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Gene network evolution

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https://www.readbyqxmd.com/read/28646210/identification-of-introns-harboring-functional-sequence-elements-through-positional-conservation
#1
Michal Chorev, Alan Joseph Bekker, Jacob Goldberger, Liran Carmel
Many human introns carry out a function, in the sense that they are critical to maintain normal cellular activity. Their identification is fundamental to understanding cellular processes and disease. However, being noncoding elements, such functional introns are poorly predicted based on traditional approaches of sequence and structure conservation. Here, we generated a dataset of human functional introns that carry out different types of functions. We showed that functional introns share common characteristics, such as higher positional conservation along the coding sequence and reduced loss rates, regardless of their specific function...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642229/evolutionary-dynamics-of-the-kinetochore-network-in-eukaryotes-as-revealed-by-comparative-genomics
#2
Jolien Je van Hooff, Eelco Tromer, Leny M van Wijk, Berend Snel, Geert Jpl Kops
During eukaryotic cell division, the sister chromatids of duplicated chromosomes are pulled apart by microtubules, which connect via kinetochores. The kinetochore is a multiprotein structure that links centromeres to microtubules, and that emits molecular signals in order to safeguard the equal distribution of duplicated chromosomes over daughter cells. Although microtubule-mediated chromosome segregation is evolutionary conserved, kinetochore compositions seem to have diverged. To systematically inventory kinetochore diversity and to reconstruct its evolution, we determined orthologs of 70 kinetochore proteins in 90 phylogenetically diverse eukaryotes...
June 22, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28641092/nuclear-mechanotransduction-sensing-the-force-from-within
#3
REVIEW
Avathamsa Athirasala, Nivi Hirsch, Amnon Buxboim
The cell nucleus is a hallmark of eukaryotic evolution, where gene expression is regulated and the genome is replicated and repaired. Yet, in addition to complex molecular processes, the nucleus has also evolved to serve physical tasks that utilize its optical and mechanical properties. Nuclear mechanotransduction of externally applied forces and extracellular stiffness is facilitated by the physical connectivity of the extracellular environment, the cytoskeleton and the nucleoskeletal matrix of lamins and chromatin...
June 19, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28627128/signatures-of-soft-sweeps-across-the-dt1-locus-underlying-determinate-growth-habit-in-soybean-glycine-max-l-merr
#4
Limei Zhong, Qiaomei Yang, Xin Yan, Chao Yu, Liu Su, Xifeng Zhang, Youlin Zhu
Determinate growth habit is an agronomically important trait associated with domestication in soybean. Previous studies have demonstrated that the emergence of determinacy is correlated with artificial selection on four non-synonymous mutations in the Dt1 gene. To better understand the signatures of the soft sweeps across the Dt1 locus and track the origins of the determinate alleles, we examined patterns of nucleotide variation in Dt1 and the surrounding genomic region of approximately 800 kb. Four local, asymmetrical hard sweeps on four determinate alleles, sized approximately 660, 120, 220 and 150 kb were identified, which constitute the soft sweeps for the adaptation...
June 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28625053/annotation-of-the-domestic-pig-genome-by-quantitative-proteogenomics
#5
Harald Marx, Hannes Hahne, Susanne E Ulbrich, Angelika Schnieke, Oswald Rottmann, Dimitrij Frishman, Bernhard Kuster
The pig is one of the earliest domesticated animals in the history of human civilization and represents one of the most important livestock animals. The recent sequencing of the Sus scrofa genome was a major step towards the comprehensive understanding of porcine biology, evolution and its utility as a promising large animal model for biomedical and xenotransplantation research. However, the functional and structural annotation of the Sus scrofa genome is far from complete. Here, we present mass spectrometry-based quantitative proteomics data of nine juvenile organs and six embryonic stages between 18 to 39 days after gestation...
