerisation rates. In conclusion, a finely tuned color intensity balance is essential for accurately measuring both fast temporal responses and detailed spatial receptive fields.

Mar 13, 2025
Castellani, F., Louboutin, A., Quetu, T., Baroux, R., Ferrari, U., Goldin, M. A.
CC BY-NC-ND
.na.character

Light color and nutrients interact to determine freshwater algal community diversity and composition

ecology
new results

Lakes experience a wide range of variation in resource availability; variation of essential resources such as light and nutrients can cause changes in algae community structure. Changes in light color and nutrient availability could lead to shifts in algal community diversity and composition, including shifting communities to be dominated by cyanobacteria. Due to eutrophication and brownification, lakes are experiencing increases in nutrient concentrations and shifts from blue towards red in the color of light available to algae for photosynthesis. We investigated whether differences in light color and nutrients affect algal community composition and diversity, and whether differences in light color alter the impact that nutrient levels have on algal communities. We used experimental microcosms with a fully factorial experimental design, crossing four light colors with two nutrient levels. We assessed community composition by enumerating algal taxa via light microscopy. We found that light color and the interaction between light color and nutrient availability led to large differences in community diversity, with blue light leading to the greatest diversity and broad light the lowest. Light color, nutrients, and the interaction between the two were all significant drivers of differences in community composition. Overall, we found that light color and nutrient availability interact to affect algal community diversity, composition, and cyanobacteria density. Consequences of light color are infrequently studied in aquatic ecology, but our results show that light color may need to be considered more broadly. Furthermore, our results suggest that concurrent eutrophication and brownification may yield environmental conditions favorable to cyanobacteria, including taxa that can form harmful algal blooms.

Mar 4, 2025
Swanson, J. A., Bruck, H., Abdulrahman, D., Richardson, T. L., Dudycha, J. L.
CC BY-NC
.na.character

Brightness demixing for simultaneous multi-target imaging in 3D single-molecule localization microscopy

biophysics
new results

Single-Molecule Localization Microscopy (SMLM) has revolutionized high-resolution imaging, but the simultaneous detection of multiple fluorophores traditionally relies on spectral-based separation, which is inherently constrained by spectral overlap. Here, we introduce Brightness Demixing, a novel method for fluorophore discrimination that exploits brightness, which directly depends on the fluorophore’s extinction coefficient and quantum yield. By oversampling blinking events, we precisely quantify photon flux as a proxy for brightness, enabling robust differentiation of fluorophores independent of their spectral properties, without requiring additional spectral separation. Brightness Demixing operates within a single detection channel, eliminating the need for additional spectral filters or cameras. We demonstrate this approach with simultaneous two- and three-target imaging in both 2D and 3D configurations. By maintaining single-wavelength excitation and minimizing chromatic aberrations, this method significantly enhances multiplexing in SMLM while remaining fully compatible with existing setups. Brightness Demixing thus offers a simple yet powerful approach for expanding multi-target imaging capabilities in super-resolution microscopy

Mar 3, 2025
Le, L., Sreenivas, S. K., Fort, E., Leveque-Fort, S.
CC BY-ND
.na.character

Color-neutral and reversible tissue transparency enables longitudinal deep-tissue imaging in live mice

bioengineering
new results

Light scattering in biological tissue presents a significant challenge for deep in vivo imaging. Our previous work demonstrated the ability to achieve optical transparency in live mice using intensely absorbing dye molecules, which created transparency in the red spectrum while blocking shorter-wavelength photons. In this paper, we extend this capability to achieve optical transparency across the entire visible spectrum by employing molecules with strong absorption in the ultraviolet spectrum and sharp absorption edges that rapidly decline upon entering the visible spectrum. This new color-neutral and reversible tissue transparency method enables optical transparency for imaging commonly used fluorophores in the green and yellow spectra. Notably, this approach facilitates tissue transparency for structural and functional imaging of the live mouse brain labeled with yellow fluorescent protein and GCaMP through the scalp and skull. We show that this method enables longitudinal imaging of the same brain regions in awake mice over multiple days during development. Histological analyses of the skin and systemic toxicology studies indicate minimal acute or chronic damage to the skin or body using this approach. This color-neutral and reversible tissue transparency technique opens new opportunities for noninvasive deep-tissue optical imaging, enabling long term visualization of cellular structures and dynamic activity with high spatiotemporal resolution and chronic tracking capabilities.

Feb 27, 2025
Keck, C. H. C., Schmidt, E. L., Roth, R. H., Floyd, B. M., Tsai, A. P., Garcia, H. B., Cui, M., Chen, X., Wang, C., Park, A., Zhao, S., Liao, P. A., Casey, K. M., Reineking, W., Cai, S., Zhang, L.-Y., Yang, Q., Yuan, L., Baghdasaryan, A., Lopez, E. R., Cooper, L., Cui, H., Esquivel, D., Brinson, K., Chen, X., Wyss-Coray, T., Coleman, T. P., Brongersma, M. L., Bertozzi, C. R., Wang, G. X., DIng, J. B., Hong, G.
CC BY-NC-ND
.na.character

Open-source Photobleacher for Fluorescent Imaging of Large Pigment-Rich Tissues

neuroscience
new results

Fluorescent imaging enables visualization of the specific molecules of interest with high contrast, and the use of multiple fluorophores in a single tissue sample allows visualization of complex relationships between biological molecules, cell types, and anatomy. The utility of fluorescent imaging in human tissue has been limited by endogenous pigments that can block the light path or emit an autofluorescence, thereby interfering with the specific imaging of target molecules. Although photobleachers have been developed to quench endogenous pigments, the lack of customizability limits their utility for a broad range of applications. Here, we present a high luminous-intensity photobleacher that is based on rigorous simulations of illumination patterns using the laws of radiation, along with the framework to maximize bleaching efficiency. This open-source project is designed to help researchers customize and scale according to the tissue types and the research goals. The photobleacher is applicable to both thin tissue slices and large-volume cleared tissue samples to enable serial three-dimensional imaging of postmortem human brain using multiplexed antibody or oligonucleotide probes.

Feb 25, 2025
Murakami, T. C., Belenko, N., Dennis, G., Wang, C., Siantoputri, M. E., Maeda, Y., Pressl, C., Heintz, N.
CC BY
.na.character

Local variations in L/M ratio influence the detection and color naming of small spots

neuroscience
new results

The distribution of long-wavelength sensitive (L) and middle-wavelength sensitive (M) cones in the retina determines how different frequencies of incident light are sampled across space, and has been hypothesized to influence spatial and color vision. We asked whether the detection and color naming of small, short-duration increment stimuli depend on the relative numbers of L and M cones illuminated. Stimuli were corrected for optical aberrations by an adaptive optics system, and targeted to locations in the parafovea where cone spectral types were known. We found that sensitivity to 680 nm light, normalized by sensitivity to 543 nm light, grew with the proportion of L cones at the stimulated locus, though intra- and intersubject variability was considerable. A similar trend was derived from a simple model of the achromatic (L+M) pathway, as well as from photoreceptor-level ideal observers, suggesting that small spot detection mainly relies on a non-opponent mechanism. Most stimuli were called achromatic, with red and green responses becoming more common as stimulus intensity and local L/M ratio symmetry increased. Our detection data confirm earlier reports that small spot psychophysics can reveal information about local cone topography, and our color naming findings suggest that chromatic sensitivity may improve when the L/M ratio approaches unity.

Feb 24, 2025
Greene, M. J., Pandiyan, V. P., Sabesan, R., Tuten, W. S.
CC BY
.na.character

Ecology and sexual conflict drive the macroevolutionary dynamics of female-limited colour polymorphisms

evolutionary biology
new results

Sexual conflict over mating has been documented in many species, both in the field and in experimental studies. In pond damselflies (family Coenagrionidae), sexual conflict maintains heritable female colour polymorphisms, with one female morph typically being a male mimic. However, it is not known whether sexual conflict can also explain the evolutionary origin of female-limited colour morphs, and if so, what ecological factors play a role in this macroevolutionary transition, by modulating the strength of the conflict. Furthermore, the effects of sexual conflict on phylogenetic diversification remain controversial, in particular, whether sexual conflict elevates speciation rates, extinction rates, or both. Here, we use phylogenetic comparative methods to show that female colour polymorphisms are more likely to evolve when population densities at breeding sites are high, and that these demographic conditions are more common at high latitudes and in open landscapes. We show that female-limited polymorphisms typically evolve from sexually dimorphic ancestors through the addition of a male-like female morph, consistent with the hypothesis of selection for male mimicry. Female colour polymorphisms increase both speciation and extinction rates, leading to higher evolutionary turnover of polymorphic lineages. We conclude that female colour polymorphisms evolve in a predictable fashion, and are likely driven by ecological conditions that increase the rate of pre-mating interactions and thus the intensity of sexual conflict. The effects of female colour polymorphisms on extinction differ from previous intraspecific studies and indicate contrasting long-term effects of sexual conflict at micro- and macroevolutionary scales.

Feb 17, 2025
Willink, B., Ho, T. A. T., Svensson, E. I.
CC BY
.na.character

Single-Cell RNA Sequencing Reveals Hemocyte Heterogeneity, Differentiation Trajectories, and Viral Tropism in Shrimp (Macrobrachium rosenbergii) Infected with Decapod Iridescent Virus 1

immunology
new results

Decapod Iridescent Virus 1 (DIV1) is a highly pathogenic virus threatening crustacean aquaculture. Hemocytes, the primary immune cells in shrimp, play crucial roles in host defense, yet their transcriptional heterogeneity and differentiation dynamics under viral infection remain poorly understood. Here, we characterize hemocyte subpopulations in Macrobrachium rosenbergii before and after DIV1 infection at single-cell resolution. We identified 12 distinct hemocyte clusters with unique molecular signatures. DIV1 infection induced significant shifts in hemocyte composition, with clusters 0, 5, 6, and 8 expanding, while clusters 9 and 10 exhibited resistance. Clusters 0, 5, and 8 were highly susceptible, showing elevated viral gene expression. Pseudo-time analysis revealed that DIV1 accelerates hemocyte differentiation, driving prohemocytes and semi-granulocytes toward terminally differentiated granulocytes and hyalinocytes, particularly the immune-active HC4 subpopulation. Functional enrichment analysis showed that susceptible hemocytes were associated with viral processes, oxidative stress, and phagocytosis, while resistant clusters exhibited distinct immune signatures. Furthermore, knockdown experiments confirmed the antiviral roles of PPO2, RAB11B, LAMP1, and Dorsal, as their silencing led to increased viral loads, higher MCP protein levels, and reduced shrimp survival. Taken together, our study provides the first single-cell resolution atlas of shrimp hemocytes under DIV1 infection, revealing their transcriptional heterogeneity, differentiation trajectories, and immune responses. These findings offer novel insights into shrimp antiviral immunity and lay the foundation for disease-resistant breeding and immunostimulatory strategies in aquaculture.

Feb 14, 2025
Xiao, B., Kang, F., Fan, T., Li, Q., Liu, M., He, J., Li, C.
CC BY-NC-ND
.na.character

Is blue the most attractive color for bees? Exploring the attractiveness of colors in vane traps

zoology
new results

Bees play important roles in shaping ecosystems through processes like pollination. However, their populations are in decline due to habitat degradation and unsustainable agriculture. This study assesses the effectiveness of color traps for bee monitoring in two distinct yet geographically close habitats in "Jenaer Forst" natural reserve in Germany. Over a 23-week period in spring and summer 2023, we tested six trap colors (blue, yellow, white, violet, blue-yellow, and violet-white) and analyzed their performance in terms of bee abundance, diversity, and species composition. Our results indicate that violet and blue-yellow traps captured the highest bee abundance and species richness. While overall bee community composition did not differ significantly between trap colors, specific species showed color preferences. The blue-yellow trap emerged as a versatile option, potentially capturing a diverse range of species through its contrasting colors. Moreover, despite the close proximity of the two sites, differences in community composition suggest that habitat-specific factors influence bee color preferences. Minor habitat changes significantly impacted trap effectiveness, emphasizing the importance of tailored trap designs. These findings highlight the importance of considering both color contrast and habitat context when designing bee monitoring strategies and understanding bee foraging behavior. This study contributes valuable insights to improve trap designs and enhance our understanding of the interactions between bees and their environments.

