Measuring Perceptual Distance of Organismal Color Pattern using the Features of Deep Neural Networks

2019 ◽  
Author(s):  
Drew C. Wham ◽  
Briana Ezray ◽  
Heather M. Hines
Keyword(s):  
Deep Neural Networks ◽  
Color Pattern ◽  
Color Contrast ◽  
Biological Processes ◽  
Color Patterns ◽  
Biologically Relevant ◽  
Perceptual Distance ◽  
Data Formats ◽  
Wide Range ◽  
Study Designs

ABSTRACTA wide range of research relies upon the accurate and repeatable measurement of the degree to which organisms resemble one another. Here, we present an unsupervised workflow for analyzing the relationships between organismal color patterns. This workflow utilizes several recent advancements in deep learning based computer vision techniques to calculate perceptual distance. We validate this approach using previously published datasets surrounding diverse applications of color pattern analysis including mimicry, population differentiation, heritability, and development. We demonstrate that our approach is able to reproduce the biologically relevant color pattern relationships originally reported in these studies. Importantly, these results are achieved without any task-specific training. In many cases, we were able to reproduce findings directly from original photographs or plates with minimum standardization, avoiding the need for intermediate representations such as a cartoonized images or trait matrices. We then present two artificial datasets designed to highlight how this approach handles aspects of color patterns, such as changes in pattern location and the perception of color contrast. These results suggest that this approach will generalize well to support the study of a wide range of biological processes in a diverse set of taxa while also accommodating a variety of data formats, preprocessing techniques, and study designs.

scholarly journals Patternize: An R Package For Quantifying Color Pattern Variation

2017 ◽  
Author(s):  
Steven M. Van Belleghem ◽  
Riccardo Papa ◽  
Humberto Ortiz-Zuazaga ◽  
Frederik Hendrickx ◽  
Chris Jiggins ◽  
...  
Keyword(s):  
Association Studies ◽  
Genetic Association Studies ◽  
Image Data ◽  
Principal Component ◽  
R Package ◽  
Color Pattern ◽  
Color Patterns ◽  
Wide Range ◽  
Potential Applications ◽  
Population Comparisons

The use of image data to quantify, study and compare variation in the colors and patterns of organisms requires the alignment of images to establish homology, followed by color-based segmentation of images. Here we describe an R package for image alignment and segmentation that has applications to quantify color patterns in a wide range of organisms. patternize is an R package that quantifies variation in color patterns obtained from image data. patternize first defines homology between pattern positions across specimens either through manually placed homologous landmarks or automated image registration. Pattern identification is performed by categorizing the distribution of colors using an RGB threshold, k-means clustering or watershed transformation. We demonstrate that patternize can be used for quantification of the color patterns in a variety of organisms by analyzing image data for butterflies, guppies, spiders and salamanders. Image data can be compared between sets of specimens, visualized as heatmaps and analyzed using principal component analysis (PCA). patternize has potential applications for fine scale quantification of color pattern phenotypes in population comparisons, genetic association studies and investigating the basis of color pattern variation across a wide range of organisms.

scholarly journals Colormesh: A novel method for quantifying variation in complex color patterns

2020 ◽  
Author(s):  
Jennifer J. Valvo ◽  
F. Helen Rodd ◽  
David Houle ◽  
J. David Aponte ◽  
Mitchel J. Daniel ◽  
...  
Keyword(s):  
Spatial Information ◽  
Color Pattern ◽  
Color Variation ◽  
Sampling Location ◽  
Continuous Measure ◽  
Color Patterns ◽  
Color Categories ◽  
Wide Range ◽  
Novel Method ◽  
Pattern Quantification

AbstractColor variation is one of the most obvious examples of variation in nature. Objective quantification and interpretation of variation in color and complex patterns is challenging. Assessment of variation in color patterns is limited by the reduction of color into categorical measures and lack of spatial information. We present Colormesh as a novel method for analyzing complex color patterns that offers unique capabilities. Compared to other methods, Colormesh maintains the continuous measure of color at individual sampling points throughout the pattern. This is particularly useful for analyses of variation in color patterns, whether interest is in specific locations or the pattern as a whole. In our approach, the use of Delaunay triangulation to determine sampling location eliminates the need for color patterns to have clearly defined pattern elements, and users are not required to identify discrete color categories. This method is complementary to several other methods available for color pattern quantification, and can be usefully deployed to address a wide range of questions about color pattern variation.

