pat‐geom : A software package for the analysis of animal patterns

Fibroblast alignment and matrix remodeling induced by a stiffness gradient in a skin-derived extracellular matrix hydrogel

Large skin injuries heal as scars. Stiffness gradually increases from normal skin to scar tissue (20x higher), due to excessive deposition and crosslinking of extracellular matrix (ECM) mostly produced by (myo)fibroblasts. Using a custom mold, skin-derived ECM hydrogels (dECM) were UV crosslinked after diffusion of ruthenium (Ru) to produce a Ru-dECM gradient hydrogel. The Ru diffusion gradient equates to a stiffness gradient and models physiology of the scarred skin. Crosslinking in Ru-dECM hydrogels results in a 23-fold increase in stiffness from a stiffness similar to that of normal skin. Collagen fiber density increases in a stiffness-dependent fashion while stress relaxation also alters, with one additional Maxwell element necessary for characterizing Ru-dECM. Alignment of fibroblasts encapsulated in hydrogels suggests that the stiffness gradient directs fibroblasts to orientate at ∼45 ° in regions below 120 kPa. In areas above 120 kPa, fibroblasts decrease the stiffness prior to adjusting their orientation. Furthermore, fibroblasts remodel their surrounding ECM in a gradient-dependent fashion, with rearrangement of cell-surrounding ECM in high-stiffness areas, and formation of interlaced collagen bundles in low-stiffness areas. Overall, this study shows that fibroblasts remodel their local environment to generate an optimal ECM mechanical and topographical environment. STATEMENT OF SIGNIFICANCE: This study developed a versatile in vitro model with a gradient stiffness using skin-derived ECM hydrogel with unchanged biochemical environment. Using Ruthenium crosslinking, a 20-fold stiffness increase was achieved as observed in fibrotic skin. The interaction between fibroblasts and matrix depends on changes in the matrix stiffness. The stiffness gradient directed the alignment of fibroblasts with ∼45° in regions with≤ 120 kPa. The cells in regions with the higher stiffness decreased stiffness first and then oriented themselves. Furthermore, fibroblasts remodeled surrounding ECM and regulated its mechanics in a gradient-dependent fashion to reach an optimal condition. Our study highlights the dynamic interplay between cells and surrounding matrix, shedding light on potential mechanisms and strategies to target scar formation and remodeling.

Preliminary evidence that eye appearance in parrots (Psittaciformes) co-varies with latitude and altitude

External eye appearance in avian taxa has been proposed to be driven by social and ecological functions. Recent research in primates suggests, instead, that, photoprotective functions are important drivers of external eye appearance. Using similar methods, we examined the variation in external eye appearance of 132 parrot species (Psittaciformes) in relation to their ecology and sociality. Breeding systems, flock size and sexual dimorphism, as well as species' latitude and maximum living altitude, and estimated UV-B incidence in species' ranges were used to explore the contribution of social and ecological factors in driving external eye appearance. We measured the hue and brightness of visible parts of the eye and the difference in measurements of brightness between adjacent parts of the eye. We found no link between social variables and our measurements. We did, however, find a negative association between the brightness of the inner part of the iris and latitude and altitude. Darker inner irises were more prevalent farther away from the equator and for those species living at higher altitudes. We found no link between UV-B and brightness measurements of the iris, or tissue surrounding the eye. We speculate that these results are consistent with an adaptation for visual functions. While preliminary, these results suggest that external eye appearance in parrots is influenced by ecological, but not social factors.

Automated workflows using Quantitative Colour Pattern Analysis (QCPA): a guide to batch processing and downstream data analysis

Animal and plant colouration presents a striking dimension of phenotypic variation, the study of which has driven general advances in ecology, evolution, and animal behaviour. Quantitative Colour Pattern Analysis (QCPA) is a dynamic framework for analysing colour patterns through the eyes of non-human observers. However, its extensive array of user-defined image processing and analysis tools means image analysis is often time-consuming. This hinders the full use of analytical power provided by QCPA and its application to large datasets. Here, we offer a robust and comprehensive batch script, allowing users to automate many QCPA workflows. We also provide a complimentary set of useful R scripts for downstream data extraction and analysis. The presented batch processing extension will empower users to further utilise the analytical power of QCPA and facilitate the development of customised semi-automated workflows. Such quantitatively scaled workflows are crucial for exploring colour pattern spaces and developing ever-richer frameworks for analysing organismal colouration accounting for visual perception in animals other than humans. These advances will, in turn, facilitate testing hypotheses on the function and evolution of vision and signals at quantitative and qualitative scales, which are otherwise computationally unfeasible.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10682-024-10291-7.

