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Gene network evolution

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https://www.readbyqxmd.com/read/28087776/seed-plant-specific-gene-lineages-involved-in-carpel-development
#1
Kai C Pfannebecker, Matthias Lange, Oliver Rupp, Annette Becker
Evolutionary innovations are important drivers of speciation and some are the defining characters of entire phyla. One such major innovation is the carpel, the unifying character and most complex plant organ, composed of many clearly distinct tissue types to ensure reproductive success. The origin of the carpel is unknown, but many components of the gene regulatory network (GRN) governing carpel development and their genetic interactions are known from the core eudicot Arabidopsis thaliana To unravel the evolution of the carpel GRN and to discriminate between "early" and "late" steps in carpel evolution we calculated thorough phylogeny reconstructions based on sequenced genomes...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087420/on-the-quirks-of-maximum-parsimony-and-likelihood-on-phylogenetic-networks
#2
Christopher Bryant, Mareike Fischer, Simone Linz, Charles Semple
Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe evolution accurately. For instance, processes like hybridization or lateral gene transfer that are commonplace in many groups of organisms and result in mosaic patterns of relationships cannot be represented by a single phylogenetic tree. This is why phylogenetic networks, which can display such events, are becoming of more and more interest in phylogenetic research...
January 10, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28086860/nicotiana-attenuata-data-hub-nadh-an-integrative-platform-for-exploring-genomic-transcriptomic-and-metabolomic-data-in-wild-tobacco
#3
Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T Baldwin, Shuqing Xu
BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28062755/evolutionary-conservation-and-divergence-of-gene-coexpression-networks-in-gossypium-cotton-seeds
#4
Guanjing Hu, Ran Hovav, Corrinne E Grover, Adi Faigenboim-Doron, Noa Kadmon, Justin T Page, Joshua A Udall, Jonathan F Wendel
The cotton genus (Gossypium) provides a superior system for the study of diversification, genome evolution, polyploidization, and human-mediated selection. To gain insight into phenotypic diversification in cotton seeds, we conducted coexpression network analysis of developing seeds from diploid and allopolyploid cotton species and explored network properties. Key network modules and functional associations were identified related to seed oil content and seed weight. We compared species-specific networks to reveal topological changes, including rewired edges and differentially coexpressed genes, associated with speciation, polyploidy, and cotton domestication...
January 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28056800/networking-in-microbes-conjugative-elements-and-plasmids-in-the-genus-alteromonas
#5
Mario López-Pérez, Nieves Ramon-Marco, Francisco Rodriguez-Valera
BACKGROUND: To develop evolutionary models for the free living bacterium Alteromonas the genome sequences of isolates of the genus have been extensively analyzed. However, the main genetic exchange drivers in these microbes, conjugative elements (CEs), have not been considered in detail thus far. In this work, CEs have been searched in several complete Alteromonas genomes and their sequence studied to understand their role in the evolution of this genus. Six genomes are reported here for the first time...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28056785/determination-of-dosage-compensation-and-comparison-of-gene-expression-in-a-triploid-hybrid-fish
#6
Li Ren, Chenchen Tang, Wuhui Li, Jialin Cui, Xingjun Tan, Yafeng Xiong, Jie Chen, Jun Wang, Jun Xiao, Yi Zhou, Jing Wang, Min Tao, Chun Zhang, Shaojun Liu
BACKGROUND: Polyploidy and hybridization are both recognized as major forces in evolution. Most of our current knowledge about differences in gene regulation in polyploid hybrids comes from plant studies. The gene expression of diverged genomes and regulatory interactions are still unclear in lower vertebrates. RESULTS: We generated 229 million cleaned reads (42.23 Gbp) from triploid of maternal grass carp (Ctenopharyngodon idellus, Cyprininae, 2n = 48) × paternal blunt snout bream (Megalobrama amblycephala, Cultrinae, 2n = 48) and their diploid parents using next-generation sequencing...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28053006/co-option-and-de-novo-gene-evolution-underlie-molluscan-shell-diversity
#7
Felipe Aguilera, Carmel McDougall, Bernard M Degnan
Molluscs fabricate shells of incredible diversity and complexity by localized secretions from the dorsal epithelium of the mantle. Although distantly-related molluscs express remarkably different secreted gene products, it remains unclear if the evolution of shell structure and pattern is underpinned by the differential co-option of conserved genes or the integration of lineage-specific genes into the mantle regulatory program. To address this, we compare the mantle transcriptomes of 11 bivalves and gastropods of varying relatedness...
January 4, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28052708/chaos-and-hyperchaos-in-simple-gene-network-with-negative-feedback-and-time-delays
#8
Tamara M Khlebodarova, Vladislav V Kogai, Stanislav I Fadeev, Vitaly A Likhoshvai
Today there are examples that prove the existence of chaotic dynamics at all levels of organization of living systems, except intracellular, although such a possibility has been theoretically predicted. The lack of experimental evidence of chaos generation at the intracellular level in vivo may indicate that during evolution the cell got rid of chaos. This work allows the hypothesis that one of the possible mechanisms for avoiding chaos in gene networks can be a negative evolutionary selection, which prevents fixation or realization of regulatory circuits, creating too mild, from the biological point of view, conditions for the emergence of chaos...