Feb 12, 2025
Renteria, E., Brehm, G.
CC BY-NC-ND
.na.character

Internet images reveal bumblebee-mimicking hoverflies have evolved to follow flower colour preferences of their models

ecology
new results

Batesian mimics, such as hoverflies, can gain protection by resembling noxious species that predators avoid, such as bees. Such resemblance can be behavioural as well as morphological. Bees commonly have a preference for blue flowers, whilst flies generally prefer yellow and white. We predicted that, driven by selection for enhanced mimicry, bee-mimicking hoverflies would have switched flower preference from yellow to blue, to follow the flower choices of their models. We gathered internet photographs of flower-visiting bees and wasps, their hoverfly mimics, and non-mimicking hoverflies, and compared the colours of the visited flowers. Flowers visited by bumblebees were “bluer” than those visited by other hymenopterans (honeybees, wasps and solitary bees). Correspondingly, flowers visited by bumblebee-mimicking hoverflies were bluer than those visited by non-mimics, and were indistinguishable in blueness from those visited by bumblebees. There was no such pattern in flower “yellowness”, where all flies and most hymenopterans preferred similar yellowness, and only bumblebees chose less yellow flowers than the others. Our study demonstrates widespread changes in microhabitat choice (specifically flower preference) among a diverse group of Batesian mimics, consistent with the idea of behavioural mimicry. Mildly noxious models such as bumblebees are thought to exert particularly strong selection for mimetic accuracy, suggesting that habitat-choice mimicry may be selected as a way of enhancing morphological mimicry.

Feb 7, 2025
Gilbert, J. D., Craig-Jackson, J., Morrell, L., Gilbert, F. S.
CC BY-NC
.na.character

Maturation-dependent complement production and C3 processing in human retinal pigment epithelium cells

cell biology
new results

Induced pluripotent stem cell-derived retinal pigment epithelial (iPSC-RPE) cells, closely resembling healthy RPE, offer valuable insights for retinal disease modelling. This study evaluates immature and mature phenotypes of iPSC-RPE and ARPE-19 cells, comparing RPE characteristics, cell-associated complement profiles, and TGF-{beta}1-mediated stress responses across transcript expression, secretion, and protein levels. Statistical analyses were performed using independent means t-test and Wilcoxon rank-sum test. Mature iPSC-RPE cells exhibited characteristic RPE-morphology, with elevated secretion of complement components (C3, FH/FHL-1, FI), unique FB secretion, and apical complement localisation. Intracellular C3 processing revealed cleavage products different from known blood-derived C3 fragments and showed maturation-dependent differences; only mature iPSC-RPE cells secreted active C3 forms (C3(H2O), C3a) and exhibited the intact C3 {beta}-chain. Mature ARPE-19 and iPSC-RPE cells demonstrated resistance to TGF-{beta}1 treatment, which reduced complement secretion without affecting C3a release. In conclusion, ARPE-19 and iPSC-RPE cells demonstrated local production of complement components and maturation-dependent intracellular processing of C3 into active forms. These findings highlight the impact of RPE maturation on local C3 activation, providing a basis for future studies on C3 functionality in the RPE and its potential pathological effects.

Feb 5, 2025
Schikora, J., Nickel, A., Bergert, J., Hähnel, R., Dort, A., Schayan-Araghi, S. Y., Banerjee, P., Wolf, H. N., May-Simera, H. L., Pauly, D.
CC BY-NC-ND
.na.character

Crossmodal pitch-luminance association in tortoises

animal behavior and cognition
new results

If you think that high-pitched sounds match bright colours more than dark ones, you are not alone. Spontaneous associations between different sensory modalities -crossmodal associations- are widely observed in humans. More recently, crossmodal associations have been reported in chimpanzees, monkeys, dogs, chickens, and tortoises, indicating a general cognitive strategy that reflects natural correlations in the environment or similarities in the architecture of the nervous system. Alternatively, or complementarily, crossmodal associations may arise from learning of species-specific occurrences. Recent research on primates has tentatively linked human pitch-luminance associations to the evolution of language. While humans and chimpanzees spontaneously match a high-pitched sound with a white shape and a low-pitched sound with a black shape, baboons and chickens do not exhibit any preferential association. Identifying spontaneous pitch-luminance associations in species that do not rely on vocal communication, such as the solitary Hermann’s tortoises, would support the idea of a language-independent phenomenon. To test this idea, we studied tortoises for pitch-luminance associations in a spontaneous food-searching task. After hearing a high-pitched (700 Hz) vs low-pitched (450 Hz) sound, animals could choose to search for food behind either a light- or dark-coloured wall. When hearing the high-pitched sound, tortoises chose the white stimulus, whereas when hearing the low-pitched sound, they chose the black stimulus, similarly to what humans and chimpanzees do. These results demonstrate crossmodal pitch-luminance associations in tortoises. While showing this commonality in the perceptual organization of phylogenetically distant species, we shift the question on whether pitch-luminance associations reflect homology or convergent evolution.

Jan 25, 2025
Loconsole, M., Malaman, B., Stancher, G., Versace, E.
CC BY-NC-ND
.na.character

Cis-regulatory Mutations Drive Tissue-specific Subfunctionalization of sRNA loci Regulating Soybean Seed Color During Domestication

plant biology
new results

Gene duplication and structural rearrangements have played a pivotal role in plant genome evolution, enabling functional divergence and the development of novel traits. In soybeans (Glycine max), the I locus, which regulates seed color through tissue-specific subfunctionalization of sRNA loci, offers an example of these mechanisms. Using long-read sequencing, we investigated structural variations underlying four major alleles (I, ii, ik, and i) at the I locus. Our study revealed that large-scale rearrangements, including duplications, inversions, and deletions, within a 180-kb CHS repeat-rich region drive allele-specific RNA silencing through small interfering RNAs (siRNAs). The dominant I allele contains a cis-regulatory region of DnaJ upstream of CHS genes, while the ii and ik alleles feature subtilisin- and P450-driven siRNA loci, respectively. The recessive i allele lacks siRNA production due to deletions or inversions disrupting CHS gene clusters. Phenotypic analyses and RNA-seq confirmed allele-specific, tissue-dependent expression of siRNAs correlating with seed coat pigmentation patterns. This study highlights the evolutionary role of repeat-rich regions in generating regulatory innovations and phenotypic diversity. Our findings underscore the importance of structural rearrangements in domestication traits and demonstrate the power of long-read sequencing for resolving complex genomic regions, advancing both evolutionary biology and crop improvement.

Jan 24, 2025
Vodkin, L., Jones, S., Cho, Y.
CC NO
.na.character

Decoding ladybird’s colours: structural mechanisms of colour production and pigment modulation.

evolutionary biology
new results

This study investigates the mechanisms underlying colour production in the family Coccinellidae, focusing on two model species: A. bipunctata (L) and C. quatuordecimguttata (L). In this family, colours have traditionally been attributed primarily to pigments such as carotenoids and melanins. We propose an alternative perspective, considering the elytra as an integrated optical medium whose optical properties result from both its architectural design and the properties of its constituent materials, including matrix and pigments. In the present work, several methods were used, ranging from optical and electron microscopies, light-based techniques, to LC-HRMS analyses. Through local pigment analyses, microstructural examination of elytra, and modelling of interaction of elytra with light, we show that, while pigments are central to patterning and contribute to colour, overall colour also results from one or more physical mechanisms that may operate simultaneously. In the light of these results, we assume that the complex and diverse colouration in the Coccinellidae can only be elucidated by considering the interplay of pigments and the optical properties of the elytron cuticle.

Jan 21, 2025
CARRADA, M., Haddad, M., San-Jose, L. M., Agez, G., Poumirol, J.-M., Magro, A.
CC BY
.na.character

Competition for light color between marine Synechococcus strains with fixed and variable pigmentation

microbiology
new results

Competition between phytoplankton species for light has triggered an extensive diversification of photosynthetic pigments. In Synechococcus cyanobacteria, three major pigment types occur in the ocean: blue light (BL) specialists that have a high ratio of the BL-absorbing chromophore phycourobilin (PUB) to the green light (GL)-absorbing chromophore phycoerythrobilin (PEB), GL specialists that have a low PUB:PEB ratio, and cells that modify their PUB:PEB ratio to match the ambient color, a process called Type IV chromatic acclimation (CA4). The abundance of CA4-capable cells in marine ecosystems suggests that CA4 confers a fitness advantage in certain light conditions compared to cells with fixed pigmentation. This hypothesis was tested by performing mono- and co-cultures of a BL specialist, a GL specialist and a CA4-capable strain in chemostats under different light conditions. Monocultures enabled us to parameterize a resource competition model that was used to predict competition between the three pigment types in co-cultures. In line with the model predictions, the BL specialist won in low blue light and the GL specialist won in low and high green light. Interestingly, we found that while the CA4-capable strain was at a disadvantage at low light, it was able to outcompete specialists in high blue light.

Jan 20, 2025
Dufour, L., Garczarek, L., Mattei, F., Gouriou, B., Clairet, J., Ratin, M., Kehoe, D. M., Huisman, J., Verspagen, J., Partensky, F.
CC BY-NC-ND
.na.character

Predator-Induced Tail Coloration Toward Diverse Dragonfly Nymphs in Tadpoles of the Japanese Tree Frog (Dryophytes japonicus)

ecology
new results

Anuran larvae can change their coloration and morphology to avoid predation. Particularly, some tadpoles in the genus Dryophytes in the Americas develop deep tail fins and bright orange tail coloration in response to predators such as dragonfly nymphs. These conspicuous tails are hypothesized to attract predator attacks, protecting vital body parts from fatal injuries. However, it remains unclear whether the extent of the induced phenotypic changes differs between various predators with distinct feeding patterns and habitats. To explore this, we reared tadpoles of the Japanese tree frog, Dryophytes japonicus, with four dragonfly species, water bug, water scorpion, or newt, and measured phenotypic changes, especially focusing on tail coloration. We found that the aeshnid Anax nigrofasciatus, a sit-and-wait predator that climbs on aquatic vegetation, induced bright orange and broad tails of tadpoles. Other odonate species that forage in and on the substrate also elicited tail coloration or deeper larval tails, but it took more time to induce the tadpoles’ response compared to A. nigrofasciatus. In contrast, non-odonate predators did not induce color and morphological changes. This study provides the first evidence of predator-induced tail coloration in an Asian species of Dryophytes, which appears to be a defensive response specifically to dragonfly nymphs, as visually adept predators. Moreover, the differences in the extent and timing of the phenotypic changes among odonate species suggest that anti-predator phenotypes are modulated based on relative predation risks, considering the predators’ foraging patterns and visual capabilities, thereby allowing tadpoles to minimize physiological costs and unintended risks associated with the induced traits.

