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Gene network evolution

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https://www.readbyqxmd.com/read/29145803/unraveling-the-evolution-and-coevolution-of-small-regulatory-rnas-and-coding-genes-in-listeria
#1
Franck Cerutti, Ludovic Mallet, Anaïs Painset, Claire Hoede, Annick Moisan, Christophe Bécavin, Mélodie Duval, Olivier Dussurget, Pascale Cossart, Christine Gaspin, Hélène Chiapello
BACKGROUND: Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with other genomic features is a powerful way to better understand their origin and assess a common functional or adaptive relationship between them. However, evolution and coevolution of sRNAs with coding genes have been sparsely investigated in bacterial pathogens. RESULTS: We designed a robust and generic phylogenomics approach that detects correlated evolution between sRNAs and protein-coding genes using their observed and inferred patterns of presence-absence in a set of annotated genomes...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29139535/contribution-of-cranial-neural-crest-cells-to-mouse-skull-development
#2
Taofen Wu, Guiqian Chen, Fei Tian, Hong-Xiang Liu
The mammalian skull vault is a highly regulated structure that evolutionally protects brain growth during vertebrate development. It consists of several membrane bones with different tissue origins (e.g. neural crest-derived frontal bone and mesoderm-derived parietal bone). Although membrane bones are formed through intramembranous ossification, the neural crest-derived frontal bone has superior capabilities for osteoblast activities and bone regeneration via TGF, BMP, Wnt, and FGF signaling pathways. Neural crest (NC) cells are multipotent, and once induced, will follow specific paths to migrate to different locations of the body where they give rise to a diverse array of cell types and tissues...
2017: International Journal of Developmental Biology
https://www.readbyqxmd.com/read/29132683/-impairment-of-dna-damage-response-and-cancer
#3
REVIEW
Chloé Rancoule, Alexis Vallard, Jean-Baptiste Guy, Sophie Espenel, Sylvie Sauvaigo, Claire Rodriguez-Lafrasse, Nicolas Magné
Maintaining the genetic integrity is a key process in cell viability and is enabled by a wide network of repair pathways. When this system is defective, it generates genomic instability and results in an accumulation of chromosomal aberrations and mutations that may be responsible for various clinical phenotypes, including susceptibility to develop cancer. Indeed, these defects can promote not only the initiation of cancer, but also allow the tumor cells to rapidly acquire mutations during their evolution. Several genes are involved in these damage repair systems and particular polymorphisms are predictive of the onset of cancer, the best described of them being BRCA...
November 10, 2017: Bulletin du Cancer
https://www.readbyqxmd.com/read/29127881/grapevine-immune-signaling-network-in-response-to-drought-stress-as-revealed-by-transcriptomic-analysis
#4
Muhammad S Haider, Mahantesh M Kurjogi, M Khalil-Ur-Rehman, Muhammad Fiaz, Tariq Pervaiz, Songtao Jiu, Jia Haifeng, Wang Chen, Jinggui Fang
Drought is a ubiquitous abiotic factor that severely impedes growth and development of horticulture crops. The challenge postured by global climate change is the evolution of drought-tolerant cultivars that could cope with concurrent stress. Hence, in this study, biochemical, physiological and transcriptome analysis were investigated in drought-treated grapevine leaves. The results revealed that photosynthetic activity and reducing sugars were significantly diminished which were positively correlated with low stomatal conductance and CO2 exchange in drought-stressed leaves...
October 31, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29127074/sensing-and-responding-to-energetic-stress-evolution-of-the-ampk-network
#5
Paul M Craig, Christopher D Moyes, Christophe M R LeMoine
AMP-activated protein kinase is an enzyme that mediates communication between cellular energy status and diverse effector proteins, particularly those that play roles in determining the metabolic phenotype. By phosphorylating metabolic enzymes, transcriptional regulators and proteins involved in cellular structure, it can modify energy metabolism in both the short term and long term. Its basic features are highly conserved, with homologues in all eukaryotes. Gene and/or genome duplications endowed early vertebrates with paralogs of AMPK subunits, though the nature of their subfunctionalization remains uncertain, even in mammals...
