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Gene network evolution

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https://www.readbyqxmd.com/read/28223401/transcriptome-analyses-of-rhesus-monkey-pre-implantation-embryos-reveal-a-reduced-capacity-for-dna-double-strand-break-repair-in-primate-oocytes-and-early-embryos
#1
Xinyi Wang, Denghui Liu, Dajian He, Shengbo Suo, Xian Xia, Xiechao He, Jing-Dong Han, Ping Zheng
Pre-implantation embryogenesis encompasses several critical events including genome reprogramming, zygotic genome activation (ZGA), and cell fate commitment, most of which remain mechanistically unclear in primates. In addition, primates display a high rate of embryo wastage without any clear molecular basis. Understanding the factors involved in genome reprogramming and ZGA will help the generation of induced pluripotent stem cells with high efficiency. Moreover, explaining the molecular basis responsible for embryo wastage in primates will greatly expand our knowledge of species evolution...
February 21, 2017: Genome Research
https://www.readbyqxmd.com/read/28217809/-generation-and-phenotype-analysis-of-zebrafish-mutations-of-obesity-related-genes-lepr-and-mc4r
#2
Fei Fei, Shao-Yang Sun, Yu-Xiao Yao, Xu Wang
Obesity has become a severe public health problem across the world, and seriously affects the health and life quality of human beings. Here we generated lepr and mc4r mutant zebrafish via the CRISPR/Cas9 technique, and performed morphological and functional characterizations of those mutants. We observed that there was no significant phenotypic difference between homozygous mutants and wild-type controls before 2.5 months post-fertilization (mpf). However, the adult lepr(-/-) and mc4r(-/-) individuals displayed increased food intake, heavier weight, and higher body fat percentage, the characteristics of obesity phenotypes...
February 25, 2017: Sheng Li Xue Bao: [Acta Physiologica Sinica]
https://www.readbyqxmd.com/read/28212112/cancer-as-robust-intrinsic-state-shaped-by-evolution-a-key-issues-review
#3
Ruoshi Yuan, Xiaomei Zhu, Gaowei Wang, Site Li, Ping Ao
Cancer is a complex disease: its pathology cannot be properly understood in terms of independent players-genes, proteins, molecular pathways, or their simple combinations. This is similar to many-body physics of a condensed phase that many important properties are not determined by a single atom or molecule. The rapidly accumulating large 'omics' data also require a new mechanistic and global underpinning to organize for rationalizing cancer complexity. A unifying and quantitative theory was proposed by some of the present authors that cancer is a robust state formed by the endogenous molecular-cellular network, which is evolutionarily built for the developmental processes and physiological functions...
February 17, 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/28207813/interacting-networks-of-resistance-virulence-and-core-machinery-genes-identified-by-genome-wide-epistasis-analysis
#4
Marcin J Skwark, Nicholas J Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Ying Ying Xu, Paul Turner, Simon R Harris, Stephen B Beres, James M Musser, Julian Parkhill, Stephen D Bentley, Erik Aurell, Jukka Corander
Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and Streptococcus pyogenes (group A Streptococcus)...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28206693/plasmid-and-clonal-interference-during-post-horizontal-gene-transfer-evolution
#5
S Bedhomme, D Perez Pantoja, I G Bravo
Plasmids are nucleic acid molecules that can drive their own replication in a living cell. They can be transmitted horizontally and can thrive in the host cell to high copy numbers. Plasmid replication and gene expression consume cellular resources and cells carrying plasmids incur fitness costs. But many plasmids carry genes that can be beneficial under certain conditions, allowing the cell to endure in the presence of antibiotics, toxins, competitors or parasites. Horizontal transfer of plasmid-encoded genes can thus instantaneously confer differential adaptation to local or transient selection conditions...
February 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28185903/the-thermodynamics-of-protein-aggregation-reactions-may-underpin-the-enhanced-metabolic-efficiency-associated-with-heterosis-some-balancing-selection-and-the-evolution-of-ploidy-levels
#6
REVIEW
B R Ginn
Identifying the physical basis of heterosis (or "hybrid vigor") has remained elusive despite over a hundred years of research on the subject. The three main theories of heterosis are dominance theory, overdominance theory, and epistasis theory. Kacser and Burns (1981) identified the molecular basis of dominance, which has greatly enhanced our understanding of its importance to heterosis. This paper aims to explain how overdominance, and some features of epistasis, can similarly emerge from the molecular dynamics of proteins...
February 6, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28185788/echinoderm-development-and-evolution-in-the-post-genomic-era
#7
REVIEW
Gregory A Cary, Veronica F Hinman
The highly recognizable animals within the phylum Echinodermata encompass an enormous disparity of adult and larval body plans. The extensive knowledge of sea urchin development has culminated in the description of the exquisitely detailed gene regulatory network (GRN) that governs the specification of various embryonic territories. This information provides a unique opportunity for comparative studies in other echinoderm taxa to understand the evolution and developmental mechanisms underlying body plan change...