Sox21b underlies the rapid diversification of a novel male genital structure between Drosophila species

The emergence and diversification of morphological novelties is a major feature of animal evolution.1,2,3,4,5,6,7,8,9 However, relatively little is known about the genetic basis of the evolution of novel structures and the mechanisms underlying their diversification. The epandrial posterior lobes of male genitalia are a novelty of particular Drosophila species.10,11,12,13 The lobes grasp the female ovipositor and insert between her abdominal tergites and, therefore, are important for copulation and species recognition.10,11,12,14,15,16,17 The posterior lobes likely evolved from co-option of a Hox-regulated gene network from the posterior spiracles10 and have since diversified in morphology in the D. simulans clade, in particular, over the last 240,000 years, driven by sexual selection.18,19,20,21 The genetic basis of this diversification is polygenic but, to the best of our knowledge, none of the causative genes have been identified.22,23,24,25,26,27,28,29,30 Identifying the genes underlying the diversification of these secondary sexual structures is essential to understanding the evolutionary impact on copulation and species recognition. Here, we show that Sox21b negatively regulates posterior lobe size. This is consistent with expanded Sox21b expression in D. mauritiana, which develops smaller posterior lobes than D. simulans. We tested this by generating reciprocal hemizygotes and confirmed that changes in Sox21b underlie posterior lobe evolution between these species. Furthermore, we found that posterior lobe size differences caused by the species-specific allele of Sox21b significantly affect copulation duration. Taken together, our study reveals the genetic basis for the sexual-selection-driven diversification of a novel morphological structure and its functional impact on copulatory behavior.

FGF2 isoforms play distinct roles in tubular epithelial-to-mesenchymal transition in diabetic nephropathy

INTRODUCTION

The role of different isoforms of Fibroblast growth factor-2 (FGF2) in tubular epithelial-to-mesenchymal transition (EMT) in diabetic nephropathy remains unknown. We aimed to evaluate the role of FGF2 isoforms in the pathogenesis of EMT.

MATERIALS AND METHODS

Western blot and immunofluorescence were used to assess the expression of FGF2 isoforms in db/db mice and high glucose-stimulated HK2 cells. The effects of specific FGF2 isoforms on EMT were explored via overexpression or knockdown of the corresponding isoform in HK2 cells cultivated in high glucose.

RESULTS

Expression of low molecular weight (LMW) FGF2 was up-regulated while high molecular weight (HMW) FGF2 was down-regulated in the kidney of db/db mice and HK2 cells cultured in high glucose that underwent EMT. Overexpression of the LMW FGF2 enhanced EMT changes, while overexpression of the HMW FGF2 attenuated EMT. Knockdown of HMW FGF2 in HK2 cells promoted the EMT process.

CONCLUSIONS

The expression and function of LMW and HMW FGF2 differed in the process of EMT in tubular cells. LMW FGF2 contributed to EMT, while HMW FGF2 played a protective role in the EMT process.

Engineering functional skin constructs: A quantitative comparison of three-dimensional bioprinting with traditional methods

Tissue engineering has been successful in reproducing human skin equivalents while incorporating new approaches such as three-dimensional (3D) bioprinting. The latter method offers a plethora of advantages including increased production scale, ability to incorporate multiple cell types and printing on demand. However, the quality of printed skin equivalents compared to those developed manually has never been assessed. To leverage the benefits of this method, it is imperative that 3D-printed skin should be structurally and functionally similar to real human skin. Here, we developed four bilayered human skin epidermal-dermal equivalents: non-printed dermis and epidermis (NN), printed dermis and epidermis (PP), printed epidermis and non-printed dermis (PN), and non-printed epidermis and printed dermis (NP). The effects of printing induced shear stress [0.025 kPa (epidermis); 0.049 kPa (dermis)] were characterized both at the cellular and at the tissue level. At cellular level, no statistically significant differences in keratinocyte colony-forming efficiency (CFE) (p = 0.1641) were observed. In the case of fibroblasts, no significant differences in the cell alignment index (p < 0.1717) and their ability to contract collagen gel (p = 0.851) were detected. At the tissue levels, all the four skin equivalents were characterized using histological and immunohistochemical analysis with no significant differences found in either epidermal basal cell count, thickness of viable epidermis, and relative intensity of filaggrin and claudin-1. Our results demonstrated that 3D printing can achieve the same high-quality skin constructs as have been developed traditionally, thus opening new avenues for numerous high-throughput industrial and clinical applications.

Sexual selection on jumping spider color pattern: investigation with a new quantitative approach

How animals assess information encoded in individual color patches have been extensively studied, yet the role of both individual color patches and gross color pattern (i.e., the combination of color patches) remains understudied. We tested the functioning of both individual color patches and gross color pattern in sexual selection using the jumping spider Siler semiglaucus as a study system. We first quantified sexual dimorphism in S. semiglaucus in both individual patches and gross color pattern using the newly developed quantitative color pattern analysis (QCPA) framework. After detecting sexual differences in color coverage and pattern contrast, we manipulated the abdomen color pattern of males and had them engage in both female mate choice and male contest trials. Females spent more time watching males with lower pattern contrast and greater red coverage during mate assessment, suggesting that they evaluate information from both individual patches and gross color pattern of males. However, male color pattern had no significant effect on the outcomes of male contests. Thus, we suggest that the observed sexual color pattern dimorphism evolved primarily through female mate choice in S. semiglaucus. This is the first study to use QCPA framework to quantify sexual dimorphism in within-pattern conspicuousness from an intraspecific perspective in invertebrates. Our study also highlights the importance of both individual color patches and gross color pattern in sexual selection.