Jan 17, 2025
Noda, A., Watanabe, K.
CC BY-NC-ND
.na.character

Deletion of the moe A gene in Flavobacterium IR1 drives structural color shift from green to blue and alters polysaccharide metabolism

microbiology
new results

Structural colors (SC), generated by light interacting with nanostructured materials, is responsible for the brightest and most vivid coloration in nature. Despite being widespread within the tree of life, there is little knowledge of the genes involved. Partial exceptions are some Flavobacteriia in which genes involved in a number of pathways, including gliding motility and polysaccharide metabolism, have been linked to SC. A previous genomic analysis of SC and non-SC bacteria suggested that the pterin pathway is involved in the organization of bacteria to form SC. Thus here, we focus on the moe A molybdopterin molybdenum transferase. When this gene was deleted from Flavobacterium IR1, the knock-out mutant showed a strong blue shift in SC of the colony, different from the green SC of the wild-type. The moe A mutant showed a particularly strong blue shift when grown on kappa-carrageenan and was upregulated for starch degradation. To further analyze the molecular changes, proteomic analysis was performed, showing the upregulation of various polysaccharide utilization loci, which supported the link between moe A and polysaccharide metabolism in SC. Overall, we demonstrated that single-gene mutations could change the optical properties of bacterial SC, which is unprecedented when compared to multicellular organisms where structural color is the result of several genes and can not yet be addressed genetically.

Jan 15, 2025
Escobar Doncel, A., Patinios, C., Campos, A., Walter Costa, M. B., Turkina, M. V., Murace, M., Staals, R. H. J., Vignolini, S., Dutilh, B. E., Ingham, C.
CC BY
.na.character

Interleukin-34 and debris clearance by mononuclear phagocytes drive retinal pigment epithelium regeneration in zebrafish

immunology
new results

The retinal pigment epithelium (RPE) surrounds the posterior eye and maintains the health and function of the photoreceptors. Consequently, RPE dysfunction or damage has a devastating impact on vision. Due to complex etiologies, there are currently no cures for patients with RPE degenerative diseases, which remain some of the most prevalent causes of vision loss worldwide. Further, owing to a limited capacity for mammalian tissue repair, we know little about how the RPE regenerates. Here, we utilize zebrafish as a model to uncover novel mechanisms driving intrinsic RPE regeneration. We show that interleukin-34 signaling from damaged RPE is required for precisely timed recruitment of mononuclear phagocytes (MNPs) to the injury site. Additionally, we find that cellular debris clearance by MNPs is indispensable for regeneration, as microglia-deficient zebrafish fail to regenerate RPE and photoreceptor tissues. Together, our results establish specific pro-regenerative functions of MNPs after RPE damage.

Jan 14, 2025
Leach, L. L., Gonzalez, R. G., Jayawardena, S. U., Gross, J. M.
CC BY-NC-ND
.na.character

Real-time Color Flow Mapping of Ultrasound Microrobots

bioengineering
new results

Visualization and tracking of microrobots in real-time pose key challenges for surgical microrobotic systems, as existing imaging modalities like MRI, CT, and X-ray are unable to monitor microscale items with real-time resolution. Ultrasound imaging-guided drug administration represents a significant advancement in this respect, offering real-time visual feedback on invasive medical procedures. However, ultrasound imaging still faces substantial inherent limitations in spatial resolution and signal attenuation, which hinder extending this method to microrobot visualization. Here, we introduce an approach for visualizing individual microrobots in real-time with Color Flow Mapping ultrasound imaging, based on acoustically induced structural oscillations of the microrobot generating a pseudo-Doppler signal. This approach enables the simultaneous localization and activation of bubble-based microrobots using two ultrasound sources operating at distinct frequency bandwidths. Our successful capture of microrobots measuring 60-80 micrometers in diameter reveals the potential of real-time ultrasonic imaging at the microscale.

Jan 14, 2025
Dillinger, C., Rasaiah, A., Vogel, A., Ahmed, D.
CC BY-NC-ND
.na.character

Biomimetic hydrogel platform reveals active force transduction from retinal pigment epithelium to photoreceptors

biophysics
new results

Retinal pigment epithelium (RPE) is an epithelial monolayer located at the back of the eye. RPE and retina interact closely, with RPE performing multiple tasks ensuring proper retinal physiology and forming a tight, interlocked structure with photoreceptor outer segments (POS). Especially, RPE participates in the essential daily renewal of POS in a phagocytosis process. However, current RPE in vitro cell culture systems lack the contact between RPE and retina, possibly limiting not only RPE maturation but also hindering the studies addressing the RPE-retina interface. We constructed a retina-mimicking structure from a soft polyacrylamide hydrogel with Matrigel coating and introduced it to RPE cells’ apical side during culturing to model the RPE-retina interface in vitro. RPE cells adhered to the hydrogels during culture, enabling further studies of the biophysical properties of the RPE-hydrogel interface with methods utilizing rheology and traction force microscopy. During phagocytosis, RPE cells generated considerable traction forces that were followed using a hydrogel coated with POS particles. Disruption of RPE’s actin cytoskeleton with Cytochalasin D significantly reduced the force generation. These results support the view of RPE as a mechanically active partner for retina. In addition, our retina-mimicking structure offers a tool for further biophysical modeling of the RPE-retina interface.

Jan 13, 2025
Korpela, S., Kauppila, M., Karema-Jokinen, V., Sukki, L., Kallio, P., Skottman, H., Nymark, S., Ihalainen, T. O.
CC BY-NC
.na.character

30-Color Longitudinal Full-Spectrum Immunophenotyping and Sorting of Human Circulating Immune Cell Subsets Implicated in Systemic Autoimmune Rheumatic Diseases

immunology
new results

This 30-color panel was developed to enable the enumeration and purification of distinct circulating immune cell subsets implicated in the pathogenesis of systemic autoimmune diseases including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), systemic sclerosis (SSc; scleroderma), Sjogren’s disease (SjD), idiopathic inflammatory myopathy (IIM), and others. While designed for application to peripheral blood mononuclear cells, the inclusion of CD45 coupled with the ability to extract cellular autofluorescence spectral signatures enables the application of this panel to other tissue types. Of the 30 total markers, this panel employs 18 markers to profile T cell subsets consisting of different memory subsets and T helper polarities, > 10 markers to profile B cell subsets including double-negative B cells, and a total of 8 lineage markers to identify immune lineages including monocyte and natural killer cell subsets, conventional dendritic cells, plasmacytoid dendritic cells, and basophils. This panel reproducibly identifies target populations with excellent resolution over several months of data acquisition with minimal batch effects, offering investigators a practical approach to sort immune cell subsets of interest for downstream applications while simultaneously collecting high parameter immunophenotypic information using a limited sample quantity.

Jan 13, 2025
Jiwrajka, N., Tuluc, F., Jaimes, M. C., Murray, J. B., Anguera, M. C.
CC NO
.na.character

Identification of ER:melanosome membrane contact sites in the retinal pigment epithelium.

cell biology
new results

The retinal pigment epithelium (RPE) forms a monolayer of cells at the blood:retina interface that plays important roles for photoreceptor renewal and function and is central to retinal health. RPE pigment is provided by melanin-containing melanosomes which offer protection against light and oxidative stress. Melanosome migration into the apical processes of the RPE following light onset is thought to contribute to preventing retinal degeneration with age, though the mechanism is not yet clear. Melanosomes are transported along microtubules to the apical surface where they are transferred to actin filaments within the apical processes. Melanosomes are lysosome-related organelles derived from endosomes and endosome transport along microtubules is heavily influenced by the endoplasmic reticulum (ER) through ER:endosome contact sites. Here we describe extensive connection between the ER and melanosomes in the RPE. We further show, in skin melanocytes, that the ER forms contact sites with all stages of melanosome maturation, but ER contact is reduced as melanosomes mature. Finally, we identify tripartite contact sites between the ER, melanosomes and mitochondria in both RPE tissue and cellular models, suggesting that the ER may influence melanosome biogenesis, maturation and interaction with mitochondria.

Jan 8, 2025
Eden, E. R., Burgoyne, T., Doncheva, D.
CC BY-NC-ND
.na.character

Ether Rhodamines with Enhanced Hydrophilicity, Fluorogenicity, and Brightness for Super-Resolution Imaging

biochemistry
new results

Rhodamine dyes are widely used fluorophores in super-resolution fluorescence imaging due to their exceptional optical properties and “aggregation-disaggregation” induced fluorogenic activation. However, their excessive lipophilicity often reduces brightness in aqueous environments and causes off-target staining, limiting their effectiveness in high-resolution imaging. To address these challenges, we introduce an ether-decorated N-terminal modification strategy for rhodamine and silicon-rhodamine (Si-rhodamine), replacing conventional N-alkyl groups. The ether chains enhance water solubility, decrease aggregate size, and improve fluorogenicity across a wide concentration range. Their flexible, hydrophilic structure forms a protective shield around the xanthene core, minimizing dye-water interactions and reducing fluorescence quenching. Additionally, the inductive effect of the ether chains decreases the electron-donating strength of the amino groups, suppressing quenching caused by twisted intramolecular charge transfer (TICT). These modifications collectively increase the quantum yields of ER and ESiR in water from 0.35 and 0.19 (for tetraethyl-substituted analogs) to 0.70 and 0.41, respectively. Probes derived from ER and ESiR exhibit outstanding fluorogenicity, enhanced signal-to-noise ratios, and improved resolution in complex aqueous environments, demonstrating superior performance in advanced super-resolution imaging techniques such as structured illumination microscopy (SIM), stimulated emission depletion (STED) microscopy, and single-molecule localization microscopy (SMLM). This work introduces an innovative strategy for fluorophore design, offering significant advancements for super-resolution imaging applications.

Jan 2, 2025
Fang, X., Qiao, Q., Li, Z., Li, H.-K., Chen, J., Xu, N., An, K., Jiang, W., Tao, Y., Bao, P., Zhang, Y., Wu, Z., Liu, X., Xu, Z.
CC NO
.na.character

Transcontinental patterns in floral pigment frequencies among animal-pollinated species

plant biology
new results

Flower coloration arises primarily from pigments that serve dual functions: attracting pollinators and mitigating environmental stresses. Among major flower pigment groups, anthocyanins and UV-absorbing phenylpropanoids are particularly notable for fulfilling both roles. Their importance suggests that both pigment types should be widespread in flowers. Here, we analyze the UV-Vis absorption profiles of major floral pigments to assess their potential protective role against UV radiation and demonstrate that this protection is largely confined to UV-absorbing phenylpropanoids. We also analyzed the floral pigment composition of 926 animal-pollinated species from California, southern Spain, and southeastern Brazil. UV-absorbing phenylpropanoids were ubiquitous, while anthocyanins occurred in ~56% of species, carotenoids in ~37%, and chlorophylls in ~17%. Pigment frequencies varied with abiotic and biotic factors, such as light environment in Spain, and pollinator type, such as insect versus hummingbird, in California. Despite these local differences, our findings reveal a consistent regional distribution of floral pigments.

Dec 26, 2024
Narbona, E., del Valle, J. C., Whittall, J. W., Leon-Osper, M., Buide, M. L., Pulgar, I., Camargo, M. G. G., Morellato, L. P. C., Rodriguez-Castaneda, N., Rossi, V., Conrad, K., Hernandez-Mena, J., Ortiz, P. L., Arista, M.
CC BY-NC-ND
.na.character

Chicken shank color determined by Inhibition of dermal melanin (ID) is mediated by a structural variation regulating CDKN2A expression

genetics
new results

It is well established that the color of a chicken’s shank is primarily determined by four genetic loci. Among these, the Inhibition of dermal melanin (ID) locus, which suppresses black pigmentation in the dermal layer of the shank, is the sole sex-linked mutation and its molecular mechanisms remained elusive. In this study, a resource family with segregating shank colors was constructed. A genome-wide association study utilizing FarmCPU software identified a top-associated SNP located on the Z chromosome. Subsequent linkage mapping further refined the candidate region, enabling the screening of the candidate structural variation. The candidate structural variation is associated with the yellow shank and characterized by a 143 bp deletion accompanied by a 2 bp insertion. Within the same Topologically Associating Domain, only the CDKN2A gene showed differential expression. Functional studies, including CRISPR/Cas9-edited cells, provided evidence that this mutation regulates CDKN2A transcription and is responsible for the ID shank color in chickens. The absence of melanocytes is likely due to their apoptosis. This study completes the puzzle of chicken shank color genetics and paves the way for the application of the ID mutation in the auto-sexing of chicks which is intensively needed in layer and broiler industries.

