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Gene network evolution

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https://www.readbyqxmd.com/read/28446174/a-scalable-metabolite-supplementation-strategy-against-antibiotic-resistant-pathogen-chromobacterium-violaceum-induced-by-nad-nadh-imbalance
#1
Deepanwita Banerjee, Dharmeshkumar Parmar, Nivedita Bhattacharya, Avinash D Ghanate, Venkateswarlu Panchagnula, Anu Raghunathan
BACKGROUND: The leading edge of the global problem of antibiotic resistance necessitates novel therapeutic strategies. This study develops a novel systems biology driven approach for killing antibiotic resistant pathogens using benign metabolites. RESULTS: Controlled laboratory evolutions established chloramphenicol and streptomycin resistant pathogens of Chromobacterium. These resistant pathogens showed higher growth rates and required higher lethal doses of antibiotic...
April 26, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28444830/gene-expression-reveals-evidence-for-egfr-dependent-proximal-distal-limb-patterning-in-a-myriapod
#2
Ralf Janssen
Evolution of segmented limbs is one of the key innovations of Arthropoda, allowing development of functionally specific specialized head and trunk appendages, a major factor behind their unmatched evolutionary success. Proximodistal limb patterning is controlled by two regulatory networks in the vinegar fly Drosophila melanogaster, and other insects. The first is represented by the function of the morphogens Wingless (Wg) and Decapentaplegic (Dpp); the second by the EGFR-signaling cascade. While the role of Wg and Dpp has been studied in a wide range of arthropods representing all main branches, that is, Pancrustacea (= Hexapoda + Crustacea), Myriapoda and Chelicerata, investigation of the potential role of EGFR-signaling is restricted to insects (Hexapoda)...
April 26, 2017: Evolution & Development
https://www.readbyqxmd.com/read/28439449/mobilizable-genomic-islands-different-strategies-for-the-dissemination-of-multidrug-resistance-and-other-adaptive-traits
#3
COMMENT
Nicolas Carraro, Nicolas Rivard, Vincent Burrus, Daniela Ceccarelli
Mobile genetic elements are near ubiquitous DNA segments that revealed a surprising variety of strategies for their propagation among prokaryotes and between eukaryotes. In bacteria, conjugative elements were shown to be key drivers of evolution and adaptation by efficiently disseminating genes involved in pathogenicity, symbiosis, metabolic pathways, and antibiotic resistance. Conjugative plasmids of the incompatibility groups A and C (A/C) are important vehicles for the dissemination of antibiotic resistance and the consequent global emergence and spread of multi-resistant pathogenic bacteria...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/28427910/stochasticity-of-gene-expression-as-a-motor-of-epigenetics-in-bacteria-from-individual-to-collective-behavior
#4
REVIEW
Stéphanie Bury-Moné, Bianca Sclavi
Measuring gene expression at the single cell and single molecule level has recently made possible the quantitative measurement of stochasticity of gene expression. This enables identification of the probable sources and roles of noise. Stochastic gene expression can result in bacterial population heterogeneity, offering specific advantages for fitness and survival in various environments. This trait is therefore selected during the evolution of the species, and is consequently regulated by specific genetic network architecture...
April 18, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28423210/intrinsic-incompatibilities-evolving-as-a-by-product-of-divergent-ecological-selection-considering-them-in-empirical-studies-on-divergence-with-gene-flow
#5
J Kulmuni, A M Westram
The possibility of intrinsic barriers to gene flow is often neglected in empirical research on local adaptation and speciation with gene flow, e.g. when interpreting patterns observed in genome scans. However, we draw attention to the fact that, even with gene flow, divergent ecological selection may generate intrinsic barriers involving both ecologically selected and other interacting loci. Mechanistically, the link between the two types of barriers may be generated by genes that have multiple functions (i...