Quantitative imagery analysis of spot patterns for the three-haplogroup classification of Triatoma dimidiata (Latreille, 1811) (Hemiptera: Reduviidae), an important vector of Chagas disease

Background

Spots and coloring patterns evaluated quantitatively can be used to discriminate and identify possible cryptic species. Species included in the Triatoma dimidiata (Reduviidae: Triatominae) complex are major disease vectors of Chagas disease. Phylogenetic studies have defined three haplogroups for Mexico and part of Central America. We report here our evaluation of the possibility of correctly discriminating these three T. dimidiata haplogroups using the pattern of the dorsal spots.

Methods

Digital images of the dorsal region of individuals from the three haplogroups were used. Image processing was used to extract primary and secondary variables characterizing the dorsal spot pattern. Statistical analysis of the variables included descriptive statistics, non-parametric Kruskal–Wallis tests, discriminant function analysis (DFA) and a neural classification network.

Results

A distinctive spot pattern was found for each haplogroup. The most differentiated pattern was presented by haplogroup 2, which was characterized by its notably larger central spots. Haplogroups 1 and 3 were more similar to each other, but there were consistent differences in the shape and orientation of the spots. Significant differences were found among haplogroups in almost all of the variables analyzed, with the largest differences seen for relative spot area, mean relative area of central spots, central spots Feret diameter and lateral spots Feret diameter and aspect ratio. Both the DFA and the neural network had correct discrimination values of > 90%.

Conclusions

Based on the results of this analysis, we conclude that the spot pattern can be reliably used to discriminate among the three haplogroups of T. dimidiata in Mexico, and possibly among triatomine species.

Pattern blending enriches the diversity of animal colorations

Animals exhibit a fascinating variety of skin patterns, but mechanisms underlying this diversity remain largely unknown, particularly for complex and camouflaged colorations. A mathematical model predicts that intricate color patterns can be formed by "pattern blending" between simple motifs via hybridization. Here, I analyzed the skin patterns of 18,114 fish species and found strong mechanistic associations between camouflaged labyrinthine patterns and simple spot motifs, showing remarkable consistency with the pattern blending hypothesis. Genomic analyses confirmed that the coloring on multiple labyrinthine fish species has originated from pattern blending by hybridization, and phylogenetic comparative analyses have further substantiated the pattern blending hypothesis in multiple major fish lineages. These findings provide a plausible mechanistic explanation for the characteristic diversity of animal markings and suggest a novel evolutionary process of complex and camouflaged colorations by means of pattern blending.

Intrinsic Color Sensing System Allows for Real-Time Observable Functional Changes on Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes

Stem-cell based in vitro differentiation for disease modeling offers great value to explore the molecular and functional underpinnings driving many types of cardiomyopathy and congenital heart diseases. Nevertheless, one major caveat in the application of in vitro differentiation of human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes (hiPSC-CMs) involves the immature phenotype of the CMs. Most of the existing methods need complex apparatus and require laborious procedures in order to monitor the cardiac differentiation/maturation process and often result in cell death. Here we developed an intrinsic color sensing system utilizing a microgroove structural color methacrylated gelatin film, which allows us to monitor the cardiac differentiation process of hiPSC-derived cardiac progenitor cells in real time. Subsequently this system can be employed as an assay system to live monitor induced functional changes on hiPSC-CMs stemming from drug treatment, the effects of which are simply revealed through color diversity. Our research shows that early intervention of cardiac differentiation through simple physical cues can enhance cardiac differentiation and maturation to some extent. Our system also simplifies the previous complex experimental processes for evaluating the physiological effects of successful differentiation and drug treatment and lays a solid foundation for future transformational applications.

Artificial intelligence reveals environmental constraints on colour diversity in insects

Explaining colour variation among animals at broad geographic scales remains challenging. Here we demonstrate how deep learning-a form of artificial intelligence-can reveal subtle but robust patterns of colour feature variation along an ecological gradient, as well as help identify the underlying mechanisms generating this biogeographic pattern. Using over 20,000 images with precise GPS locality information belonging to nearly 2,000 moth species from Taiwan, our deep learning model generates a 2048-dimension feature vector that accurately predicts each species' mean elevation based on colour and shape features. Using this multidimensional feature vector, we find that within-assemblage image feature variation is smaller in high elevation assemblages. Structural equation modeling suggests that this reduced image feature diversity is likely the result of colder environments selecting for darker colouration, which limits the colour diversity of assemblages at high elevations. Ultimately, with the help of deep learning, we will be able to explore the endless forms of natural morphological variation at unpreceded depths.