November 7, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/29104147/advances-in-esophageal-cancer-a-new-perspective-on-pathogenesis-associated-with-long-non-coding-rnas
#6
Xiaomei Huang, Xi Zhou, Qing Hu, Binyu Sun, Mingming Deng, Xiaolong Qi, Muhan Lü
Esophageal cancer is a malignant digestive tract cancer with high mortality. Although studies have found that esophageal cancer is involved in a complex and important gene regulation network, the pathogenesis remains unclear. The recently described long non-coding RNAs (lncRNAs) are one effective part of the gene regulation network. However, in past decades, lncRNAs were thought to be "transcript noise" or "pseudogenes" and were thus ignored. Early studies indicated that lncRNAs play pivotal roles during evolution...
November 10, 2017: Cancer Letters
https://www.readbyqxmd.com/read/29097405/the-evolution-of-gene-specific-transcriptional-noise-is-driven-by-selection-at-the-pathway-level
#7
Gustavo Valadares Barroso, Natasa Puzovic, Julien Y Dutheil
Biochemical reactions within individual cells result from the interactions of molecules, typically in small numbers. Consequently, the inherent stochasticity of binding and diffusion processes generate noise along the cascade that leads to the synthesis of a protein from its encoding gene. As a result, isogenic cell populations display phenotypic variability even in homogeneous environments. The extent and consequences of this stochastic gene expression have only recently been assessed on a genome-wide scale, in particular owing to the advent of single cell transcriptomics...
November 2, 2017: Genetics
https://www.readbyqxmd.com/read/29095827/co-option-of-the-bzip-transcription-factor-vrille-as-the-activator-of-doublesex1-in-environmental-sex-determination-of-the-crustacean-daphnia-magna
#8
Nur Syafiqah Mohamad Ishak, Quang Dang Nong, Tomoaki Matsuura, Yasuhiko Kato, Hajime Watanabe
Divergence of upstream regulatory pathways of the transcription factor Doublesex (Dsx) serves as a basis for evolution of sex-determining mechanisms in animals. However, little is known about the regulation of Dsx in environmental sex determination. In the crustacean Daphnia magna, environmental sex determination is implemented by male-specific expression of the Dsx ortholog, Dsx1. Transcriptional regulation of Dsx1 comprises at least three phases during embryogenesis: non-sex-specific initiation, male-specific up-regulation, and its maintenance...
November 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29081784/eqtls-regulating-transcript-variations-associated-with-rapid-internode-elongation-in-deepwater-rice
#9
Takeshi Kuroha, Keisuke Nagai, Yusuke Kurokawa, Yoshiaki Nagamura, Miyako Kusano, Hideshi Yasui, Motoyuki Ashikari, Atsushi Fukushima
To avoid low oxygen, oxygen deficiency or oxygen deprivation, deepwater rice cultivated in flood planes can develop elongated internodes in response to submergence. Knowledge of the gene regulatory networks underlying rapid internode elongation is important for an understanding of the evolution and adaptation of major crops in response to flooding. To elucidate the genetic and molecular basis controlling their deepwater response we used microarrays and performed expression quantitative trait loci (eQTL) and phenotypic QTL (phQTL) analyses of internode samples of 85 recombinant inbred line (RIL) populations of non-deepwater (Taichung 65)- and deepwater rice (Bhadua)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29076617/appendages-and-gene-regulatory-networks-lessons-from-the-limbless
#10
REVIEW
Carlos R Infante, Ashley M Rasys, Douglas B Menke
Among squamate reptiles, dozens of lineages have independently evolved complete or partial limb reduction. This remarkable convergence of limbless and limb-reduced phenotypes provides multiple natural replicates of different ages to explore the evolution and development of the vertebrate limb and the gene regulatory network that controls its formation. The most successful and best known of the limb-reduced squamates are snakes, which evolved a limb-reduced body form more than 100 million years ago. Recent studies have revealed the unexpected finding that many ancient limb enhancers are conserved in the genomes of snakes...
