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https://www.readbyqxmd.com/read/28913870/mimicry-in-butterflies-co-option-and-a-bag-of-magnificent-developmental-genetic-tricks
#1
REVIEW
Riddhi Deshmukh, Saurav Baral, A Gandhimathi, Muktai Kuwalekar, Krushnamegh Kunte
Butterfly wing patterns are key adaptations that are controlled by remarkable developmental and genetic mechanisms that facilitate rapid evolutionary change. With swift advancements in the fields of genomics and genetic manipulations, identifying the regulators of wing development and mimetic wing patterns has become feasible even in nonmodel organisms such as butterflies. Recent mapping and gene expression studies have identified single switch loci of major effects such as transcription factors and supergenes as the main drivers of adaptive evolution of mimetic and polymorphic butterfly wing patterns...
September 14, 2017: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/28900415/perinatal-western-diet-consumption-leads-to-profound-plasticity-and-gabaergic-phenotype-changes-within-hypothalamus-and-reward-pathway-from-birth-to-sexual-maturity-in-rat
#2
Julie Paradis, Pierre Boureau, Thomas Moyon, Sophie Nicklaus, Patricia Parnet, Vincent Paillé
Perinatal maternal consumption of energy dense food increases the risk of obesity in children. This is associated with an overconsumption of palatable food that is consumed for its hedonic property. The underlying mechanism that links perinatal maternal diet and offspring preference for fat is still poorly understood. In this study, we aim at studying the influence of maternal high-fat/high-sugar diet feeding [western diet (WD)] during gestation and lactation on the reward pathways controlling feeding in the rat offspring from birth to sexual maturity...
2017: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/28893204/predicted-networks-of-protein-protein-interactions-in-stegodyphus-mimosarum-by-cross-species-comparisons
#3
Xiu Wang, Yongfeng Jin
BACKGROUND: Stegodyphus mimosarum is a candidate model organism belonging to the class Arachnida in the phylum Arthropoda. Studies on the biology of S. mimosarum over the past several decades have consisted of behavioral research and comparison of gene sequences based on the assembled genome sequence. Given the lack of systematic protein analyses and the rich source of information in the genome, we predicted the relationships of proteins in S. mimosarum by bioinformatics comparison with genome-wide proteins from select model organisms using gene mapping...
September 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28892639/genetic-networks-in-plant-vascular-development
#4
Raili Ruonala, Donghwi Ko, Ykä Helariutta
Understanding the development of vascular tissues in plants is crucial because the evolution of vasculature enabled plants to thrive on land. Various systems and approaches have been used to advance our knowledge about the genetic regulation of vasculature development, from the scale of single genes to networks. In this review, we provide a perspective on the major approaches used in studying plant vascular development, and we cover the mechanisms and genetic networks underlying vascular tissue specification, patterning, and differentiation...
September 11, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28886704/differentiated-transcriptional-signatures-in-the-maize-landraces-of-chiapas-mexico
#5
Matthew A Kost, Hugo R Perales, Saranga Wijeratne, Asela J Wijeratne, Eric Stockinger, Kristin L Mercer
BACKGROUND: Landrace farmers are the keepers of crops locally adapted to the environments where they are cultivated. Patterns of diversity across the genome can provide signals of past evolution in the face of abiotic and biotic change. Understanding this rich genetic resource is imperative especially since diversity can provide agricultural security as climate continues to shift. RESULTS: Here we employ RNA sequencing (RNA-seq) to understand the role that conditions that vary across a landscape may have played in shaping genetic diversity in the maize landraces of Chiapas, Mexico...
September 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28885180/next-generation-sequencing-sheds-new-light-on-small-rnas-in-plant-reproductive-development
#6
Xiaobai Li
Reproductive development is a key step of the plant life cycles and indicates the start of a new life cycle. The reproductive organs including flower, fruit and seed, have diverse and complex structures, which is a syndrome in the evolution of angiosperms. The development of plant reproductive organs depends on the correct spatial and temporal expression of numerous genes acting in concert to form regulatory networks. Small non-coding RNAs (sRNAs) play a key role in the reproductive development through different modes of sequence-specific interaction with their targets...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28883798/eye-development-in-sepia-officinalis-embryo-what-the-uncommon-gene-expression-profiles-tell-us-about-eye-evolution
#7
Boudjema Imarazene, Aude Andouche, Yann Bassaglia, Pascal-Jean Lopez, Laure Bonnaud-Ponticelli
In metazoans, there is a remarkable diversity of photosensitive structures; their shapes, physiology, optical properties, and development are different. To approach the evolution of photosensitive structures and visual function, cephalopods are particularly interesting organisms due to their most highly centralized nervous system and their camerular eyes which constitute a convergence with those of vertebrates. The eye morphogenesis in numerous metazoans is controlled mainly by a conserved Retinal Determination Gene Network (RDGN) including pax, six, eya, and dac playing also key developmental roles in non-retinal structures and tissues of vertebrates and Drosophila...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28878023/maximal-aggregation-of-polynomial-dynamical-systems
#8
Luca Cardelli, Mirco Tribastone, Max Tschaikowski, Andrea Vandin
Ordinary differential equations (ODEs) with polynomial derivatives are a fundamental tool for understanding the dynamics of systems across many branches of science, but our ability to gain mechanistic insight and effectively conduct numerical evaluations is critically hindered when dealing with large models. Here we propose an aggregation technique that rests on two notions of equivalence relating ODE variables whenever they have the same solution (backward criterion) or if a self-consistent system can be written for describing the evolution of sums of variables in the same equivalence class (forward criterion)...