June 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28623182/mygenefriends-a-social-network-linking-genes-genetic-diseases-and-researchers
#6
Alexis Allot, Kirsley Chennen, Yannis Nevers, Laetitia Poidevin, Arnaud Kress, Raymond Ripp, Julie Dawn Thompson, Olivier Poch, Odile Lecompte
BACKGROUND: The constant and massive increase of biological data offers unprecedented opportunities to decipher the function and evolution of genes and their roles in human diseases. However, the multiplicity of sources and flow of data mean that efficient access to useful information and knowledge production has become a major challenge. This challenge can be addressed by taking inspiration from Web 2.0 and particularly social networks, which are at the forefront of big data exploration and human-data interaction...
June 16, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28620026/learning-to-read-and-write-in-evolution-from-static-pseudoenzymes-and-pseudosignalers-to-dynamic-gear-shifters
#7
REVIEW
Abulikemu Abudukelimu, Thierry D G A Mondeel, Matteo Barberis, Hans V Westerhoff
We present a systems biology view on pseudoenzymes that acknowledges that genes are not selfish: the genome is. With network function as the selectable unit, there has been an evolutionary bonus for recombination of functions of and within proteins. Many proteins house a functionality by which they 'read' the cell's state, and one by which they 'write' and thereby change that state. Should the writer domain lose its cognate function, a 'pseudoenzyme' or 'pseudosignaler' arises. GlnK involved in Escherichia coli ammonia assimilation may well be a pseudosignaler, associating 'reading' the nitrogen state of the cell to 'writing' the ammonium uptake activity...
June 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28619134/genetic-antigenic-and-pathogenic-characteristics-of-avian-infectious-bronchitis-viruses-genotypically-related-to-793-b-in-china
#8
Zongxi Han, Wenjun Zhao, Yuqiu Chen, Qianqian Xu, Junfeng Sun, Tingting Zhang, Yan Zhao, Shuling Liang, Mengying Gao, Qiuling Wang, Xiangang Kong, Shengwang Liu
In this study, 20 infectious bronchitis virus (IBV) strains, which were genotypically related to 793/B, as assessed by an S1 gene comparison and a complete genomic sequence analysis, were isolated and identified from 2009 to 2014 in China. Phylogenetic analysis, network tree, similarity plot analysis, Recombination Detection Program 4(RDP4) and sequence comparison revealed that 12 of the 20 isolates were likely the reisolated vaccine virus. One isolate, ck/CH/LSD/110857, was shown to have originated from recombination events between H120- and 4/91-like vaccine strains that did not result in changes of antigenicity and pathogenicity...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28615505/topological-features-of-a-gene-co-expression-network-predict-patterns-of-natural-diversity-in-environmental-response
#9
David L Des Marais, Rafael F Guerrero, Jesse R Lasky, Samuel V Scarpino
Molecular interactions affect the evolution of complex traits. For instance, adaptation may be constrained by pleiotropic or epistatic effects, both of which can be reflected in the structure of molecular interaction networks. To date, empirical studies investigating the role of molecular interactions in phenotypic evolution have been idiosyncratic, offering no clear patterns. Here, we investigated the network topology of genes putatively involved in local adaptation to two abiotic stressors-drought and cold-in Arabidopsis thaliana Our findings suggest that the gene-interaction topologies for both cold and drought stress response are non-random, with genes that show genetic variation in drought expression response (eGxE) being significantly more peripheral and cold response genes being significantly more central than genes which do not show GxE...