October 27, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/29070832/prediction-of-cross-resistance-and-collateral-sensitivity-by-gene-expression-profiles-and-genomic-mutations
#11
Takaaki Horinouchi, Shingo Suzuki, Hazuki Kotani, Kumi Tanabe, Natsue Sakata, Hiroshi Shimizu, Chikara Furusawa
In adaptive evolution, an increase in fitness to an environment is frequently accompanied by changes in fitness to other environmental conditions, called cross-resistance and sensitivity. Although the networks between fitness changes affect the course of evolution substantially, the mechanisms underlying such fitness changes are yet to be fully elucidated. Herein, we performed high-throughput laboratory evolution of Escherichia coli under various stress conditions using an automated culture system, and quantified how the acquisition of resistance to one stressor alters the resistance to other stressors...
October 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29070508/coordinated-functional-divergence-of-genes-after-genome-duplication-in-arabidopsis-thaliana
#12
Riet De Smet, Ehsan Sabaghian, Zhen Li, Yvan Saeys, Yves Van de Peer
Gene and genome duplications have been rampant during the evolution of flowering plants. Unlike small-scale gene duplications, whole-genome duplications (WGDs) copy entire pathways or networks, and as such create the unique situation in which such duplicated pathways or networks could evolve novel functionality through the coordinated sub- or neo-functionalization of its constituent genes. Here, we describe a remarkable case of coordinated gene expression divergence following WGDs in Arabidopsis thaliana. We identified a set of 92 homoeologous gene pairs that all show a similar pattern of tissue-specific gene expression divergence following WGD, with one homoeolog showing predominant expression in aerial tissues and the other homoeolog showing biased expression in tip-growth tissues...
October 25, 2017: Plant Cell
https://www.readbyqxmd.com/read/29068047/a-multivariate-assessment-of-the-dali-hominin-cranium-from-china-morphological-affinities-and-implications-for-pleistocene-evolution-in-east-asia
#13
Sheela Athreya, Xinzhi Wu
OBJECTIVES: A nearly complete hominin fossil cranium from Dali in Shaanxi Province, China was excavated in 1978. We update and expand on previous research by providing a multivariate analysis of the specimen relative to a large sample of Middle and Late Pleistocene hominins. MATERIALS AND METHODS: We apply principal components analysis, discriminant function analysis, and a method of assessing group membership based on a soft independent model of class analogy (SIMCA) to the study of Dali's cranial morphology...
October 25, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/29067016/pivotal-impacts-of-retrotransposon-based-invasive-rnas-on-evolution
#14
REVIEW
Laleh Habibi, Hamzeh Salmani
RNAs have long been described as the mediators of gene expression; they play a vital role in the structure and function of cellular complexes. Although the role of RNAs in the prokaryotes is mainly confined to these basic functions, the effects of these molecules in regulating the gene expression and enzymatic activities have been discovered in eukaryotes. Recently, a high-resolution analysis of the DNA obtained from different organisms has revealed a fundamental impact of the RNAs in shaping the genomes, heterochromatin formation, and gene creation...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29058744/hybrid-deterministic-stochastic-simulation-of-complex-biochemical-systems
#15
Paola Lecca, Fabio Bagagiolo, Marina Scarpa
In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by complex networks of chemical reactions involving genes, proteins, and enzymes. Accurate computational models are indispensable means for understanding the mechanisms behind the evolution of a complex system, not always explored with wet lab experiments. To serve their purpose, computational models, however, should be able to describe and simulate the complexity of a biological system in many of its aspects...