February 6, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28185563/exploring-phylogenetic-hypotheses-via-gibbs-sampling-on-evolutionary-networks
#8
Yun Yu, Christopher Jermaine, Luay Nakhleh
BACKGROUND: Phylogenetic networks are leaf-labeled graphs used to model and display complex evolutionary relationships that do not fit a single tree. There are two classes of phylogenetic networks: Data-display networks and evolutionary networks. While data-display networks are very commonly used to explore data, they are not amenable to incorporating probabilistic models of gene and genome evolution. Evolutionary networks, on the other hand, can accommodate such probabilistic models, but they are not commonly used for exploration...
November 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28185554/evolution-of-transcriptional-networks-in-yeast-alternative-teams-of-transcriptional-factors-for-different-species
#9
Adriana Muñoz, Daniella Santos Muñoz, Aleksey Zimin, James A Yorke
BACKGROUND: The diversity in eukaryotic life reflects a diversity in regulatory pathways. Nocedal and Johnson argue that the rewiring of gene regulatory networks is a major force for the diversity of life, that changes in regulation can create new species. RESULTS: We have created a method (based on our new "ping-pong algorithm) for detecting more complicated rewirings, where several transcription factors can substitute for one or more transcription factors in the regulation of a family of co-regulated genes...
November 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28180060/gprc6a-jack-of-all-metabolism-or-master-of-none
#10
REVIEW
Min Pi, Satoru Kenneth Nishimoto, L Darryl Quarles
BACKGROUND: GPRC6A, a widely expressed G-protein coupled receptor, is proposed to be a master regulator of complex endocrine networks and metabolic processes. GPRC6A is activated by multiple ligands, including osteocalcin (Ocn), testosterone (T), basic amino acids, and various cations. SCOPE OF REVIEW: We review the controversy surrounding GPRC6A functions. In mice, GPRC6A is proposed to integrate metabolic functions through the coordinated secretion of hormones, including insulin, GLP-1, T, and IL-6, and direct effects of this receptor to control glucose and fat metabolism in the liver, skeletal muscle, and fat...
February 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/28179101/molecular-phylogenomic-study-and-the-role-of-exogenous-spermidine-in-the-metabolic-adjustment-of-endogenous-polyamine-in-two-rice-cultivars-under-salt-stress
#11
Jayita Saha, Kalyan Giri
Compelling evidences anticipated the well acclamation of involvement of exogenous and endogenous polyamines (PAs) in conferring salt tolerance in plants. Intracellular PA's anabolism and catabolism should have contributed to maintain endogenous PAs homeostasis to induce stress signal networks. In this report, the evolutionary study has been conducted to reveal the phylogenetic relationship of genes encoding enzymes of the anabolic and catabolic pathway of PAs among the five plant lineages including green algae, moss, lycophyte, dicot and monocot along with their respective exon-intron structural patterns...
April 20, 2017: Gene
https://www.readbyqxmd.com/read/28164039/quorum-sensing-n-acyl-homoserine-lactones-sdia-suppresses-escherichia-coli-pseudomonas-aeruginosa-conjugation-through-inhibiting-trai-expression
#12
Yang Lu, Jianming Zeng, Binning Wu, Shunmei E, Lina Wang, Renxin Cai, Ni Zhang, Youqiang Li, Xianzhang Huang, Bin Huang, Cha Chen
Conjugation is a key mechanism for horizontal gene transfer and plays an important role in bacterial evolution, especially with respect to antibiotic resistance. However, little is known about the role of donor and recipient cells in regulation of conjugation. Here, using an Escherichia coli (SM10λπ)-Pseudomonas aeruginosa (PAO1) conjugation model, we demonstrated that deficiency of lasI/rhlI, genes associated with generation of the quorum sensing signals N-acyl homoserine lactones (AHLs) in PAO1, or deletion of the AHLs receptor SdiA in the donor SM10λπ both facilitated conjugation...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28161902/phylogenomic-analysis-of-gene-co-expression-networks-reveals-the-evolution-of-functional-modules
#13
Colin Ruprecht, Sebastian Proost, Marcela Hernandez-Coronado, Carlos Ortiz-Ramirez, Daniel Lang, Stefan A Rensing, Jörg D Becker, Klaas Vandepoele, Marek Mutwil
Molecular evolutionary studies correlate genomic and phylogenetic information with the emergence of new traits of organisms. These traits are, however, the consequence of dynamic gene networks composed of functional modules, which might not be captured by genomic analyses. Here, we established a method, which combines large-scale genomic and phylogenetic data with gene co-expression networks, to extensively study the evolutionary make-up of modules in the moss Physcomitrella patens and in the angiosperms Arabidopsis thaliana and rice...
February 5, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28161289/climbing-brain-levels-of-organisation-from-genes-to-consciousness
#14
REVIEW
Jean-Pierre Changeux
Given the tremendous complexity of brain organisation, here I propose a strategy that dynamically links stages of brain organisation from genes to consciousness, at four privileged structural levels: genes; transcription factors (TFs)-gene networks; synaptic epigenesis; and long-range connectivity. These structures are viewed as nested and reciprocally inter-regulated, with a hierarchical organisation that proceeds on different timescales during the course of evolution and development. Interlevel bridging mechanisms include intrinsic variation-selection mechanisms, which offer a community of bottom-up and top-down models linking genes to consciousness in a stepwise manner...