Dec 24, 2024
Li, J., Wang, L., Yang, S., Zhou, X., Gou, Q., Cai, J., Yang, H., Wang, Q., Li, S.
CC NO
.na.character

RGB color indices as proxy for symbiont cell density and chlorophyll content during coral bleaching

ecology
new results

Coral bleaching, the breakdown of the symbiosis between the coral host and endosymbiotic microalgae, is the main cause of widespread coral reef degradation. Current methods for assessing coral health based on visual appearance, such as the use of color reference cards, are limited by subjective human color perception and low resolution. Digital photography with RGB (Red, Green, Blue) color channel analyses offers a fast, non-invasive, and standardized alternative to estimate physiological parameters. However, the link between coral color and physiological parameters during bleaching may vary depending on the type of stressor. While such approaches are extensively used in plant studies, their application in estimating Symbiodiniaceae cell density and chlorophyll content in corals requires further attention. In this study, we analyzed the correlation between Symbiodiniaceae cell density and chlorophyll content across three coral species (Acropora muricata, Pocillopora verrucosa, and Stylophora pistillata) with 19 color indices derived from the RGB channels currently established as predictors of chlorophyll content in plants. Corals were exposed to three bleaching conditions (acute short-term and chronic long-term heat stress and menthol bleaching) to identify the best color indices for assessing coral health through image analysis. We found that the Red index had the strongest linear correlation with symbiont cell density and chlorophyll content across species (R2 up to 0.97), so that relative changes in this color index can be directly interpreted as corresponding changes in tissue parameters. To train a model that predicts symbiont densities of a distinct sample set using the Red index, we found 10 to 12 samples to be sufficient to achieve an accuracy of > 95 % of the models trained on the full datasets. This research contributes to improved image analysis as a reliable and non-invasive tool for monitoring, by providing guidelines for a systematic use of RGB data to interpret coral health.

Dec 22, 2024
Ferrara, E. F., Bauer, L., Puntin, G., Bautz, F. R., Celayir, S., Do, M.-S., Eck, F. L., Heider, M. C., Wissel, P. M.-C., Arnold, A., Wilke, T., Reichert, J., Ziegler, M.
CC BY-NC
.na.character

Genomics of experimental adaptive radiation in the cryptic coloration of feather lice

evolutionary biology
new results

A major challenge faced by living organisms is adaptation to novel environments. This process is poorly understood because monitoring genetic changes in natural populations is difficult. One way to simplify the task is to focus on organisms that can be studied in captivity under conditions that remain largely natural. Feather lice (Insecta, Phthiraptera, Ischnocera) are host-specific parasites of birds that live, feed, and breed solely on feathers. Birds defend themselves against lice, which damage feathers, by killing them with their beaks during bouts of preening. In response, feather lice have evolved background-matching cryptic coloration to help them avoid preening. We experimentally manipulated the color backgrounds of host-specific pigeon lice (Columbicola columbae) by confining them to different colored breeds of rock pigeon (Columba livia) over a period of four years (ca. 60 louse generations). Over the course of the experiment, we sampled lice from pigeons every six months for genomic resequencing, and then calculated allele frequency differences and trajectories to identify putative genomic sites under selection. We documented many loci that changed in response to selection for color. Most loci putatively under selection were unshared among replicate populations of lice, indicating that independent adaptation of distinct lineages to the same novel environment resulted in similar phenotypes driven by different genotypes.

Dec 22, 2024
Baldwin-Brown, J. G., Villa, S., Waight, E., Johnson, K. P., Bush, S. E., Clayton, D. H., Shapiro, M.
CC BY
.na.character

Temporal evolution of color representations measured with MEG reveals a ‘coarse to fine’ dynamic

neuroscience
new results

Color perception is based on the differential spectral responses of the L, M and S-cones, subsequent subcortical and cortical computations, and may include the influence of higher order factors such as language. Although the early subcortical stages of color vision are well characterised, the organization of cortical representations of color remain elusive, despite numerous models based on discrimination thresholds, appearance and categorization. An underexplored aspect of cortical color representations is their dynamic evolution. Here we compare the evolution of three different color representations over time using magnetoencephalography (MEG). We measured neural responses to 14 hues at each of 3 achromatic offsets (increment, isoluminant and decrement) while participants attended either to the exact color of the stimulus or its color category. We used a series of classification analyses, combined with multidimensional scaling (MDS) and Representational Similarity Analysis, to ask how cortical representations of color unfold over time from stimulus onset. We compared the performance of ‘higher order’ models based on hue and color category with a model based simply on stimulus cone contrast and found that all models had significant correlations with the data. However, the unique variance accounted for by each model revealed a dynamic change in hue responses over time, that was consistent with a ‘coarse to fine’ transition from a broad clustering into categorical groups to a finer within category representation. Notably, these dynamics were replicated across datasets from both tasks, suggesting they reflect a robust reorganization of cortical hue responses over time.

Dec 20, 2024
Goddard, E., Mullen, K. T.
CC NO
.na.character

Genetic basis of an adaptive polymorphism controlling butterfly silver iridescence

evolutionary biology
new results

Identifying the genes and mutations that drive phenotypic variation and which are subject to selection is crucial for understanding evolutionary processes. Mormon Fritillary butterflies (Speyeria mormonia) exhibit a striking wing color polymorphism throughout their range: typical morphs bear silver spots on their ventral surfaces, and can co-occur with unsilvered morphs displaying a dull coloration. Through genome-wide association studies in two polymorphic populations, we fine-map this difference in silvering to the 3’ region of the transcription factor gene optix. The expression of optix is confined to the unsilvered regions that surround the spots, and these patterns are transformed to a silver identity upon optix RNAi knockdown, implicating optix as a repressor of silver scales in this butterfly. We show that the unsilvered optix haplotype shows signatures of recent selective sweeps, and that this allele is shared with the monomorphic, unsilvered species Speyeria hydaspe, suggesting that introgressions facilitate the exchange of variants of adaptive potential across species. Remarkably, these findings parallel the role of introgressions and cis-regulatory modulation of optix in shaping the aposematic red patterns of Heliconius butterflies, a lineage that separated from Speyeria 45 million years ago. The genetic basis of adaptive variation can thus be more predictable than often presumed, even for traits that appear divergent across large evolutionary distances.

Dec 17, 2024
Livraghi, L., Hanly, J. J., Loh, L. S., Henry, A., Keck, C. M. T., Shirey, V. M., Tsai, C.-C., Yu, N., Van Belleghem, S. M., Roberts, W. M., Boggs, C. L., Martin, A.
CC BY-NC
.na.character

Two-fold Red Excess (TREx): A simple and novel digital color index that enables non-invasive real-time health assessment of green-leaved as well as anthocyanin-rich crops

plant biology
new results

Background: Digital color indices provide a reliable means for assessing plant health status by enabling real-time estimation of chlorophyll (Chl) content, and are thus adopted widely for crop monitoring. However, as all prevalent leaf color indices used for this purpose have been developed using green-leaved plants, they do not perform reliably for anthocyanin (Anth)-rich red-leaved varieties. Hence, the present study investigates digital color indices for six types of leafy vegetables with different levels of Anth to identify congruent trends that could be implemented universally for non-invasive crop monitoring irrespective of species and leaf Anth content. For this, datasets from three digital color spaces, viz., RGB (Red, Green, Blue), HSV (Hue, Saturation, Value), and Lab* (Lightness, Redness-greenness, Yellowness-blueness), as well as various derived plant color indices were compared with SPAD Chl meter readings and Anth/Chl ratio of n = 320 leaf samples. Results: While most digital color features and indices presented abrupt shifts between Anth-rich and green-leaved samples, the newly-developed color index Two-fold Red Excess (TREx) as well as the color feature R showed very strong correlation with SPAD readings (R2 > 0.84), and did not exhibit any deviation due to leaf Anth content. Moreover, both parameters could predict SPAD values reliably (R2 > 0.75). Further, logarithmic decline of G/R and Augmented Green-Red Index (AGRI) with increasing Anth/Chl ratio (R2 > 0.82) revealed that relative Anth content affected digital color indices markedly by shifting the R:G balance until the Anth/Chl ratio reached a certain threshold. Conclusion: The present study provides the first in-depth assessment of variations in RGB-based digital color indices due to high leaf Anth contents, and uses the data for Anth-rich as well as green-leaved crops belonging to different species to develop a universal digital color index TREx that can be used as a reliable alternative to handheld Chl meters for rapid high-throughput monitoring of green-leaved as well as red-leaved crop varieties.

Dec 12, 2024
Agarwal, A., Colwell, F. d. J., Galvis, V. A. C., Hill, T. R., Boonham, N., Prashar, A.
CC BY-NC-ND
.na.character

Relationship between concentration of cytokinin for efficient shoot regeneration and seed coat color in leaf lettuce

plant biology
new results

Lettuce (Lactuca sativa L.) is an economically important leafy vegetable crop around the world. Recently, transgenic lettuce has been developed to improve agronomic traits. Although plant regeneration is a key step in plant genetic transformation, it depends strongly on the cultivar. In this study, shoot regeneration efficiency was measured by using two leaf lettuce cultivars, Chima-sanchi, white seed cultivar, and Chirimen-chisya, brown seed cultivar, a basal salt mixture, and a combination of the cytokinin, 6-benzylaminopurine (BAP), and an auxin, 1-naphthaleneacetic acid (NAA). Efficient shoot regeneration in Chima-sanchi was thus obtained on 1 x Murashige and Skoog medium (MS) with 0.05 mg L-1 BAP and 0.1 mg L-1 NAA. However, the highest efficiency was obtained in Chirimen-chisya on 1 x MS with 0.5 mg L-1 BAP and 0.1 mg L-1 NAA. Therefore, the BAP concentration for efficient shoot regeneration differs significantly between the two cultivars. These cultivars also have different seed coat colors. Due to the similar results obtained from analyzing 4 additional cultivars, 2 white seed cultivars and 2 brown seed cultivars, we demonstrated a strong correlation between the BAP concentration for efficient shoot regeneration and the seed coat color in leaf lettuce.

Dec 12, 2024
Kimura, M., Yoshizumi, T.
CC NO
.na.character

Cryo-EM of PMEL Amyloids Reveals Pathogenic Mechanism of Pigment Dispersion Syndrome

cell biology
new results

PMEL amyloids provide a vital scaffold for melanin deposition in melanosomes, playing a central role in pigmentation. Despite their importance, the high-resolution structure of PMEL amyloids has remained elusive. Here, we determined near-atomic resolution structures of wild-type PMEL amyloids using cryo-electron microscopy, revealing two distinct polymorphic forms with unique structural features. We further examined the pathogenic G175S mutation linked to pigment dispersion syndrome (PDS). Structural analysis showed that the G175S mutation introduces an additional hydrogen bond, stabilizing a novel fibril conformation. In vitro assays demonstrated a fourfold increase in polymerization efficiency for the G175S mutant compared to the wild-type. This enhanced polymerization correlated with a ~70% increase in secreted amyloids in G175S-expressing cells without detectable changes in melanosome morphology or number. These findings suggest that the G175S mutation promotes amyloidogenesis within melanosomes, increasing amyloid load and contributing to PDS pathophysiology. This study provides insights into the molecular basis of PMEL amyloid formation in both physiological and pathological contexts, offering new perspectives on their structural diversity and dysregulation in pigmentation disorders.