November 29, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28052243/networks-of-cultured-ipsc-derived-neurons-reveal-the-human-synaptic-activity-regulated-adaptive-gene-program
#9
Priit Pruunsild, C Peter Bengtson, Hilmar Bading
Long-term adaptive responses in the brain, such as learning and memory, require synaptic activity-regulated gene expression, which has been thoroughly investigated in rodents. Using human iPSC-derived neuronal networks, we show that the human and the mouse synaptic activity-induced transcriptional programs share many genes and both require Ca(2+)-regulated synapse-to-nucleus signaling. Species-specific differences include the noncoding RNA genes BRE-AS1 and LINC00473 and the protein-coding gene ZNF331, which are absent in the mouse genome, as well as several human genes whose orthologs are either not induced by activity or are induced with different kinetics in mice...
January 3, 2017: Cell Reports
https://www.readbyqxmd.com/read/28050020/identification-and-evolutionary-dynamics-of-two-novel-human-coronavirus-oc43-genotypes-associated-with-acute-respiratory-infections-phylogenetic-spatiotemporal-and-transmission-network-analyses
#10
Xiang Yong Oong, Kim Tien Ng, Yutaka Takebe, Liang Jie Ng, Kok Gan Chan, Jack Bee Chook, Adeeba Kamarulzaman, Kok Keng Tee
Human coronavirus OC43 (HCoV-OC43) is commonly associated with respiratory tract infections in humans, with five genetically distinct genotypes (A to E) described so far. In this study, we obtained the full-length genomes of HCoV-OC43 strains from two previously unrecognized lineages identified among patients presenting with severe upper respiratory tract symptoms in a cross-sectional molecular surveillance study in Kuala Lumpur, Malaysia, between 2012 and 2013. Phylogenetic, recombination and comparative genomic analyses revealed two distinct clusters diverging from a genotype D-like common ancestor through recombination with a putative genotype A-like lineage in the non-structural protein (nsp) 10 gene...
January 4, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/28049761/an-evolutionary-framework-for-carpel-developmental-control-genes
#11
Kai C Pfannebecker, Matthias Lange, Oliver Rupp, Annette Becker
Carpels are the female reproductive organs of flowering plants (angiosperms), enclose the ovules, and develop into fruits. The presence of carpels unites angiosperms, and they are suggested to be the most important autapomorphy of the angiosperms, e.g., they prevent inbreeding and allow efficient seed dispersal. Many transcriptional regulators and coregulators essential for carpel development are encoded by diverse gene families and well characterized in Arabidopsis thaliana Among these regulators are AGAMOUS (AG), ETTIN (ETT), LEUNIG (LUG), SEUSS (SEU), SHORT INTERNODE/STYLISH (SHI/STY), and SEPALLATA1, 2, 3, 4 (SEP1, 2, 3, 4)...
October 20, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28049420/horizontal-gene-transfer-drives-the-evolution-of-rh50-permeases-in-prokaryotes
#12
Giorgio Matassi
BACKGROUND: Rh50 proteins belong to the family of ammonia permeases together with their Amt/MEP homologs. Ammonia permeases increase the permeability of NH3/NH4(+) across cell membranes and are believed to be involved in excretion of toxic ammonia and in the maintenance of pH homeostasis. RH50 genes are widespread in eukaryotes but absent in land plants and fungi, and remarkably rare in prokaryotes. The evolutionary history of RH50 genes in prokaryotes is just beginning to be unveiled...
January 3, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28044340/dancing-in-the-dark-darkness-as-a-signal-in-plants
#13
REVIEW
Adam Seluzicki, Yogev Burko, Joanne Chory
Daily cycles of light and dark provide an organizing principle and temporal constraints under which life on Earth evolved. While light is often the focus of plant studies, it is only half the story. Plants continuously adjust to their surroundings, taking both dawn and dusk as cues to organize their growth, development and metabolism to appropriate times of day. In this review, we examine the effects of darkness on plant physiology and growth. We describe the similarities and differences between seedlings grown in the dark versus those grown in light-dark cycles, and the evolution of etiolated growth...
January 3, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28036280/pan-organ-transcriptome-variation-across-21-cancer-types
#14
Wangxiong Hu, Yanmei Yang, Xiaofen Li, Shu Zheng
It is widely accepted that some messenger RNAs are evolutionarily conserved across species, both in sequence and tissue-expression specificity. To date, however, little effort has been made to exploit the transcriptome divergence between cancer and adjacent normal tissue at the pan-organ level. In this work, a transcriptome sequencing dataset from 675 normal-tumor pairs, representing 21 solid organs in The Cancer Genome Atlas, is used to evaluate expression evolution. The results show that in most cancer types, gene expression divergence and organ-specificity are reduced in cancer tissue compared to adjacent normal tissue...