June 14, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28611792/structural-and-functional-insights-into-wrky3-and-wrky4-transcription-factors-to-unravel-the-wrky-dna-w-box-complex-interaction-in-tomato-solanum-lycopersicum-l-a-computational-approach
#10
Mohd Aamir, Vinay K Singh, Mukesh Meena, Ram S Upadhyay, Vijai K Gupta, Surendra Singh
The WRKY transcription factors (TFs), play crucial role in plant defense response against various abiotic and biotic stresses. The role of WRKY3 and WRKY4 genes in plant defense response against necrotrophic pathogens is well-reported. However, their functional annotation in tomato is largely unknown. In the present work, we have characterized the structural and functional attributes of the two identified tomato WRKY transcription factors, WRKY3 (SlWRKY3), and WRKY4 (SlWRKY4) using computational approaches...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28603022/variation-analysis-of-norovirus-among-children-with-diarrhea-in-rural-hebei-province-north-of-china
#11
Niu Qiao, Song-Mei Wang, Jin-Xia Wang, Bin Kang, Shan-Shan Zhen, Xin-Jiang Zhang, Zhi-Yong Hao, Jing-Chen Ma, Chao Qiu, Yu-Liang Zhao, Lei Liu, Xuan-Yi Wang
To understand the distribution of genotyping, as well as evolution of norovirus circulating among children<5yrs., a population-based diarrhea surveillance targeted children<5yrs. was conducted in rural Zhengding County, Hebei Province, China between October 2011 and March 2012. RT-PCR was used to amplify the capsid-encoding region of GI and GII norovirus to identify norovirus infection. All PCR products were sequenced and analyzed for genotyping and constructing phylogenetic tree. Dynamic distribution network was constructed by TempNet to illustrate the genetic relationships at two different time points...
June 7, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28602572/the-near-east-as-a-cradle-of-biodiversity-a-phylogeography-of-banded-newts-genus-ommatotriton-reveals-extensive-inter-and-intraspecific-genetic-differentiation
#12
Isolde van Riemsdijk, Jan W Arntzen, Sergé Bogaerts, Michael Franzen, Spartak N Litvinchuk, Kurtuluş Olgun, Ben Wielstra
The banded newt (genus Ommatotriton) is widely distributed in the Near East (Anatolia, Caucasus and the Levant) - an understudied region from the perspective of phylogeography. The genus is polytypic, but the number of species included and the phylogenetic relationships between them are not settled. We sequenced two mitochondrial and two nuclear DNA markers throughout the range of Ommatotriton. For mtDNA we constructed phylogenetic trees, estimated divergence times using fossil calibration, and investigated changes in effective population size with Bayesian skyline plots and mismatch analyses...
June 13, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28588592/in-depth-genomic-and-transcriptomic-analysis-of-five-k-transporter-gene-families-in-soybean-confirm-their-differential-expression-for-nodulation
#13
Hafiz M Rehman, Muhammad A Nawaz, Zahid Hussain Shah, Ihsanullah Daur, Sadia Khatoon, Seung Hwan Yang, Gyuhwa Chung
Plants have evolved a sophisticated network of K(+) transport systems to regulate growth and development. Limited K(+) resources are now forcing us to investigate how plant demand can be satisfied. To answer this complex question, we must understand the genomic and transcriptomic portfolio of K(+) transporters in plants. Here, we have identified 70 putative K(+) transporter genes from soybean, including 29 HAK/KT/KUP genes, 16 genes encoding voltage-gated K(+) channels, 9 TPK/KCO genes, 4 HKT genes, and 12 KEA genes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28588590/a-conserved-carbon-starvation-response-underlies-bud-dormancy-in-woody-and-herbaceous-species
#14
Carlos Tarancón, Eduardo González-Grandío, Juan C Oliveros, Michael Nicolas, Pilar Cubas
Plant shoot systems give rise to characteristic above-ground plant architectures. Shoots are formed from axillary meristems and buds, whose growth and development is modulated by systemic and local signals. These cues convey information about nutrient and water availability, light quality, sink/source organ activity and other variables that determine the timeliness and competence to maintain development of new shoots. This information is translated into a local response, in meristems and buds, of growth or quiescence...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28587860/the-oyster-immunity
#15
Lingling Wang, Xiaorui Song, Linsheng Song
Oysters, the common name for a number of different bivalve molluscs, are the worldwide aquaculture species and also play vital roles in the function of ecosystem. As invertebrate, oysters have evolved an integrated, highly complex innate immune system to recognize and eliminate various invaders via an array of orchestrated immune reactions, such as immune recognition, signal transduction, synthesis of antimicrobial peptides, as well as encapsulation and phagocytosis of the circulating haemocytes. The hematopoietic tissue, hematopoiesis, and the circulating haemocytes have been preliminary characterized, and the detailed annotation of the Pacific oyster Crassostrea gigas genome has revealed massive expansion and functional divergence of innate immune genes in this animal...