Functional significance of preserved color patterns of mollusks from the Gosport Sand (Eocene) of Alabama

1988 ◽  
Vol 62 (01) ◽  
pp. 83-87 ◽  
Author(s):  
Patricia H. Kelley ◽  
Charles T. Swann
Keyword(s):  
Functional Morphology ◽  
Functional Significance ◽  
Intraspecific Variability ◽  
Color Pattern ◽  
Color Patterns ◽  
Historical Factors ◽  
Life Mode ◽  
Molluscan Fauna ◽  
Excellent Preservation ◽  
Architectural Constraints

The excellent preservation of the molluscan fauna from the Gosport Sand (Eocene) at Little Stave Creek, Alabama, has made it possible to describe the preserved color patterns of 15 species. In this study the functional significance of these color patterns is tested in the context of the current adaptationist controversy. The pigment of the color pattern is thought to be a result of metabolic waste disposal. Therefore, the presence of the pigment is functional, although the patterns formed by the pigment may or may not have been adaptive. In this investigation the criteria proposed by Seilacher (1972) for testing the functionality of color patterns were applied to the Gosport fauna and the results compared with life mode as interpreted from knowledge of extant relatives and functional morphology. Using Seilacher's criteria of little ontogenetic and intraspecific variability, the color patterns appear to have been functional. However, the functional morphology studies indicate an infaunal life mode which would preclude functional color patterns. Particular color patterns are instead interpreted to be the result of historical factors, such as multiple adaptive peaks or random fixation of alleles, or of architectural constraints including possibly pleiotropy or allometry. The low variability of color patterns, which was noted within species and genera, suggests that color patterns may also serve a useful taxonomic purpose.

scholarly journals Energetics of mesoscale cell turbulence in two-dimensional monolayers

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Shao-Zhen Lin ◽  
Wu-Yang Zhang ◽  
Dapeng Bi ◽  
Bo Li ◽  
Xi-Qiao Feng
Keyword(s):  
Kinetic Energy ◽  
Tumor Metastasis ◽  
Cell Types ◽  
Boltzmann Distribution ◽  
Scaling Exponent ◽  
Biological Processes ◽  
Two Dimensional ◽  
Cell Monolayers ◽  
Wide Range ◽  
Epithelial Cell Monolayers

AbstractInvestigation of energy mechanisms at the collective cell scale is a challenge for understanding various biological processes, such as embryonic development and tumor metastasis. Here we investigate the energetics of self-sustained mesoscale turbulence in confluent two-dimensional (2D) cell monolayers. We find that the kinetic energy and enstrophy of collective cell flows in both epithelial and non-epithelial cell monolayers collapse to a family of probability density functions, which follow the q-Gaussian distribution rather than the Maxwell–Boltzmann distribution. The enstrophy scales linearly with the kinetic energy as the monolayer matures. The energy spectra exhibit a power-decaying law at large wavenumbers, with a scaling exponent markedly different from that in the classical 2D Kolmogorov–Kraichnan turbulence. These energetic features are demonstrated to be common for all cell types on various substrates with a wide range of stiffness. This study provides unique clues to understand active natures of cell population and tissues.

Recent advances in multivalent carbon nanoform-based glycoconjugates

2021 ◽  
Vol 28 ◽  
Author(s):  
Javier Ramos-Soriano ◽  
Mattia Ghirardello ◽  
M. Carmen Galan
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Level ◽  
Biological Processes ◽  
Biologically Relevant ◽  
Disease Mechanisms ◽  
Recent Advances

: Multivalent carbohydrate-mediated interactions are fundamental to many biological processes, including disease mechanisms. To study these significant glycan-mediated interactions at a molecular level, carbon nanoforms such as fullerenes, carbon nanotubes, or graphene and their derivatives have been identified as promising biocompatible scaffolds that can mimic the multivalent presentation of biologically relevant glycans. In this minireview, we will summarize the most relevant examples of the last few years in the context of their applications.

scholarly journals Reversing resistance: different routes and common themes across pathogens