September 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28866362/gene-cell-and-organ-multiplication-drives-inner-ear-evolution
#9
REVIEW
Bernd Fritzsch, Karen L Elliott
We review the development and evolution of the ear neurosensory cells, the aggregation of neurosensory cells into an otic placode, the evolution of novel neurosensory structures dedicated to hearing and the evolution of novel nuclei in the brain and their input dedicated to processing those novel auditory stimuli. The evolution of the apparently novel auditory system lies in duplication and diversification of cell fate transcription regulation that allows variation at the cellular level [transforming a single neurosensory cell into a sensory cell connected to its targets by a sensory neuron as well as diversifying hair cells], organ level [duplication of organ development followed by diversification and novel stimulus acquisition] and brain nuclear level [multiplication of transcription factors to regulate various neuron and neuron aggregate fate to transform the spinal cord into the unique hindbrain organization]...
August 31, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28866096/regulation-and-evolution-of-the-interaction-of-the-seed-b3-transcription-factors-with-nf-y-subunits
#10
REVIEW
C Boulard, A Fatihi, L Lepiniec, B Dubreucq
The LAFL genes (LEC2, ABI3, FUS3, LEC1) encode transcription factors that regulate different aspects of seed development, from early to late embryogenesis and accumulation of storage compounds. These transcription factors form a complex network, with members able to interact with various other players to control the switch between embryo development and seed maturation and, at a later stage in the plant life cycle, between the mature seed and germination. In this review, we first summarize our current understanding of the role of each member in the network in the light of recent advances regarding their regulation and structure/function relationships...
September 1, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28861068/protein-protein-interactions-in-virus-host-systems
#11
REVIEW
Anderson F Brito, John W Pinney
To study virus-host protein interactions, knowledge about viral and host protein architectures and repertoires, their particular evolutionary mechanisms, and information on relevant sources of biological data is essential. The purpose of this review article is to provide a thorough overview about these aspects. Protein domains are basic units defining protein interactions, and the uniqueness of viral domain repertoires, their mode of evolution, and their roles during viral infection make viruses interesting models of study...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28854629/position-matters-network-centrality-considerably-impacts-rates-of-protein-evolution-in-the-human-protein-protein-interaction-network
#12
David Alvarez-Ponce, Felix Feyertag, Sandip Chakraborty
The proteins of any organism evolve at disparate rates. A long list of factors affecting rates of protein evolution have been identified. However, the relative importance of each factor in determining rates of protein evolution remains unresolved. The prevailing view is that evolutionary rates are dominantly determined by gene expression, and that other factors such as network centrality have only a marginal effect, if any. However, this view is largely based on analyses in yeasts, and accurately measuring the importance of the determinants of rates of protein evolution is complicated by the fact that the different factors are often correlated with each other, and by the relatively poor quality of available functional genomics data sets...
June 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28853706/evolutionary-routes-to-biochemical-innovation-revealed-by-integrative-analysis-of-a-plant-defense-related-specialized-metabolic-pathway
#13
Gaurav D Moghe, Bryan J Leong, Steven M Hurney, A Daniel Jones, Robert L Last
The diversity of life on Earth is a result of continual innovations in molecular networks influencing morphology and physiology. Plant specialized metabolism produces hundreds of thousands of compounds, offering striking examples of these innovations. To understand how this novelty is generated, we investigated the evolution of the Solanaceae family-specific, trichome-localized acylsugar biosynthetic pathway using a combination of mass spectrometry, RNA-seq, enzyme assays, RNAi and phylogenomics in different non-model species...
August 30, 2017: ELife
https://www.readbyqxmd.com/read/28851849/functional-constraints-on-replacing-an-essential-gene-with-its-ancient-and-modern-homologs
#14
Betül Kacar, Eva Garmendia, Nurcan Tuncbag, Dan I Andersson, Diarmaid Hughes
Genes encoding proteins that carry out essential informational tasks in the cell, in particular where multiple interaction partners are involved, are less likely to be transferable to a foreign organism. Here, we investigated the constraints on transfer of a gene encoding a highly conserved informational protein, translation elongation factor Tu (EF-Tu), by systematically replacing the endogenous tufA gene in the Escherichia coli genome with its extant and ancestral homologs. The extant homologs represented tuf variants from both near and distant homologous organisms...