June 3, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28584165/phylogenomic-synteny-network-analysis-of-mads-box-transcription-factor-genes-reveals-lineage-specific-transpositions-ancient-tandem-duplications-and-deep-positional-conservation
#16
Tao Zhao, Rens Holmer, Suzanne de Bruijn, Gerco C Angenent, Harrold A van den Burg, M Eric Schranz
Conserved genomic context provides critical information for comparative evolutionary analysis. With the increase in numbers of sequenced plant genomes, synteny analysis can provide new insight into gene family evolution. Here, we exploit a network analysis approach to organize and interpret massive pairwise syntenic relationships. Specifically, we analyzed synteny networks of the MADS-box transcription factor gene family using fifty-one completed plant genomes. In combination with phylogenetic profiling, several novel evolutionary patterns were inferred and visualized from synteny network clusters...
June 5, 2017: Plant Cell
https://www.readbyqxmd.com/read/28584121/applying-gene-regulatory-network-logic-to-the-evolution-of-social-behavior
#17
Nicole M Baran, Patrick T McGrath, J Todd Streelman
Animal behavior is ultimately the product of gene regulatory networks (GRNs) for brain development and neural networks for brain function. The GRN approach has advanced the fields of genomics and development, and we identify organizational similarities between networks of genes that build the brain and networks of neurons that encode brain function. In this perspective, we engage the analogy between developmental networks and neural networks, exploring the advantages of using GRN logic to study behavior. Applying the GRN approach to the brain and behavior provides a quantitative and manipulative framework for discovery...
June 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28584112/causes-and-evolutionary-consequences-of-primordial-germ-cell-specification-mode-in-metazoans
#18
Carrie A Whittle, Cassandra G Extavour
In animals, primordial germ cells (PGCs) give rise to the germ lines, the cell lineages that produce sperm and eggs. PGCs form in embryogenesis, typically by one of two modes: a likely ancestral mode wherein germ cells are induced during embryogenesis by cell-cell signaling (induction) or a derived mechanism whereby germ cells are specified by using germ plasm-that is, maternally specified germ-line determinants (inheritance). The causes of the shift to germ plasm for PGC specification in some animal clades remain largely unknown, but its repeated convergent evolution raises the question of whether it may result from or confer an innate selective advantage...
June 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28584099/genome-wide-use-of-high-and-low-affinity-tbrain-transcription-factor-binding-sites-during-echinoderm-development
#19
Gregory A Cary, Alys M Cheatle Jarvela, Rene D Francolini, Veronica F Hinman
Sea stars and sea urchins are model systems for interrogating the types of deep evolutionary changes that have restructured developmental gene regulatory networks (GRNs). Although cis-regulatory DNA evolution is likely the predominant mechanism of change, it was recently shown that Tbrain, a Tbox transcription factor protein, has evolved a changed preference for a low-affinity, secondary binding motif. The primary, high-affinity motif is conserved. To date, however, no genome-wide comparisons have been performed to provide an unbiased assessment of the evolution of GRNs between these taxa, and no study has attempted to determine the interplay between transcription factor binding motif evolution and GRN topology...
June 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28584090/paleogenomics-of-echinoids-reveals-an-ancient-origin-for-the-double-negative-specification-of-micromeres-in-sea-urchins
#20
Jeffrey R Thompson, Eric M Erkenbrack, Veronica F Hinman, Brenna S McCauley, Elizabeth Petsios, David J Bottjer
Establishing a timeline for the evolution of novelties is a common, unifying goal at the intersection of evolutionary and developmental biology. Analyses of gene regulatory networks (GRNs) provide the ability to understand the underlying genetic and developmental mechanisms responsible for the origin of morphological structures both in the development of an individual and across entire evolutionary lineages. Accurately dating GRN novelties, thereby establishing a timeline for GRN evolution, is necessary to answer questions about the rate at which GRNs and their subcircuits evolve, and to tie their evolution to paleoenvironmental and paleoecological changes...
June 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
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