ColSci preprints

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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
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