2017 ◽  
Vol 284 (1863) ◽  
pp. 20171619 ◽  
Author(s):  
Richard C. Allen ◽  
Jan Engelstädter ◽  
Sebastian Bonhoeffer ◽  
Bruce A. McDonald ◽  
Alex R. Hall
Keyword(s):  
Fitness Cost ◽  
Biological Processes ◽  
Short Supply ◽  
Compensatory Evolution ◽  
Wide Range ◽  
Different Types ◽  
Cost Of Resistance

Resistance spreads rapidly in pathogen or pest populations exposed to biocides, such as fungicides and antibiotics, and in many cases new biocides are in short supply. How can resistance be reversed in order to prolong the effectiveness of available treatments? Some key parameters affecting reversion of resistance are well known, such as the fitness cost of resistance. However, the population biological processes that actually cause resistance to persist or decline remain poorly characterized, and consequently our ability to manage reversion of resistance is limited. Where do susceptible genotypes that replace resistant lineages come from? What is the epidemiological scale of reversion? What information do we need to predict the mechanisms or likelihood of reversion? Here, we define some of the population biological processes that can drive reversion, using examples from a wide range of taxa and biocides. These processes differ primarily in the origin of revertant genotypes, but also in their sensitivity to factors such as coselection and compensatory evolution that can alter the rate of reversion, and the likelihood that resistance will re-emerge upon re-exposure to biocides. We therefore argue that discriminating among different types of reversion allows for better prediction of where resistance is most likely to persist.

scholarly journals Cooperative subunit dynamics modulate p97 function

2018 ◽  
Vol 116 (1) ◽  
pp. 158-167 ◽  
Author(s):  
Rui Huang ◽  
Zev A. Ripstein ◽  
John L. Rubinstein ◽  
Lewis E. Kay
Keyword(s):  
Bound State ◽  
Nmr Studies ◽  
Biologically Relevant ◽  
Aaa Atpase ◽  
Cellular Processes ◽  
Allosteric Communication ◽  
Functional Dynamics ◽  
Nmr Study ◽  
Wide Range

p97 is an essential hexameric AAA+ ATPase involved in a wide range of cellular processes. Mutations in the enzyme are implicated in the etiology of an autosomal dominant neurological disease in which patients are heterozygous with respect to p97 alleles, containing one copy each of WT and disease-causing mutant genes, so that, in vivo, p97 molecules can be heterogeneous in subunit composition. Studies of p97 have, however, focused on homohexameric constructs, where protomers are either entirely WT or contain a disease-causing mutation, showing that for WT p97, the N-terminal domain (NTD) of each subunit can exist in either a down (ADP) or up (ATP) conformation. NMR studies establish that, in the ADP-bound state, the up/down NTD equilibrium shifts progressively toward the up conformation as a function of disease mutant severity. To understand NTD functional dynamics in biologically relevant p97 heterohexamers comprising both WT and disease-causing mutant subunits, we performed a methyl-transverse relaxation optimized spectroscopy (TROSY) NMR study on a series of constructs in which only one of the protomer types is NMR-labeled. Our results show positive cooperativity of NTD up/down equilibria between neighboring protomers, allowing us to define interprotomer pathways that mediate the allosteric communication between subunits. Notably, the perturbed up/down NTD equilibrium in mutant subunits is partially restored by neighboring WT protomers, as is the two-pronged binding of the UBXD1 adaptor that is affected in disease. This work highlights the plasticity of p97 and how subtle perturbations to its free-energy landscape lead to significant changes in NTD conformation and adaptor binding.

scholarly journals Ultrabithorax Is a Micromanager of Hindwing Identity in Butterflies and Moths

2021 ◽  
Vol 9 ◽  
Author(s):  
Amruta Tendolkar ◽  
Aaron F. Pomerantz ◽  
Christa Heryanto ◽  
Paul D. Shirk ◽  
Nipam H. Patel ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Targeted Mutagenesis ◽  
Junonia Coenia ◽  
Wing Venation ◽  
Loss Of Function ◽  
Color Patterns ◽  
Wide Range ◽  
Range Of Functions ◽  
Gene Regulatory ◽  
Pyralid Moth