Dec 12, 2024
Yanagisawa, H., Arai, H., Miyazawa, H., Kikkawa, M., Oda, T.
CC BY
.na.character

Truncated and “double-headed” derivatives of TO1-B dye for Mango-based imaging systems with increased brightness and selectivity and large Stocks shift

biophysics
new results

Fluorogenic dyes that light up in complexes with genetically encodable RNA aptamers are increasingly used for intracellular RNA imaging. The growing toolbox of dyes and aptamers allows simultaneous or sequential monitoring of different RNAs. However, few orthogonal aptamer-dye pairs meet all the requirements of multiplex imaging in terms of brightness, contrast, etc., thus necessitating their optimization and further diversification. Here, we report new fluorogenic ligands for the Mango II aptamer, one of the most stable and widely used RNA tags. They are based on the cognate Mango ligand TO1-B, which is a thiazole orange (TO) derivative with a biotinylated tetraethylene glycol (TEG) residue attached via an amide linker, and its analogue with an isosteric triazolyl linker (TO1-triazolyl-TEG-biotin). Structural data suggested that the biotin residue might be dispensable for interactions with Mango, so we replaced it with a second TO residue or the alternative push-pull system, namely the dimethylaminophenyl (DMAP) group linked to the benzothiazolyl (BzT) group via the ethenyl linker. The resulting “double-headed” symmetric and asymmetric dyes showed reduced fluorescence in the free state due to intramolecular TO/TO or TO/DMAP-BzT interactions. The asymmetric dye exhibited intramolecular FRET in complex with Mango, resulting in a remarkably large (130 nm) Stocks shift, which may be advantageous for multiplex imaging. The main limitation of the “double-headed” dyes was their low brightness. To improve brightness, we further optimized the truncated (biotin-free) TO1-triazolyl-TEG dye by introducing a hydroxy or a methoxy group into the methylqunolinium (MQ) fragment of its push-pull system. The brightness of the methoxy-MQ derivative was increased by 40% compared to the reported TO1-triazolyl-TEG-biotin. Importantly, the methoxy-MQ derivative also showed increased selectivity for Mango over other noncanonical nucleic acids structures, making it a promising alternative to known TO-based dyes for high-contrast RNA imaging.

Dec 12, 2024
Svetlova, J. I., Slushko, G. K., Fayzieva, A. S., Belyaev, E. S., Kamzeeva, P. N., Aralov, A. V.
CC BY-NC
.na.character

The effect of illumination cues on color constancy in simultaneous identification of illumination and reflectance changes

neuroscience
new results

To provide a stable percept of the surface color of objects, the visual system needs to account for variation in illumination chromaticity. This ability is called color constancy. The details of how the visual system disambiguates effects of illumination and reflectance on the light reaching the eye are still unclear. Here we asked how independent illumination and reflectance judgments are of each other, whether color constancy depends on explicitly identifying the illumination chromaticity, and what kinds of contextual cues support this identification. We studied the simultaneous identification of illumination and reflectance changes with realistically rendered, abstract 3D-scenes. Observers were tasked to identify both of these changes between sequentially presented stimuli. The stimuli included a central object whose reflectance could vary, and a background that only varied due to changes in illumination chromaticity. We manipulated the visual cues available in the background: local contrast and specular highlights. Identification of illumination and reflectance changes was not independent: While reflectance changes were rarely mis-identified as illumination changes, illumination changes clearly biased reflectance judgments. However, correct identification of reflectance changes was also not fully dependent on correctly identifying the illumination change: Only when there was no illumination change in the stimulus did it lead to better color constancy, that is, correctly identifying the reflectance change. Discriminability of illumination changes did not vary based on available visual cues, but discriminability of reflectance changes was improved with local contrast, and to a lesser extent with specular highlights, in the stimulus. We conclude that a failure of color constancy does not depend on a failure to identify illumination changes, but additional visual cues still improve color constancy through better disambiguation of illumination and reflectance changes.

Dec 10, 2024
Virtanen, L. S., Olkkonen, M., Saarela, T. P.
CC BY
.na.character

Pigmentation and retinal pigment epithelium thickness: a study of the phenotypic and genotypic relationships between ocular and extraocular pigmented tissues.

genetics
new results

The retinal pigment epithelium (RPE) is a specialised monolayer of pigmented epithelial cells in the outer retina. The embryology and biology of pigmentation in the RPE differs from other pigmented tissues such as the hair, skin and iris. The extent to which RPE pigmentation is related to that of other tissues remains unclear, and this study aims to address this knowledge gap. Here, we utilised RPE thickness measured using optical coherence tomography (OCT) imaging as a surrogate phenotype for RPE melanin content. We used UK Biobank data to assess the phenotypic relationships between RPE thickness and fundus pigmentation (principally a measure of choroidal pigmentation), hair colour, skin colour, and ability to tan. We subsequently performed a genome-wide association study (GWAS) to identify genetic loci associated with RPE thickness. We utilised the obtained genetic data to explore the global and local genetic correlation between RPE thickness and other pigmentation-related traits. We found that RPE thickness is not phenotypically or globally genetically correlated with hair colour, skin colour or ability to tan. Whilst RPE thickness was phenotypically correlated with retinal pigmentation score, there was not significant global genetic correlation. Despite this, variants in key pigmentation loci including TYR, and OCA2-HERC2 were found to be significant in our GWAS of RPE thickness. Furthermore, we identified four genetic regions in which RPE thickness is locally genetically correlated with other pigmentation-related traits, all of which contain protein-coding genes that are central to melanogenesis and melanosome transport. In conclusion, our study supports our assertion that pigmentation plays a role in RPE thickness, and highlights both shared and divergent features of RPE and other pigmentation-related traits.

Dec 7, 2024
Julian, T. H., Fitzgerald, T., UK Biobank Eye and Vision Consortium, , Birney, E., Sergouniotis, P. I.
CC BY
.na.character

Multiple pathways to red carotenoid coloration: House finches(Haemorhous mexicanus) do not use CYP2J19 to produce red plumage

evolutionary biology
new results

The carotenoid-based colors of birds are a celebrated example of biological diversity and an important system for the study of evolution. Recently, a two-step mechanism, with the enzymes cytochrome P450 2J19 (CYP2J19) and 3-hydroxybutyrate dehydrogenase 1-like (BDH1L), was described for the biosynthesis of red ketocarotenoids from yellow dietary carotenoids in the retina and plumage of birds. A common assumption has been that all birds with ketocarotenoid-based plumage coloration used this CYP2J19/BDH1L mechanism to produce red feathers. We tested this assumption in house finches (Haemorhous mexicanus) by examining the catalytic function of the house finch homologs of these enzymes and tracking their expression in molting birds. We found that CYP2J19 and BDH1L did not catalyze the production of 3-hydroxy-echinenone (3-OH-echinenone), the primary red plumage pigment of house finches, when provided with common dietary carotenoid substrates. Moreover, gene expression analyses revealed little to no expression of CYP2J19 in liver tissue or growing feather follicles, the putative sites of pigment metabolism in molting house finches. Finally, although the hepatic mitochondria of house finches have high concentrations of 3-OH-echinenone, observations using fluorescent markers suggest that both CYP2J19 and BDH1L localize to the endomembrane system rather than the mitochondria. We propose that house finches and other birds that deposit 3-OH-echinenone as their primary red plumage pigment use an alternative enzymatic pathway to produce their characteristic red ketocarotenoid-based coloration.

Nov 30, 2024
Koch, R. E., Truong, C. N., Reeb, H. R., Joski, B. H., Hill, G. E., Zhang, Y., Toomey, M. B.
CC NO
.na.character

Characterization of widely conserved novel pigment production in Bacillus subtilis species

microbiology
new results

Bacillus subtilis is widely studied in the microbial secondary metabolite (SM) field due to its rich variety of important natural products and genetic tractability. However, identification of novel SMs and their biosynthetic gene clusters (BGCs), has become increasingly difficult, especially in Bacilli, as the tools for screening and genome mining are dependent on clear function or similarity to already known BGCs. Pigments are SMs identified by their absorption of visible light, resulting in a certain color perceived by our eyes at sufficient concentrations. Thereby, pigments provide the evidence of a BGC without knowing the sequence or function. Expanding the known repertoire of SM BGCs with novel BGCs will further reinforce identification of a broader set of BGCs by mining tools such as antiSMASH. Here, we study a pigment observed in B. subtilis soil isolate MB9_B4 on certain media. We characterize the conditions where this pigment is produced and identify the corresponding BGC using a comparative genomic approach exploiting our strain collection containing other isolates with pigment production ability. The responsible BGC carried several genes, which were annotated as parts of the tryptophan biosynthesis pathway, possibly originating from a duplication and divergence of an originally primary metabolism. Identification of the pigment gene cluster additionally lead to the discovery of additional pigment BGC carrier B. subtilis isolates, some of which were described at the earliest in 1896 under the name Bacillus aterrimus, with a name referring to a dark pigmentation (the Latin aterrimus meaning very black). In addition, we employed solid-state nuclear magnetic resonance and Fourier transform infrared spectroscopies to characterize the chemical groups of the pigment. This study describes the chemical and biological features of a new class of SM BGC, which we hope will serve to improve the current BGC discovery pipelines in Bacilli.

Nov 28, 2024
Stannius, R. O., Dunlap, C. A., Morvan, E., Berbon, M., Lecomte, S., Loquet, A., Kovacs, A. T.
CC BY-NC-ND
.na.character

Molecular and genetic characterization of sex-linked orange coat color in the domestic cat

genetics
new results

The Sex-linked orange mutation in domestic cats causes variegated patches of reddish/yellow hair and is a defining signature of random X-inactivation in female tortoiseshell and calico cats. Unlike the situation for most coat color genes, there is no apparent homolog for Sex-linked orange in other mammals. We show that the Sex-linked orange is caused by a 5 kb deletion that leads to ectopic and melanocyte-specific expression of the Rho GTPase Activating Protein 36 (Arhgap36) gene. Single cell RNA-seq studies from fetal cat skin reveal that red/yellow hair color is caused by reduced expression of melanogenic genes that are normally activated by the Melanocortin 1 receptor (Mc1r)-cyclic adenosine monophosphate (cAMP)-protein kinase A (PKA) pathway, but the Mc1r gene and its ability to stimulate cAMP accumulation is intact. Instead, we show that increased expression of Arhgap36 in melanocytes leads to reduced levels of the PKA catalytic subunit (PKAC); thus, Sex-linked orange is genetically and biochemically downstream of Mc1r. Our findings solve a comparative genomic conundrum, provide in vivo evidence for the ability of Arhgap36 to inhibit PKA, and reveal a molecular explanation for a charismatic color pattern with a rich genetic history.