December 27, 2016: Oncotarget
https://www.readbyqxmd.com/read/28032149/dtni-a-novel-toxicogenomics-data-analysis-tool-for-identifying-the-molecular-mechanisms-underlying-the-adverse-effects-of-toxic-compounds
#15
Diana M Hendrickx, Terezinha Souza, Danyel G J Jennen, Jos C S Kleinjans
Unravelling gene regulatory networks (GRNs) influenced by chemicals is a major challenge in systems toxicology. Because toxicant-induced GRNs evolve over time and dose, the analysis of global gene expression data measured at multiple time points and doses will provide insight in the adverse effects of compounds. Therefore, there is a need for mathematical methods for GRN identification from time-over-dose-dependent data. One of the current approaches for GRN inference is Time Series Network Identification (TSNI)...
December 28, 2016: Archives of Toxicology
https://www.readbyqxmd.com/read/28028477/emergent-adaptive-behaviour-of-grn-controlled-simulated-robots-in-a-changing-environment
#16
Yao Yao, Veronique Storme, Kathleen Marchal, Yves Van de Peer
We developed a bio-inspired robot controller combining an artificial genome with an agent-based control system. The genome encodes a gene regulatory network (GRN) that is switched on by environmental cues and, following the rules of transcriptional regulation, provides output signals to actuators. Whereas the genome represents the full encoding of the transcriptional network, the agent-based system mimics the active regulatory network and signal transduction system also present in naturally occurring biological systems...
2016: PeerJ
https://www.readbyqxmd.com/read/28027290/single-cell-based-analysis-highlights-a-surge-in-cell-to-cell-molecular-variability-preceding-irreversible-commitment-in-a-differentiation-process
#17
Angélique Richard, Loïs Boullu, Ulysse Herbach, Arnaud Bonnafoux, Valérie Morin, Elodie Vallin, Anissa Guillemin, Nan Papili Gao, Rudiyanto Gunawan, Jérémie Cosette, Ophélie Arnaud, Jean-Jacques Kupiec, Thibault Espinasse, Sandrine Gonin-Giraud, Olivier Gandrillon
In some recent studies, a view emerged that stochastic dynamics governing the switching of cells from one differentiation state to another could be characterized by a peak in gene expression variability at the point of fate commitment. We have tested this hypothesis at the single-cell level by analyzing primary chicken erythroid progenitors through their differentiation process and measuring the expression of selected genes at six sequential time-points after induction of differentiation. In contrast to population-based expression data, single-cell gene expression data revealed a high cell-to-cell variability, which was masked by averaging...
December 2016: PLoS Biology
https://www.readbyqxmd.com/read/28018170/mrna-transcriptomics-of-galectins-unveils-heterogeneous-organization-in-mouse-and-human-brain
#18
Sebastian John, Rashmi Mishra
Background: Galectins, a family of non-classically secreted, β-galactoside binding proteins is involved in several brain disorders; however, no systematic knowledge on the normal neuroanatomical distribution and functions of galectins exits. Hence, the major purpose of this study was to understand spatial distribution and predict functions of galectins in brain and also compare the degree of conservation vs. divergence between mouse and human species. The latter objective was required to determine the relevance and appropriateness of studying galectins in mouse brain which may ultimately enable us to extrapolate the findings to human brain physiology and pathologies...
2016: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28005004/functional-evolution-of-a-morphogenetic-gradient
#19
Chun Wai Kwan, Jackie Gavin-Smyth, Edwin L Ferguson, Urs Schmidt-Ott
Bone Morphogenetic Proteins (BMPs) pattern the dorsal-ventral axis of bilaterian embryos; however, their roles in the evolution of body plan are largely unknown. We examined their functional evolution in fly embryos. BMP signaling specifies two extraembryonic tissues, the serosa and amnion, in basal-branching flies such as Megaselia abdita, but only one, the amnioserosa, in Drosophila melanogaster. The BMP signaling dynamics are similar in both species until the beginning of gastrulation, when BMP signaling broadens and intensifies at the edge of the germ rudiment in Megaselia, while remaining static in Drosophila...
December 22, 2016: ELife
https://www.readbyqxmd.com/read/28000736/unraveling-the-genetic-basis-of-xylose-consumption-in-engineered-saccharomyces-cerevisiae-strains
#20
Leandro Vieira Dos Santos, Marcelo Falsarella Carazzolle, Sheila Tiemi Nagamatsu, Nádia Maria Vieira Sampaio, Ludimila Dias Almeida, Renan Augusto Siqueira Pirolla, Guilherme Borelli, Thamy Lívia Ribeiro Corrêa, Juan Lucas Argueso, Gonçalo Amarante Guimarães Pereira
The development of biocatalysts capable of fermenting xylose, a five-carbon sugar abundant in lignocellulosic biomass, is a key step to achieve a viable production of second-generation ethanol. In this work, a robust industrial strain of Saccharomyces cerevisiae was modified by the addition of essential genes for pentose metabolism. Subsequently, taken through cycles of adaptive evolution with selection for optimal xylose utilization, strains could efficiently convert xylose to ethanol with a yield of about 0...
December 21, 2016: Scientific Reports
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