April 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28421087/evolutionary-analysis-of-the-lafl-genes-involved-in-the-land-plant-seed-maturation-program
#6
Jing-Dan Han, Xia Li, Chen-Kun Jiang, Gane K-S Wong, Carl J Rothfels, Guang-Yuan Rao
Seeds are one of the most significant innovations in the land plant lineage, critical to the diversification and adaptation of plants to terrestrial environments. From perspective of seed evo-devo, the most crucial developmental stage in this innovation is seed maturation, which includes accumulation of storage reserves, acquisition of desiccation tolerance, and induction of dormancy. Based on previous studies of seed development in the model plant Arabidopsis thaliana, seed maturation is mainly controlled by the LAFL regulatory network, which includes LEAFY COTYLEDON1 (LEC1) and LEC1-LIKE (L1L) of the NF-YB gene family, and ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2 (LEAFY COTYLEDON2) of the B3-AFL gene family...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28410570/natural-selection-drove-metabolic-specialization-of-the-chromatophore-in-paulinella-chromatophora
#7
Cecilio Valadez-Cano, Roberto Olivares-Hernández, Osbaldo Resendis-Antonio, Alexander DeLuna, Luis Delaye
BACKGROUND: Genome degradation of host-restricted mutualistic endosymbionts has been attributed to inactivating mutations and genetic drift while genes coding for host-relevant functions are conserved by purifying selection. Unlike their free-living relatives, the metabolism of mutualistic endosymbionts and endosymbiont-originated organelles is specialized in the production of metabolites which are released to the host. This specialization suggests that natural selection crafted these metabolic adaptations...
April 14, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28410373/parallel-reorganization-of-protein-function-in-the-spindle-checkpoint-pathway-through-evolutionary-paths-in-the-fitness-landscape-that-appear-neutral-in-laboratory-experiments
#8
Alex N Nguyen Ba, Bob Strome, Selma Osman, Elizabeth-Ann Legere, Taraneh Zarin, Alan M Moses
Regulatory networks often increase in complexity during evolution through gene duplication and divergence of component proteins. Two models that explain this increase in complexity are: 1) adaptive changes after gene duplication, such as resolution of adaptive conflicts, and 2) non-adaptive processes such as duplication, degeneration and complementation. Both of these models predict complementary changes in the retained duplicates, but they can be distinguished by direct fitness measurements in organisms with short generation times...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28408285/from-epigenetic-landscape-to-phenotypic-fitness-landscape-evolutionary-effect-of-pathogens-on-host-traits
#9
Mark Jayson V Cortez, Jomar F Rabajante, Jerrold M Tubay, Ariel L Babierra
The epigenetic landscape illustrates how cells differentiate through the control of gene regulatory networks. Numerous studies have investigated epigenetic gene regulation but there are limited studies on how the epigenetic landscape and the presence of pathogens influence the evolution of host traits. Here, we formulate a multistable decision-switch model involving several phenotypes with the antagonistic influence of parasitism. As expected, pathogens can drive dominant (common) phenotypes to become inferior through negative frequency-dependent selection...
April 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28405712/emergence-of-new-srnas-in-enteric-bacteria-is-associated-with-low-expression-and-rapid-evolution
#10
Fenil R Kacharia, Jess A Millar, Rahul Raghavan
Non-coding small RNAs (sRNAs) are critical to post-transcriptional gene regulation in bacteria. However, unlike for protein-coding genes, the evolutionary forces that shape sRNAs are not understood. We investigated sRNAs in enteric bacteria and discovered that recently emerged sRNAs evolve at significantly faster rates than older sRNAs. Concomitantly, younger sRNAs are expressed at significantly lower levels than older sRNAs. This process could potentially facilitate the integration of newly emerged sRNAs into bacterial regulatory networks...