Nov 22, 2024
Kaelin, C. B., McGowan, K. A., Koroma, D. C., Trotman, J., David, V. A., Menotti-Raymond, M., Graff, E., Schmidt-Kuentzel, A., Oancea, E., Barsh, G. S.
CC NO
.na.character

A deletion at the X-linked ARHGAP36 gene locus is associated with the orange coloration of tortoiseshell and calico cats

genetics
new results

The X-linked orange (O) locus in domestic cats controls an unknown molecular mechanism that causes the suppression of black-brownish pigmentation in favor of orange coloration. The alternating black-brownish and orange patches seen in tortoiseshell and calico cats are considered as classic examples of the phenotypic expression of random X-chromosome inactivation (XCI) occurring in female mammals. However, the O gene in the cat genome has not been identified, and the genetic variation responsible for the orange coloration remains unknown. We report here that a 5.1-kilobase (kb) deletion within an intron of the X-linked ARHGAP36 gene, encoding a Rho GTPase activating protein, is closely and exclusively associated with orange coloration. The deleted region contains a highly conserved putative regulatory element, whose removal presumably cause altered ARHGAP36 expression. Notably, ARHGAP36 expression in cat skin tissues is linked to the suppression of many melanogenesis genes, potentially shifting pigment synthesis from eumelanin to pheomelanin. Furthermore, we find evidence that the gene undergoes XCI in female human and mouse cells, and XCI-dependent CpG island methylation consistent with random XCI in female domestic cats. The 5.1-kb deletion seems widespread in domestic cats with orange coat coloration, suggesting a single origin of this coat color phenotype.

Nov 21, 2024
Toh, H., Au Yeun, W. K., Unoki, M., Matsumoto, Y., Miki, Y., Matsumura, Y., Baba, Y., Sado, T., Nakamura, Y., Matsuda, M., Sasaki, H.
CC BY-NC-ND
.na.character

Long-term balancing selection maintains cryptic color polymorphism in frogs

evolutionary biology
new results

Color polymorphism can influence the evolutionary fate of cryptic species because it increases populations’ chances of survival in heterogenous or variable environments. Yet, little is known about the molecular and evolutionary mechanisms underlying the persistence of cryptic color polymorphisms, or the impact these polymorphisms have on the macro-evolutionary dynamics of lineages. Here, we examine the evolutionary history of the most widespread cryptic color polymorphism in anurans, involving green and brown morphs. Using an order-scale comparative analysis, we show that these morphs can co-exist within species over long periods of evolutionary time and that polymorphic lineages switch habitat more frequently and have greater diversification rates than other groups. We then identify the locus responsible for the green/brown polymorphism in a group of African grass frogs, and demonstrate that this genomic region is evolving under long-term balancing selection, resulting in trans-specific polymorphism. These results provide a micro-evolutionary mechanism for the long-term persistence of color polymorphism observed at a macro-evolutionary scale. This study highlights the importance of cryptic color polymorphism in the ecology and evolution of anurans, and provides a framework for future research on the genetic architecture and selective forces underlying cryptic traits.

Nov 18, 2024
Goutte, S., Boissinot, S.
CC NO
.na.character

From aerial drone to QTL: Leveraging next-generation phenotyping to reveal the genetics of color and height in field-grown Lactuca sativa

plant biology
new results

In recent years, the automation of genotyping has significantly enhanced the efficiency of genome-wide association studies. Due to this development, phenotyping is now usually the rate-limiting step, especially in the field. Efforts are now focused on further automating in-field phenotyping. Here we present a GWAS study on 194 field-grown accessions of lettuce (Lactuca sativa). These accessions were non-destructively phenotyped at two time points 15 days apart using an unmanned aerial vehicle. Our high throughput phenotyping approach integrates an RGB camera, a multispectral camera to measure the reflectance at 5 wavelengths (blue, green, red, red edge, near-infrared), and precise height estimation. We used the mean and other descriptives such as median, quantiles, minimum and maximum to quantify different aspects of color and height variation in lettuce from the drone images. Using this approach, we confirm several previously described QTLs, now in populations grown under field conditions and identify several new QTLs for plant-height and color.

Nov 8, 2024
Dijkhuizen, R. F., van Eijnatten, A. L., Mehrem, S. L., van den Bergh, E. S., van Lieshout, J., Spaninks, K., Kaandorp, S., Offringa, R., Proveniers, M., Van den Ackerveken, G., Snoek, B. L.
CC BY-NC
.na.character

Development of glowing plastic bricks from waste plastic and florescent pyoverdine pigment of Pseudomonas aeruginosa

microbiology
new results

The extensive increase in non-biodegradable plastic waste is leading to heightened pollution and severe impacts on the climate. The marine environment withstands the worst of plastic pollution, with a documented accumulation of 86 million tons of plastic debris globally. Humans are directly impacted by degraded plastic waste through direct consumption (e.g., in tap water), indirect consumption (via the consumption of contaminated animals), and interference with various hormonal mechanisms. In the 20th century, human-produced plastics constituted approximately 3% of the world’s total biomass. In addressing this issue, we embarked on the development of plastic bricks, emphasizing the repurposing of plastic waste. To distinguish our approach, we incorporated a luminescent quality using the inherent fluorescent property of the pyoverdine pigment produced by Pseudomonas aeruginosa. This luminescence aims to mitigate nocturnal visibility issues, which contribute to accidents involving both human and speechless fauna.

Nov 6, 2024
Pandey, K., Oderdara, R., Patel, R. B.
CC NO
.na.character

Iridescent structural coloration in a crested Cretaceous enantiornithine bird from Jehol Biota

evolutionary biology
new results

A combination of sectioning and microscopy techniques, along with the application of finite-difference-time-domain modeling on a fossil feather, novelly results in the estimation of the range of iridescent colors from fossilized melanosomes preserved in the elongate head crest feathers of a new Cretaceous enantiornithine bird. The densely packed rod-like melanosomes yield are estimated to have yielded from red to deep blue iridescent coloration of the head feathers. The shape and density of these melanosome may have also further increased the feathers structural strength. This occurrence on a likely male individual is highly suggestive of both a signaling function of the iridescent crest, and a potential behavioral role in adjusting the angle of light incidence to control the display of this iridescent structural coloration.

Oct 25, 2024
LI, Z., Hu, J., Stidham, T., Ye, M., Wang, M., Pan, Y., Zhao, T., Li, J., Zhou, Z., Clarke, J.
CC BY
.na.character

Disentangling the effect of heritability and plasticity on Populus fremontii leaf reflectance across a temperature gradient

ecology
new results

We quantified the relative effect of plasticity and heritability on Populus fremontii (Fremont cottonwood) leaf reflectance using clonal replicates propagated from 16 populations and grown across three common gardens spanning a mean annual temperature gradient of 10.7-22.3{degrees}C. We used variance partitioning to decompose phenotypic variation expressed in the leaf spectra into genotypic versus environmental components and estimate broad-sense heritability and found that heritability was most strongly expressed in the red-edge (~680-750nm) and SWIR (~1400-3000nm). Support vector machine models predicted P. fremontii source population and garden location at 78% and 93% accuracy, respectively, demonstrating that genotypic and environmental variation can be differentiated from the same leaf spectra. However, model accuracy declined by ~49% when using leaf reflectance from any two common gardens to predict the source population at the third site. Prediction accuracies were lowest for the hottest site, which was linked to leaf stress responses in the visible and red-edge wavelengths (400-750nm). We conclude that leaf spectra display heritability and plasticity across different parts of the spectrum. When mapping in regions/seasons with extreme climates, spectral plasticity linked to heat stress can decrease spectral heritability but may offer opportunities to understand phenological responses to extreme temperatures at large scales.

Oct 24, 2024
Seeley, M. M., Thomson, E., Allan, G. J., Whitham, T. G., Hultine, K., Cooper, H. F., Wiebe, B. C., Asner, G. P., Corbin, J. P., Doughty, C. E.
CC BY-NC-ND
.na.character

Morph-specific selection pressures drive phenotypic divergence in a color polymorphic bird

evolutionary biology
new results

There is a long tradition of using heritable color polymorphisms in natural populations to study selection, gene flow, and other evolutionary processes. However, we still have only limited knowledge on how continuous color variation within genetically discrete morphs affects selective dynamics, which narrows our understanding of how color polymorphisms persist. Our comprehensive analysis of 43 years of plumage color scores from a bi-morphic Finnish population of tawny owls (Strix aluco) reveals that intra-morph variation is substantial, but also unexpectedly dynamic. We show that both morphs recently diverged in their plumage coloration: while the brown morph is on a steady trajectory toward more intense plumage pigmentation, the gray morph has recently shifted toward lighter plumage, following a series of extreme winters. Evidence suggests that this divergence is driven by the brown morph’s higher reproductive success and greater plasticity in response to seasonality, while the gray morph, with its more genetically determined plumage color and limited standing variation, has a reduced capacity to respond to selection and track new phenotypic optima. Our study confirms the presence of substantial and dynamic phenotypic variation within genetically discrete color morphs, and demonstrates its relevance for the evolutionary potential of populations to respond to environmental change.

Oct 20, 2024
Passarotto, A., Lurig, M. D., Aaltonen, E., Karell, P.
CC BY-NC-ND
.na.character

Facial Coloration as a Social Signal in a Neotropical Cichlid: Testing the Facial Expression Hypothesis

animal behavior and cognition
new results

The face is a uniquely distinctive stimulus for humans, encapsulating a wealth of information. Among the myriad of social cues conveyed by the face, emotional signals, known as facial expressions, are paramount not only for humans but also for numerous social animals. The evolution of facial expressions in these animals can also manifest in taxa other than mammals, as suggested by various studies highlighting the socio-ecological benefits of facial expressions. In this study, we elucidated the social function of facial coloration, determined by melanophores, in the neotropical social cichlid Symphysodon aequifasciatus. In this species, facial coloration exhibits flexibility and instantaneous changes in response to varying social contexts. Through behavioral observations and experimental manipulation, we confirmed that facial coloration in S. aequifasciatus serves to attenuate unnecessary aggressive competition among conspecifics. Furthermore, we observed that the facial area subjected to coloration in this species is innervated by the adenosine triphosphate- and noradrenaline-ergic nervous system. These findings indicated that facial expression in S. aequifasciatus depends on the sympathetic nervous system and has evolved independently of mammalian facial expressions. Our study highlights teleost fishes as valuable animal models for exploring the universality of facial expressions and their underlying cognitive mechanisms in vertebrates.

Oct 18, 2024
Satoh, S., Fukuda, K., Matsuo, S., Banda, T., Banda, T., Kanbe, K., Konno, A., Takei, S., Kohda, M., Kutsukake, N.
CC BY-NC-ND
.na.character

Enhancing pigment production by a chromogenic bacterium (Exiguobacterium aurantiacum) using tomato waste extract: A Statistical approach

microbiology
confirmatory results

There is high demand for microbial pigments as promising alternative for synthetic pigments basically for safety and economic reasons. This study aimed at the optimization of yellowish-orange pigment production by Exiguobacterium aurantiacum using agro-waste extract as growth substrate. Air samples were collected using depositional method. Pure cultures of pigment producing bacteria were isolated by subsequent culturing on fresh nutrient agar medium and the potent isolate was identified using MALDI-TOF technique. Culture conditions were screened using Plackett-Burman design and the most three significant variables were optimized by response surface methodology. Fermentation was conducted in 150 mL agro-waste decoctions from which tomato waste extract was selected because of higher optical density of the culture compared to other agro-waste extracts. Pigment was extracted by solvent extraction method and the best solvent was selected based on its ability to dissolve the culture suspension. The pigment was characterized using spectroscopic and chromatographic techniques. Culture agitation rate, initial medium pH and concentration of yeast extract were identified as the most significant (p< 0.0001) variables affecting pigment production. At optimized conditions, 0.96 g/L of pigment was extracted from 4.73 g/L of culture biomass and the extracted pigment under optimized conditions was 1.6 times higher than the pigment extracted under un-optimized conditions. The spectroscopic and chromatographic analyses demonstrated the presence of different functional groups and carotenoids were identified as parts of the molecule responsible for the yellowish-orange pigmentation of the extract. This study demonstrated the potential for optimization of pigment production by bacteria using agro-waste extract as substrate. Hence, the current findings strongly encourage for further study at a large-scale level for industrial production.