October 23, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/29058036/the-road-less-traveled-from-genotype-to-phenotype-in-flies-and-humans
#16
Robert R H Anholt, Trudy F C Mackay
Understanding how genomic variation gives rise to phenotypic variation is essential for elucidating mechanisms of adaptive evolution, plant and animal breeding, and precision medicine. However, identifying causal links between DNA sequence variants and variation in phenotypes is challenging in human populations, due to large blocks of linkage disequilibrium in the genome and heterogeneous developmental histories, lifestyles, and social and physical environments. Drosophila melanogaster presents a powerful genetic model, since linkage disequilibrium decays rapidly, facilitating assignment of causality to polymorphisms associated with phenotypic variation, and large numbers of individuals can be reared under defined environmental conditions, economically, and without regulatory restrictions...
October 20, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/29048529/the-rhizome-of-lokiarchaeota-illustrates-the-mosaicity-of-archaeal-genomes
#17
Anthony Levasseur, Vicky Merhej, Emeline Baptiste, Vikas Sharma, Pierre Pontarotti, Didier Raoult
Genome remodeling and exchange of sequences are widespread in the prokaryotic world and mosaic genomes challenge the classification of prokaryotes, which cannot be properly achieved in terms of a single gene or group of genes. Here, we studied individually the gene collection of the archaic microorganism Lokiarchaeum sp., suggested as an archaeal host close to the emergence of the eukaryotes. The network or rhizome of all Lokiarchaeum sp. genes revealed that the genomic repertoire is mainly composed of genes from archaeal (∼36%) and bacterial origin (∼28%), distantly followed by components of eukaryotic origin (∼2%)...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29046583/parallel-genome-reduction-in-symbionts-descended-from-closely-related-free-living-bacteria
#18
Vittorio Boscaro, Martin Kolisko, Michele Felletti, Claudia Vannini, Denis H Lynn, Patrick J Keeling
Endosymbiosis plays an important role in ecology and evolution, but fundamental aspects of the origin of intracellular symbionts remain unclear. The extreme age of many symbiotic relationships, lack of data on free-living ancestors and uniqueness of each event hinder investigations. Here, we describe multiple strains of the bacterium Polynucleobacter that evolved independently and under similar conditions from closely related, free-living ancestors to become obligate endosymbionts of closely related ciliate hosts...
August 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/29046437/modulation-of-global-transcriptional-regulatory-networks-as-a-strategy-for-increasing-kanamycin-resistance-of-the-translational-elongation-factor-g-mutants-in-escherichia-coli
#19
Aalap Mogre, Reshma T V, Aswin Sai Narain Seshasayee
Evolve and resequence experiments have provided us a tool to understand bacterial adaptation to antibiotics. In our previous work, we had used short term evolution to isolate mutants resistant to the ribosome targeting antibiotic kanamycin, and reported that Escherichia coli develops low cost resistance to kanamycin via  different point mutations in the translation Elongation Factor-G (EF-G). Furthermore, we had shown that the resistance of EF-G mutants could be increased by second site mutations in the genes rpoD / cpxA / topA / cyaA Mutations in three of these genes had been discovered in earlier screens for aminoglycoside resistance...
October 18, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29045649/understanding-evolutionary-impacts-of-seasonality-an-introduction-to-the-symposium
#20
Caroline M Williams, Gregory J Ragland, Gustavo Betini, Lauren B Buckley, Zachary A Cheviron, Kathleen Donohue, Joe Hereford, Murray M Humphries, Simeon Lisovski, Katie E Marshall, Paul S Schmidt, Kimberly S Sheldon, Øystein Varpe, Marcel E Visser
Seasonality is a critically important aspect of environmental variability, and strongly shapes all aspects of life for organisms living in highly seasonal environments. Seasonality has played a key role in generating biodiversity, and has driven the evolution of extreme physiological adaptations and behaviors such as migration and hibernation. Fluctuating selection pressures on survival and fecundity between summer and winter provide a complex selective landscape, which can be met by a combination of three outcomes of adaptive evolution: genetic polymorphism, phenotypic plasticity, and bet-hedging...
October 16, 2017: Integrative and Comparative Biology
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