August 29, 2017: MBio
https://www.readbyqxmd.com/read/28851604/regulatory-logic-underlying-diversification-of-the-neural-crest
#15
REVIEW
Megan L Martik, Marianne E Bronner
The neural crest is a transient, multipotent population of cells that arises at the border of the developing nervous system. After closure of the neural tube, these cells undergo an epithelial-to-mesenchymal transition (EMT) to delaminate and migrate, often to distant locations in the embryo. Neural crest cells give rise to a diverse array of derivatives including neurons and glia of the peripheral nervous system, melanocytes, and bone and cartilage of the face. A gene regulatory network (GRN) controls the specification, delamination, migration, and differentiation of this fascinating cell type...
August 26, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28833068/pervasive-gene-expression-responses-to-a-fluctuating-diet-in-drosophila-melanogaster
#16
Jelle Zandveld, Joost van den Heuvel, Maarten Mulder, Paul M Brakefield, Thomas B L Kirkwood, Daryl P Shanley, Bas J Zwaan
Phenotypic plasticity is an important concept in life history evolution, and most organisms, including Drosophila melanogaster, show a plastic life-history response to diet. However, little is known about how these life-history responses are mediated. In this study, we compared adult female flies fed an alternating diet (yoyo flies) with flies fed a constant low (CL) or high (CH) diet and tested how whole genome expression was affected by these diet regimes and how the transcriptional responses related to different life history traits...
August 21, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28831143/genome-wide-comparative-analysis-of-h3k4me3-profiles-between-diploid-and-allotetraploid-cotton-to-refine-genome-annotation
#17
Qi You, Xin Yi, Kang Zhang, Chunchao Wang, Xuelian Ma, Xueyan Zhang, Wenying Xu, Fuguang Li, Zhen Su
Polyploidy is a common evolutionary occurrence in plants. Recently, published genomes of allotetraploid G. hirsutum and its donors G. arboreum and G. raimondii make cotton an accessible polyploid model. This study used chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq) to investigate the genome-wide distribution of H3K4me3 in G. arboreum and G. hirsutum, and explore the conservation and variation of genome structures between diploid and allotetraploid cotton. Our results showed that H3K4me3 modifications were associated with active transcription in both cottons...
August 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28830343/divergence-of-functional-effects-among-bacterial-srna-paralogs
#18
I-Chen Kimberly Chen, Gregory J Velicer, Yuen-Tsu Nicco Yu
BACKGROUND: Non-coding small RNAs (sRNAs) regulate a variety of important biological processes across all life domains, including bacteria. However, little is known about the functional evolution of sRNAs in bacteria, which might occur via changes in sRNA structure and/or stability or changes in interactions between sRNAs and their associated regulatory networks, including target mRNAs. The sRNA Pxr functions as a developmental gatekeeper in the model cooperative bacterium Myxococcus xanthus...
August 22, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28818668/a-bipolar-role-of-the-transcription-factor-erg-for-cnidarian-germ-layer-formation-and-apical-domain-patterning
#19
Aldine R Amiel, Hereroa Johnston, Taylor Chock, Paul Dahlin, Marta Iglesias, Michael Layden, Eric Röttinger, Mark Q Martindale
Germ layer formation and axial patterning are biological processes that are tightly linked during embryonic development of most metazoans. In addition to canonical WNT, it has been proposed that ERK-MAPK signaling is involved in specifying oral as well as aboral territories in cnidarians. However, the effector and the molecular mechanism underlying latter phenomenon is unknown. By screening for potential effectors of ERK-MAPK signaling in both domains, we identified a member of the ETS family of transcription factors, Nverg that is bi-polarily expressed prior to gastrulation...
August 14, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28816684/a-multiobjective-evolutionary-algorithm-based-on-structural-and-attribute-similarities-for-community-detection-in-attributed-networks
#20
Zhangtao Li, Jing Liu, Kai Wu
Most of the existing community detection algorithms are based on vertex connectivity. While in many real networks, each vertex usually has one or more attributes describing its properties which are often homogeneous in a cluster. Such networks can be modeled as attributed graphs, whose attributes sometimes are equally important to topological structure in graph clustering. One important challenge is to detect communities considering both topological structure and vertex properties simultaneously. To this propose, a multiobjective evolutionary algorithm based on structural and attribute similarities (MOEA-SA) is first proposed to solve the attributed graph clustering problems in this paper...
August 16, 2017: IEEE Transactions on Cybernetics
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