Oct 17, 2024
Zeleke, B., Muleta, D., Dinka, H. A., Tsegaye, D. A., Hassen, J.
CC BY
.na.character

Manipulation of the brown glume and internode 1 gene leads to alterations in lignified tissue coloration, lignification, and pathogen resistance in wheat

plant biology
new results

Lignin is a crucial component of the cell wall, providing mechanical support and protection against biotic and abiotic stresses. However, little is known about wheat lignin-related mutants and their roles in pathogen defense. In this study, we identified an ethyl methanesulfonate (EMS)-derived Aegilops tauschii mutant named brown glume and internode 1 (bgi1), which exhibits reddish-brown pigmentation in various tissues, including internodes, spikes, and glumes. Using map-based cloning and single nucleotide polymorphism (SNP) analysis, we identified AET6Gv20438400 (BGI1) as the leading candidate gene, encoding the TaCAD1 protein. The mutation occurred in the splice acceptor site of the first intron, resulting in a premature stop codon in BGI1. We validated the function of BGI1 using loss-of-function EMS and gene editing knockout mutants, both of which displayed reddish-brown pigmentation in lignified tissues. BGI1 knockout mutants exhibited reduced lignin content and shearing force relative to wild type, while BGI1 overexpression transgenic plants showed increased lignin content and enhanced disease resistance against common root rot and Fusarium crown rot. We confirmed that BGI1 exhibits CAD activity both in vitro and in vivo, playing an important role in lignin biosynthesis. BGI1 was highly expressed in the stem and spike and localized in the cytoplasm. Transcriptome analysis revealed the regulatory networks associated with BGI1. Finally, we demonstrated that BGI1 interacts with TaPYL-1D, potentially involved in the abscisic acid signaling pathway. The identification and functional characterization of BGI1 significantly advance our understanding of CAD proteins in lignin biosynthesis and plant defense against pathogen infection in wheat.

Oct 15, 2024
Hua, L., Song, R., Hao, X., Zhang, J., Liu, Y., Luo, J., Ren, X., Li, H., Wang, G., Rehman, S. u., Wu, J., Fu, D., Dong, Y., Wang, X., Zhang, C., Chen, S.
CC BY-NC-ND
.na.character

Growth-coupled microbial biosynthesis of the animal pigment xanthommatin

synthetic biology
new results

The mining of genomes across life has unearthed a bounty of biosynthetic potential to diverse molecules key to a biobased future. While the heterologous expression of metabolic pathways has achieved broad success, most approaches suffer a similar fate in low initial production levels that require extensive, resource-heavy iterative strain engineering refinement. Herein we introduce a growth-coupled biosynthetic (GrowBio) strategy that irrevocably connects microbial growth with specialized compound production. We demonstrate the plug-and-play versatility of GrowBio in the production of the structurally complex animal biopigment xanthommatin, a color-changing ommochrome with material and cosmetic potential. Xanthommatin biosynthesis directly fuels growth of a newly designed Pseudomonas putida 5,10-methylenetetrahydrofolate auxotroph (PUMA). Aided by genome-scale metabolic modeling, PUMA was designed and built to be controlled by endogenous formate co-produced as a coupled biosynthetic byproduct in the multistep conversion of tryptophan to xanthommatin. Adaptive laboratory evolution was utilized to streamline xanthommatin’s gram-scale bioproduction via growth rate selection, establishing GrowBio as a promising biotechnological approach for establishing and optimizing the microbial production of value-added molecules.

Oct 6, 2024
Bushin, L. B., Alter, T. B., Alvan-Vargas, M. V. G., Dürr, L., Olson, E. C., Avila, M. J., Puiggene, O., Kim, T., Deravi, L. F., Feist, A. M., Nikel, P. I., Moore, B. S.
CC NO
.na.character

A massive community-science flower color dataset reveals convergent evolution of delayed flowering phenology in North American red-flowering plants

evolutionary biology
new results

The radiation of angiosperms is marked by a phenomenal diversity of floral size, shape, color, scent, and reward. Through hundreds of years of documentation and quantification scientists have sought to make sense of this variation by defining pollination syndromes as the convergent evolution of common suits of floral traits across distantly related species that have evolved by selection to optimize pollination strategies. Now, with the rise in popularity of community science platforms like iNaturalist, anyone - not just scientists - can collect data. Thanks to the availability of high-quality community-science datasets, we have an unprecedented number of observations of natural flowering plant diversity. These datasets provide an opportunity to develop new tools and to examine new traits, such as flowering time, that may help further characterize pollination syndromes. Here we test the hypothesis that flowering phenology can also be an important trait of a pollination syndrome; particularly of the “hummingbird flower” syndrome, which is usually characterized by red color, long corolla tubes, and exserted stamens. We produced a novel flower color dataset by using GPT-4 with Vision (GPT-4V) to assign flower color to 11,729 North American flowering plant species from community science photographs. We then mapped those species-specific colors to 1,674,908 citizen scientist observations of flowering plants. We demonstrate constrained flowering time in the eastern U.S. for species with red or orange flowers relative to species with flowers of other colors. Importantly, the onset of flowering corresponds closely to the arrival of hummingbirds. Our findings reveal an opportunity to expand the suite of traits included in pollination syndrome and suggest that the hummingbird pollination syndrome can include flowering phenology. Our methods demonstrate an effective pipeline for leveraging the enormous amount of community science data by extracting valuable information about patterns of trait variation.

Sep 27, 2024
McKenzie, P. F., Berardi, A. E., Hopkins, R.
CC BY-NC
.na.character

Novel color vision assessment tool: AIM Color Detection and Discrimination

neuroscience
new results

Color vision assessment is essential in clinical practice, yet different tests exhibit distinct strengths and limitations. Here we apply a psychophysical paradigm, Angular Indication Measurement (AIM) for color detection and discrimination. AIM is designed to address some of the shortcomings of existing tests, such as prolonged testing time, limited accuracy and sensitivity, and the necessity for clinician oversight. AIM presents adaptively generated charts, each a NM (here 44) grid of stimuli, and participants are instructed to indicate either the orientation of the gap in a cone-isolating Landolt C optotype or the orientation of the edge between two colors in an equiluminant color space. The contrasts or color differences of the stimuli are adaptively selected for each chart based on performance of prior AIM charts. In a group of 23 color-normal and 15 people with color vision deficiency (CVD), we validate AIM color against Hardy-Rand-Rittler (HRR), Farnsworth-Munsell 100 hue test (FM100), and anomaloscope color matching diagnosis and use machine learning techniques to classify the type and severity of CVD. The results show that AIM has classification accuracies comparable to that of the anomaloscope, and while HRR and FM100 are less accurate than AIM and an anomaloscope, HRR is very rapid. We conclude that AIM is a computer-based, self-administered, response-adaptive and rapid tool with high test-retest repeatability that has the potential to be suitable for both clinical and research applications.

Sep 27, 2024
He, J., Skerswetat, J., Bex, P. J.
CC BY-NC-ND
.na.character

The role of pigments in light color variation of the firefly Photinus pyralis

evolutionary biology
new results

Fireflies use bioluminescent signals to communicate with their mates. Luciferase has been thought to be the sole contributor to light color; however, populations of the Photinus pyralis firefly display variation in the color of their emitted signals yet have identical luciferase sequences. Here, we examined whether pigments could be present in the light organs of the twilight-active species P. pyralis and contribute to this variation. We detected patterns of expression that suggest ommochrome and pterin screening pigments are expressed in P. pyralis light organs and could filter light emitted by luciferase and play a role in signal tuning. There were no significant differences between the pigment gene expression of P. pyralis individuals with yellower and greener signals. Our study provides alternative mechanisms that could influence pigments in P. pyralis light organs that could also play a role in modifying signal color.

Sep 25, 2024
Popecki, M. S., Rogers, R. L., Archer-Hartmann, S. A., Wares, J. P., Stanger-Hall, K. F.
CC NO
.na.character

Pollinator visitation pattern and differential reproductive compatibilities maintain bract colour polymorphism in a nocturnal ginger from Western Ghats, India

ecology
new results

Polymorphism, the presence of discrete floral morphs within a population, can be maintained by positive or negative frequency selection. Pollinators often show a positive frequency-dependent foraging which confers reproductive advantage to common morphs over rare morphs. However, pollinator-mediated selections often act on visual floral displays. Here, we investigate hawkmoth-mediated selection in a nocturnal Curcuma caulina (Zingiberaceae) with bract colour polymorphism, where the role of visual display is minimal. We used path analyses to explain maintenance of differential morph abundances in C. caulina. For this, we quantified inter-morph trait variations in floral structures, nectar traits, pollinator visitations, physiological compatibilities and reproductive fitness. We noted that the rarest morph was self-compatible, exhibited higher nectar reward and pollinator visits, and low reproductive fitness, whereas the two common morphs were complete to partially self-incompatible, with lower nectar rewards and pollinator visits, but higher reproductive fitness. We conclude that while hawkmoths show a positive response to floral rewards, self-compatibility confers lower reproductive fitness to the nectar-rich rare morphs. In contrast, self-incompatibility confers higher fitness to the common morphs despite lower pollinator visits. Thus, colour polymorphism in nocturnal C. caulina is explained by floral traits associated with bract colour, which are under pollinator-mediated selection.

Sep 24, 2024
Shrotri, S., Gowda, V.
CC BY-NC-ND
.na.character

Ocean carbon export can be predicted from ocean color-based phytoplankton communities

ecology
new results

Carbon flux to the deep sea can be dictated by surface ocean phytoplankton community composition, but translating surface ocean observations into quantitative predictions of carbon export requires additional consideration of the underlying ecosystem drivers. Here, we used genetic tracers of phytoplankton detected in surface seawater and within sinking particles collected in the mesopelagic ocean to identify mechanistic links between surface communities and carbon export in the North Pacific and North Atlantic Oceans. Phytoplankton 18S rRNA sequences were sampled over a one-month period in surface seawater and within bulk-collected and individually-isolated sinking particles using mesopelagic sediment traps (100-500m). Nearly all phytoplankton amplicon sequence variants (ASVs) exported from the surface were packaged in large (>300 m) particles. Individually, these particles contained only a few distinct phytoplankton ASVs, but collectively, large particles transported about half of the surface taxonomic diversity into the mesopelagic. The relative sequence abundances of the surface community detected within particles were quantitatively related to measured POC fluxes: a linear model based on the relative sequence abundance of just two pigment-based phytoplankton taxa, diatoms and photosynthetic Hacrobia, was predictive of POC flux magnitude. These two taxa were also enriched within the ecologically-distinct particle classes that had the greatest influence on carbon export magnitude. As global, hyperspectral ocean color satellites begin to quantify these taxonomic groups in the surface ocean, the relationship of these taxa to carbon fluxes demonstrated here may help generate more accurate global estimates of export.