April 12, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28397602/effects-of-isolation-by-continental-islands-in-the-seto-inland-sea-japan-on-genetic-diversity-of-the-large-japanese-field-mouse-apodemus-speciosus-rodentia-muridae-inferred-from-the-mitochondrial-dloop-region
#11
Jun J Sato, Yurina Tasaka, Ryoya Tasaka, Kentaro Gunji, Yuya Yamamoto, Yasushi Takada, Yasushi Uematsu, Eiichi Sakai, Takashi Tateishi, Yasunori Yamaguchi
To study the effects of post-glacial isolation by islands on population genetic diversity and differentiation of the large Japanese field mouse, Apodemus speciosus, we examined partial nucleotide sequences of the mitochondrial Dloop region (ca. 300 bp) in 231 individuals collected from islands in the Seto Inland Sea and adjacent regions on Honshu and Shikoku Islands in the western part of the Japanese archipelago. Molecular phylogenetic and network analyses showed that haplotypes in each island tended to form monophyletic groups, while those in Honshu and Shikoku (the major Japanese islands) showed scattered relationships and were connected with island haplotypes...
April 2017: Zoological Science
https://www.readbyqxmd.com/read/28390909/deep-reticulation-and-incomplete-lineage-sorting-obscure-the-diploid-phylogeny-of-rain-lilies-and-allies-amaryllidaceae-tribe-hippeastreae
#12
Nicolás García, Ryan A Folk, Alan W Meerow, Srikar Chamala, Matthew A Gitzendanner, Renata Souza de Oliveira, Douglas E Soltis, Pamela S Soltis
Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups...
April 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28373969/the-molecular-apgar-score-a-key-to-unlocking-evolutionary-principles
#13
John S Torday, Heber C Nielsen
One of the first "tools" used for systematically evaluating successful newborn transitional physiology at birth was the Apgar Score, devised by Virginia Apgar in 1953. This objective assessment tool allowed clinicians to immediately gauge the relative success of a newborn infant making the transition from the in utero liquid immersive environment to the ex utero gas environment in the delivery room during the first minutes after birth. The scoring system, although eponymous, is generally summarized as an acronym based on Appearance, Pulse, Grimace, Activity, and Respiration, criteria evaluated and scored at 1 and 5 min after birth...
2017: Frontiers in Pediatrics
https://www.readbyqxmd.com/read/28369921/global-chondrocyte-gene-expression-after-a-single-anabolic-loading-period-time-evolution-and-re-inducibility-of-mechano-responses
#14
Simone Scholtes, Elisabeth Krämer, Melanie Weisser, Wolfgang Roth, Reto Luginbühl, Tobias Grossner, Wiltrud Richter
OBJECTIVE: A genome-wide identification of mechano-regulated genes and candidate pathways in human chondrocytes subjected to a single anabolic loading episode and characterization of time evolution and re-inducibility of the response. DESIGN: Osteochondral constructs consisting of a chondrocyte-seeded collagen-scaffold connected to β-tricalcium-phosphate were pre-cultured for 35 days and subjected to dynamic compression (25% strain, 1 Hz, 9 × 10 minutes over 3h) before microarray-profiling was performed...
March 28, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28369658/tracking-the-evolution-of-3d-gene-organization-demonstrates-its-connection-to-phenotypic-divergence
#15
Alon Diament, Tamir Tuller
It has recently been shown that the organization of genes in eukaryotic genomes, and specifically in 3D, is strongly related to gene expression and function and partially conserved between organisms. However, previous studies of 3D genomic organization analyzed each organism independently from others. Here, we propose an approach for unified inter-organismal analysis of gene organization based on a network representation of Hi-C data. We define and detect four classes of spatially co-evolving orthologous modules (SCOMs), i...
March 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28364793/signaling-networks-in-tmprss2-erg-positive-prostate-cancers-do-we-need-a-pied-piper-or-sharpshooter-to-deal-with-at-large-fused-oncoprotein
#16
REVIEW
X Lin, M Z Qureshi, M A Romero, I Yaylim, S Arif, I Ucak, S Fayyaz, A A Farooqi, Q Mansoor, M Ismail
Overwhelmingly increasing scientific evidence has provided near complete resolution of prostate cancer landscape and it is now more understandable that wide ranging factors underlies its development and progression. Increasingly it is being realized that genetic/epigenetic factors, Intra-tumoral and inter-tumoral heterogeneity, loss of apoptosis, dysregulations of spatio-temporally controlled signaling cascades, Darwinian evolution in response to therapeutic pressures play instrumental role in prostate carcinogenesis...