February 1, 2017: Trends in Cognitive Sciences
https://www.readbyqxmd.com/read/28144250/evolution-and-expression-patterns-of-tcp-genes-in-asparagales
#15
Yesenia Madrigal, Juan F Alzate, Natalia Pabón-Mora
CYCLOIDEA-like genes are involved in the symmetry gene network, limiting cell proliferation in the dorsal regions of bilateral flowers in core eudicots. CYC-like and closely related TCP genes (acronym for TEOSINTE BRANCHED1, CYCLOIDEA, and PROLIFERATION CELL FACTOR) have been poorly studied in Asparagales, the largest order of monocots that includes both bilateral flowers in Orchidaceae (ca. 25.000 spp) and radially symmetrical flowers in Hypoxidaceae (ca. 200 spp). With the aim of assessing TCP gene evolution in the Asparagales, we isolated TCP-like genes from publicly available databases and our own transcriptomes of Cattleya trianae (Orchidaceae) and Hypoxis decumbens (Hypoxidaceae)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28142200/chlamydomonas-carries-out-fatty-acid-%C3%AE-oxidation-in-ancestral-peroxisomes-using-a-bona-fide-acyl-coa-oxidase
#16
Fantao Kong, Yuanxue Liang, Bertrand Légeret, Audrey Beyly-Adriano, Stéphanie Blangy, Richard P Haslam, Johnathan A Napier, Fred Beisson, Gilles Peltier, Yonghua Li-Beisson
Peroxisomes are thought to have played a key role in the evolution of metabolic networks of photosynthetic organisms by connecting oxidative and biosynthetic routes operating in different compartments. While the various oxidative pathways operating in the peroxisomes of higher plants are fairly well characterized, the reactions present in the primitive peroxisomes (microbodies) of algae are poorly understood. Screening of a Chlamydomonas insertional mutant library identified a strain strongly impaired in oil remobilization and defective in Cre05...
January 31, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28131339/review-epistasis-and-dominance-in-the-emergence-of-catalytic-function-as-exemplified-by-the-evolution-of-plant-terpene-synthases
#17
REVIEW
Jitender Cheema, Juan A Faraldos, Paul E O'Maille
Epistasis, the interaction between mutations and the genetic background, is a pervasive force in evolution that is difficult to predict yet derives from a simple principle - biological systems are interconnected. Therefore, one effect may be intimately linked to another, hence interdependent. Untangling epistatic interactions between and within genes is a vibrant area of research. Deriving a mechanistic understanding of epistasis is a major challenge. Particularly, elucidating how epistasis can attenuate the effects of otherwise dominant mutations that control phenotypes...
February 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28127303/reverse-engineering-gene-regulatory-networks-from-measurement-with-missing-values
#18
Oyetunji E Ogundijo, Abdulkadir Elmas, Xiaodong Wang
BACKGROUND: Gene expression time series data are usually in the form of high-dimensional arrays. Unfortunately, the data may sometimes contain missing values: for either the expression values of some genes at some time points or the entire expression values of a single time point or some sets of consecutive time points. This significantly affects the performance of many algorithms for gene expression analysis that take as an input, the complete matrix of gene expression measurement. For instance, previous works have shown that gene regulatory interactions can be estimated from the complete matrix of gene expression measurement...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/28126286/beyond-genomics-studying-evolution-with-gene-coexpression-networks
#19
REVIEW
Colin Ruprecht, Neha Vaid, Sebastian Proost, Staffan Persson, Marek Mutwil
Understanding how genomes change as organisms become more complex is a central question in evolution. Molecular evolutionary studies typically correlate the appearance of genes and gene families with the emergence of biological pathways and morphological features. While such approaches are of great importance to understand how organisms evolve, they are also limited, as functionally related genes work together in contexts of dynamic gene networks. Since functionally related genes are often transcriptionally coregulated, gene coexpression networks present a resource to study the evolution of biological pathways...
January 23, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/28118844/single-cell-epigenomic-variability-reveals-functional-cancer-heterogeneity
#20
Ulrike M Litzenburger, Jason D Buenrostro, Beijing Wu, Ying Shen, Nathan C Sheffield, Arwa Kathiria, William J Greenleaf, Howard Y Chang
BACKGROUND: Cell-to-cell heterogeneity is a major driver of cancer evolution, progression, and emergence of drug resistance. Epigenomic variation at the single-cell level can rapidly create cancer heterogeneity but is difficult to detect and assess functionally. RESULTS: We develop a strategy to bridge the gap between measurement and function in single-cell epigenomics. Using single-cell chromatin accessibility and RNA-seq data in K562 leukemic cells, we identify the cell surface marker CD24 as co-varying with chromatin accessibility changes linked to GATA transcription factors in single cells...
January 24, 2017: Genome Biology
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