Sep 24, 2024
Kramer, S. J., Jones, E. L., Estapa, M. L., Paul, N. L., Rynearson, T. A., Santoro, A. E., Sudek, S., Durkin, C. A.
CC BY-NC-ND
.na.character

More than fruity scents: floral biology, scent and spectral reflectance of twelve Annonaceae species

ecology
new results

The pantropical family Annonaceae possesses a broad array of floral phenotypes and pollination specialisations. Being the most species-rich lineage in the magnoliids, Annonaceae are a major flowering plant component of tropical rainforests, and are important in the plant-pollinator network of this biome. Insects such as beetles, flies, bees, cockroaches and thrips have been reported as their pollinators. Although there has been considerable effort to assess their interactions with pollinators, attempts to characterise the visual and olfactory communication channels between them are scarce. Here, we report the floral phenology and characterise the spectral reflectance and odour of 12 Annonaceae species from five genera, viz. Meiogyne, Monoon, Polyalthia, Pseuduvaria, and Uvaria. Pseuduvaria species are either monoecious or dioecious while the four genera produce hermaphroditic flowers. The Meiogyne species are likely pollinated by small beetles; the Polyalthia and Pseuduvaria species are likely pollinated by both beetles and flies; and the Uvaria species is likely pollinated by both beetles and bees. All species produce flowers that are not reflective in the 300-350 nm UV spectrum, and have various spectral reflectance profile across the remaining UV and visible spectra. We detected diverse floral volatiles across all the species assessed. The flowers of the small beetle-pollinated species, including Meiogyne species and Polyalthia xanthocarpa, emitted mostly branched-chain esters, including isobutyl acetate and isoamyl acetate. The Pseuduvaria species emitted scent reminiscent of rotten fruit, largely consisting of 2,3-butanediol, a common by-product in yeast fermentation. The flowers of Uvaria concava, which were visited by both bees and beetles, released mainly straight-chain esters, including methyl hexanoate and methyl (Z)-4-octenoate. A corrugated inner petal outgrowth was observed in Meiogyne and Pseuduvaria; this functions as a food body reward in Meiogyne, but as a nectary gland for Pseuduvaria. This study provides insights into how Annonaceae flowers attract different guilds of pollinators.

Sep 20, 2024
Liu, M.-F., Chen, J., Pang, C.-C., Scharaschkin, T., Saunders, R. M. K.
CC NO
.na.character

Circadian modulation of mosquito host-seeking persistence by Pigment-Dispersing Factor impacts daily biting patterns

neuroscience
new results

Daily rhythms in mosquito attraction to humans are thought to drive biting patterns and contribute to disease transmission dynamics. Behavioral rhythms in many insects are controlled by specialized clock cells in the brain that are coordinated by the neuropeptide Pigment-Dispersing Factor (PDF). We show that female Aedes aegypti mosquitoes with genetically disrupted PDF display altered daily behavioral timing with reduced locomotor activity and biting in the morning. Using an automated behavioral tracking system, we also report that mosquitoes exhibit daily modulation of response persistence to the host cue carbon dioxide and loss of PDF alters this pattern. These findings indicate that PDF regulates temporal features of host-seeking behavior that promote biting success at specific times of day and may underlie blood feeding patterns observed in the field.

Sep 19, 2024
Dong, L., Hormigo, R., Barnett, J. M., Greppi, C., Duvall, L. B.
CC BY-NC
.na.character

Density-Dependent Colour Scanning Electron Microscopy (DDC-SEM). Applications in the study of calcified tissues and visual impact.

scientific communication and education
confirmatory results

Scanning Electron Microscopy (SEM) is widely used as a technique for materials characterization. It has also been successfully applied to the imaging of biological samples, providing invaluable insights into the topography, morphology and composition of biological structures. A particular method combining different SEM detectors, named Density-Dependent Coloured SEM (DDC-SEM), has proven to be most useful for the identification and visualization of minerals in soft tissues. The method consists of a manipulation of original greyscale SEM images to produce coloured images that provide both topography and density information for samples with components of different densities. Here we provide a discussion on how to use DDC-SEM to aid the visualization and intuitive understanding of pathological calcification. This method has become popular not only for its scientific improvement of conventional SEM greyscale images, but also for its aesthetical merits.

Sep 19, 2024
Tsolaki, E., Hunter, L., Chester, A. H., Bertazzo, S.
CC NO
.na.character

Interaction between facial expression and color in modulating EPR P3

neuroscience
new results

The relationships between facial expression and color affect human cognition functions such as perception and memory. However, whether these relationships influence attention remains unclear. Additionally, whether facial expressions affect selective attention is unknown; for example, reddish angry faces increase negative social evaluation or emotion intensity, but it is unclear whether selective attention is similarly enhanced. To investigate these questions, we examined whether event-related potentials for faces vary depending on facial expression and color by recording electroencephalography (EEG) data. We conducted an oddball task using stimuli that combined facial expressions (angry, neutral) and facial colors (original, red, green). The participants counted the number of times a rarely appearing target face stimulus appeared among the standard face stimuli. The results indicated that the difference in P3 amplitudes for the target and standard faces depended on the combinations of facial expressions and facial colors; the P3 amplitudes for red angry faces were greater than those for red neutral faces. Additionally, there was no significant main effect or interaction effect of facial expression or facial color on P1 amplitudes for the target, and there were significant main effects of facial expression only on the N170 amplitude. These findings suggest that the intensity of a human’s selective attention to facial expressions varies according to the higher-order semantic processing of the relationship between emotion and color rather than simple facial expression or facial color effects individually. Our results support the idea that red color increases the human response to anger from an EEG perspective.

Sep 17, 2024
Hasegawa, Y., Tamura, H., Nakauchi, S., Minami, T.
CC BY-NC-ND
.na.character

Functional characterisation of neuropeptides that act as ligands for both calcitonin-type and pigment-dispersing factor-type receptors in a deuterostome

neuroscience
new results

The calcitonin (CT) family of related peptides exert their diverse physiological effects in mammals via two G-protein coupled receptors, CTR and the CTR-like receptor CLR. Analysis of the phylogenetic distribution of CT-type signaling has revealed the occurrence of CT-type peptides and CTR/CLR-type proteins in deuterostome and protostome invertebrates. Furthermore, experimental studies have revealed that in the protostome Drosophila melanogaster the CT-like peptide DH31 can act as a ligand for a CTR/CLR-type receptor and a pigment-dispersing factor (PDF) receptor. Here we investigated the signaling mechanisms and functions of CT-type neuropeptides in a deuterostome invertebrate, the sea cucumber Apostichopus japonicus (phylum Echinodermata). In A. japonicus, a single gene encodes two CT-type peptides (AjCT1 and AjCT2), both of which act as ligands for a CTR/CLR-type receptor (AjCTR) and two PDF-type receptors (AjPDFR1, AjPDFR2), but with differential activation of downstream cAMP/PKA, Gq/Ca2+/PKC and ERK1/2 signaling pathways. Analysis of the expression of the gene encoding AjCT1 and AjCT2 revealed transcripts in a variety of organ systems, but with highest expression in the circumoral nervous system. In vitro pharmacological experiments revealed that AjCT1 and/or AjCT2 cause dose-dependent relaxation of longitudinal body wall muscle and intestine preparations. Furthermore, in vivo pharmacological experiments and loss-of-function tests revealed a potential physiological role for AjCT2 signaling in promoting feeding and growth in A. japonicus. This is the first study to obtain evidence that CT-type peptides can act as ligands for both CTR/CLR-type and PDF-type receptors in a deuterostome. Furthermore, because of the economic importance of A. japonicus as a foodstuff, discovery of the potential role for CT-type peptides as regulators of feeding and growth in this species may provide a basis for practical applications in aquaculture.

Aug 30, 2024
Cong, X., Liu, H., Elphick, M. R., Chen, M.
CC NO
.na.character

Damsels in a hidden colour: development of ultraviolet sensitivity and colour patterns in damselfishes (Pomacentridae)

ecology
new results

Damselfishes (Pomacentridae) are widespread and highly abundant on tropical coral reefs. They exhibit diverse body colouration within and between the ~250 species and across ontogenetic stages. In addition to human visible colours (i.e., 400-700 nm), most adult damselfishes reflect ultraviolet (UV, 300-400 nm) colour patches. UV sensitivity and UV colour signals are essential for feeding and form the basis for a secret communication channel invisible to the many UV-blind predatory fish on the reef; however, how these traits develop across ontogenetic stages, and their distribution across the damselfish family is poorly characterised. Here, we used UV photography, phylogenetic reconstructions of opsin genes, differential gene expression analysis (DGE) of retinal samples, to investigate the development of UV vision and colour patterns in three ontogenetic stages (pre-settlement larval, juvenile, and adult) of eleven damselfish species. Using DGE, we found similar gene expression between juveniles and adults, which strongly differed from larvae. All species and all stages expressed at least one UV-sensitive sws1 opsin gene. However, UV body colour patterns only started to appear at the juvenile stage. Moreover, Pomacentrus species displayed highly complex UV body patterns that were correlated with the expression of two sws1 copies. This could mean that some damselfishes can discriminate colours that change only in their UV component. We demonstrate dramatic shifts in both UV sensitivity and UV colouration across the development stages of damselfish, while highlighting the importance of considering ontogeny when studying the coevolution of visual systems and colour signals.

Aug 23, 2024
Tettamanti, V., Marshall, J., Cheney, K., Cortesi, F.
CC NO
.na.character

Facial and body colouration are linked to social rank in the African cichlid, Astatotilapia burtoni

animal behavior and cognition
new results

Animal colouration is fundamentally important for social communication within conspecifics to advertising threat to competitors or fitness to possible mates. Social status and animal colouration are covarying traits that are plastic in response to dynamic environments. In the African cichlid, Astatotilapia burtoni, body colouration and behaviour have been extensively reported to vary with social rank. However, the nature of the interaction between these two traits is poorly understood. We hypothesise that pigmentation patterns could be linked to the behavioural repertoires underlying social status and can be resolved to regions on the cichlid body plan. To test this hypothesis, we generated Territorial (T) and Non-territorial (NT) males and employed computer vision tools to quantify and visualise patterns/colour enrichment associated with stereotyped T/NT male behaviour. We report colour-behaviour interactions localised in specific areas of the body and face for two colour morphs, illustrating a more nuanced view of social behaviour and pigmentation. Since behavioural and morphological variation are key drivers of selection in the East African Great Rift Lakes, we surmise our data may be translatable to other cichlid lineages and underline the importance of trait covariance in sexual selection and male competition.

Aug 22, 2024
Peros, M., Chang, A., Martashvili, A., Alvarado, S. G.
CC BY-NC-ND
.na.character

Dialogues in colour and behaviour - Integration of complex signalling traits and physiology

animal behavior and cognition
new results

Animal communication can be complex, often involving multiple static and dynamic traits. The extent to which these traits are correlated can elucidate their function as either redundant or multiple messages. Using the agamid lizard, Psammophilus dorsalis, as a model system we examined patterns of trait expression and the role of steroid hormones in mediating these traits during social interactions. We staged male-male interactions in the lab and measured the repertoire of display behaviour and colours, which change dynamically in the visible and ultraviolet ranges in different body regions. Additionally, we measured testosterone and corticosterone levels before and after the social trials. Our results show that within behaviour and colour trait categories, components were strongly correlated within individuals, suggesting either a shared physiological pathway or redundant information content. However, across trait categories, correlation patterns varied. The chromatic contrast of the (yellow) dorsal region of lizards was correlated with both body size and level of aggression, whereas the size of UV patches was correlated with body size only. We also found a negative association between baseline corticosterone levels, body size and dorsal yellow chromatic contrast, suggesting a mechanistic link between these traits. However, social interaction induced testosterone and corticosterone levels were uncorrelated with the expression of the dynamic behavioural and colour displays during the social interactions itself. Notably, the intensity of colour and behavioural displays of males were matched by their opponents. Overall, our results suggest that multiple signalling traits can ensure both redundancy as well as provide multiple messages to receivers, thus improving the robustness of information transfer, particularly during competitions which have high fitness consequences.

Aug 19, 2024
Patro, S., Saravanan, T., Parag, A., Thaker, M.
CC BY-NC-ND
.na.character
No matching items