The forewings and hindwings of butterflies and moths (Lepidoptera) are differentiated from each other, with segment-specific morphologies and color patterns that mediate a wide range of functions in flight, signaling, and protection. The Hox gene Ultrabithorax (Ubx) is a master selector gene that differentiates metathoracic from mesothoracic identities across winged insects, and previous work has shown this role extends to at least some of the color patterns from the butterfly hindwing. Here we used CRISPR targeted mutagenesis to generate Ubx loss-of-function somatic mutations in two nymphalid butterflies (Junonia coenia, Vanessa cardui) and a pyralid moth (Plodia interpunctella). The resulting mosaic clones yielded hindwing-to-forewing transformations, showing Ubx is necessary for specifying many aspects of hindwing-specific identities, including scale morphologies, color patterns, and wing venation and structure. These homeotic phenotypes showed cell-autonomous, sharp transitions between mutant and non-mutant scales, except for clones that encroached into the border ocelli (eyespots) and resulted in composite and non-autonomous effects on eyespot ring determination. In the pyralid moth, homeotic clones converted the folding and depigmented hindwing into rigid and pigmented composites, affected the wing-coupling frenulum, and induced ectopic scent-scales in male androconia. These data confirm Ubx is a master selector of lepidopteran hindwing identity and suggest it acts on many gene regulatory networks involved in wing development and patterning.

scholarly journals The RhoA-ROCK pathway in the regulation of T and B cell responses

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2295 ◽  
Author(s):  
Edd Ricker ◽  
Luvana Chowdhury ◽  
Woelsung Yi ◽  
Alessandra B. Pernis
Keyword(s):  
Immune Responses ◽  
Biological Processes ◽  
Dynamic Interactions ◽  
Cell Responses ◽  
Important Mediator ◽  
Downstream Effectors ◽  
Wide Range ◽  
Response To Stress ◽  
The Impact ◽  
Rho Kinases

Effective immune responses require the precise regulation of dynamic interactions between hematopoietic and non-hematopoietic cells. The Rho subfamily of GTPases, which includes RhoA, is rapidly activated downstream of a diverse array of biochemical and biomechanical signals, and is emerging as an important mediator of this cross-talk. Key downstream effectors of RhoA are the Rho kinases, or ROCKs. The ROCKs are two serine-threonine kinases that can act as global coordinators of a tissue’s response to stress and injury because of their ability to regulate a wide range of biological processes. Although the RhoA-ROCK pathway has been extensively investigated in the non-hematopoietic compartment, its role in the immune system is just now becoming appreciated. In this commentary, we provide a brief overview of recent findings that highlight the contribution of this pathway to lymphocyte development and activation, and the impact that dysregulation in the activation of RhoA and/or the ROCKs may exert on a growing list of autoimmune and lymphoproliferative disorders.

scholarly journals Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species

2021 ◽  
Vol 17 (2) ◽  
pp. e1008767
Author(s):  
Zutan Li ◽  
Hangjin Jiang ◽  
Lingpeng Kong ◽  
Yuanyuan Chen ◽  
Kun Lang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Prediction Accuracy ◽  
Cross Validation ◽  
Biological Processes ◽  
Biological Functions ◽  
Learning Framework ◽  
Wide Range ◽  
Genomic Scale ◽  
Downstream Gene Expression ◽  
Fold Cross Validation

N6-methyladenine (6mA) is an important DNA modification form associated with a wide range of biological processes. Identifying accurately 6mA sites on a genomic scale is crucial for under-standing of 6mA’s biological functions. However, the existing experimental techniques for detecting 6mA sites are cost-ineffective, which implies the great need of developing new computational methods for this problem. In this paper, we developed, without requiring any prior knowledge of 6mA and manually crafted sequence features, a deep learning framework named Deep6mA to identify DNA 6mA sites, and its performance is superior to other DNA 6mA prediction tools. Specifically, the 5-fold cross-validation on a benchmark dataset of rice gives the sensitivity and specificity of Deep6mA as 92.96% and 95.06%, respectively, and the overall prediction accuracy is 94%. Importantly, we find that the sequences with 6mA sites share similar patterns across different species. The model trained with rice data predicts well the 6mA sites of other three species: Arabidopsis thaliana, Fragaria vesca and Rosa chinensis with a prediction accuracy over 90%. In addition, we find that (1) 6mA tends to occur at GAGG motifs, which means the sequence near the 6mA site may be conservative; (2) 6mA is enriched in the TATA box of the promoter, which may be the main source of its regulating downstream gene expression.

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