February 28, 2017: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/28358137/identification-and-evolution-of-a-plant-cell-wall-specific-glycoprotein-glycosyl-transferase-exad
#17
Svenning Rune Møller, Xueying Yi, Silvia Melina Velásquez, Sascha Gille, Pernille Louise Munke Hansen, Christian P Poulsen, Carl Erik Olsen, Martin Rejzek, Harriet Parsons, Yang Zhang, Hans H Wandall, Henrik Clausen, Robert A Field, Markus Pauly, Jose M Estevez, Jesper Harholt, Peter Ulvskov, Bent Larsen Petersen
Extensins are plant cell wall glycoproteins that act as scaffolds for the deposition of the main wall carbohydrate polymers, which are interlocked into the supramolecular wall structure through intra- and inter-molecular iso-di-tyrosine crosslinks within the extensin backbone. In the conserved canonical extensin repeat, Ser-Hyp4, serine and the consecutive C4-hydroxyprolines (Hyps) are substituted with an α-galactose and 1-5 β- or α-linked arabinofuranoses (Arafs), respectively. These modifications are required for correct extended structure and function of the extensin network...
March 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28350855/diversification-of-spatiotemporal-expression-and-copy-number-variation-of-the-echinoid-hbox12-pmar1-micro1-multigene-family
#18
Vincenzo Cavalieri, Fabiana Geraci, Giovanni Spinelli
Changes occurring during evolution in the cis-regulatory landscapes of individual members of multigene families might impart diversification in their spatiotemporal expression and function. The archetypal member of the echinoid hbox12/pmar1/micro1 family is hbox12-a, a homeobox-containing gene expressed exclusively by dorsal blastomeres, where it governs the dorsal/ventral gene regulatory network during embryogenesis of the sea urchin Paracentrotus lividus. Here we describe the inventory of the hbox12/pmar1/micro1 genes in P...
2017: PloS One
https://www.readbyqxmd.com/read/28348857/comparative-genomics-and-evolution-of-transcriptional-regulons-in-proteobacteria
#19
Semen A Leyn, Inna A Suvorova, Alexey E Kazakov, Dmitry A Ravcheev, Vita V Stepanova, Pavel S Novichkov, Dmitry A Rodionov
Comparative genomics approaches are broadly used for analysis of transcriptional regulation in bacterial genomes. In this work, we identified binding sites and reconstructed regulons for 33 orthologous groups of transcription factors (TFs) in 196 reference genomes from 21 taxonomic groups of Proteobacteria. Overall, we predict over 10 600 TF binding sites and identified more than 15 600 target genes for 1896 TFs constituting the studied orthologous groups of regulators. These include a set of orthologues for 21 metabolism-associated TFs from Escherichia coli and/or Shewanella that are conserved in five or more taxonomic groups and several additional TFs that represent non-orthologous substitutions of the metabolic regulators in some lineages of Proteobacteria...
July 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28333240/structure-of-the-transcriptional-regulatory-network-correlates-with-regulatory-divergence-in-drosophila
#20
Bing Yang, Patricia J Wittkopp
Transcriptional control of gene expression is regulated by biochemical interactions between cis-regulatory DNA sequences and trans-acting factors that form complex regulatory networks. Genetic changes affecting both cis- and trans-acting sequences in these networks have been shown to alter patterns of gene expression as well as higher-order organismal phenotypes. Here, we investigate how the structure of these regulatory networks relates to patterns of polymorphism and divergence in gene expression. To do this, we compared a transcriptional regulatory network inferred for Drosophila melanogaster to differences in gene regulation observed between two strains of D...
February 25, 2017: Molecular Biology and Evolution
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