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Gene environment interactions

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https://www.readbyqxmd.com/read/28345060/genome-reduction-and-microbe-host-interactions-drive-adaptation-of-a-sulfur-oxidizing-bacterium-associated-with-a-cold-seep-sponge
#1
Ren-Mao Tian, Weipeng Zhang, Lin Cai, Yue-Him Wong, Wei Ding, Pei-Yuan Qian
As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored "differential coverage binning" method on 22-Gb metagenomic sequences, we recovered the nearly complete genome of a sulfur-oxidizing bacterium (SOB) that dominates the microbiota of the cold seep sponge Suberites sp. Phylogenetic analyses suggested that this bacterium (an unclassified gammaproteobacterium termed "Gsub") may represent a new deep-sea SOB group...
March 2017: MSystems
https://www.readbyqxmd.com/read/28344339/the-evolution-and-expression-pattern-of-human-overlapping-lncrna-and-protein-coding-gene-pairs
#2
Qianqian Ning, Yixue Li, Zhen Wang, Songwen Zhou, Hong Sun, Guangjun Yu
Long non-coding RNA overlapping with protein-coding gene (lncRNA-coding pair) is a special type of overlapping genes. Protein-coding overlapping genes have been well studied and increasing attention has been paid to lncRNAs. By studying lncRNA-coding pairs in human genome, we showed that lncRNA-coding pairs were more likely to be generated by overprinting and retaining genes in lncRNA-coding pairs were given higher priority than non-overlapping genes. Besides, the preference of overlapping configurations preserved during evolution was based on the origin of lncRNA-coding pairs...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28342734/integration-of-microbiome-and-epigenome-to-decipher-the-pathogenesis-of-autoimmune-diseases
#3
REVIEW
Beidi Chen, Luxi Sun, Xuan Zhang
The interaction between genetic predisposition and environmental factors are of great significance in the pathogenesis and development of autoimmune diseases (AIDs). The human mucosa is the most frequent site that interacts with the exterior environment, and commensal microbiota at the gut and other human mucosal cavities play a crucial role in the regulation of immune system. Growing evidence has shown that the compositional and functional changes of mucosal microbiota are closely related to AIDs. Gut dysbiosis not only influence the expression level of Toll-like receptors (TLRs) of antigen presenting cells, but also contribute to Th17/Treg imbalance...
March 22, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28341680/phar-a-negative-regulatory-protein-of-phap-modulates-the-colonization-of-burkholderia-gut-symbiont-in-the-midgut-of-the-host-insect-riptortus-pedestris
#4
Seong Han Jang, Ho Am Jang, Jun Beom Lee, Jong Uk Kim, Seung Ah Lee, Kyoung-Eun Park, Byung Hyun Kim, Yong Hun Jo, Bok Luel Lee
Five genes encoding PhaP family proteins and one phaR gene have been identified in the genome of Burkholderia RPE75. PhaP proteins function as the surface proteins of polyhydroxyalkanoate (PHA) granules, and PhaR protein acts as a negative regulator of PhaP biosynthesis. Recently, we characterized one phaP gene to understand the molecular cross-talk between Riptortus insects and Burkholderia gut symbionts. In this study, we constructed four other phaP gene-depleted mutants (ΔphaP1, ΔphaP2, ΔphaP3, ΔphaP4), one phaR gene-depleted mutant (ΔphaR) and a phaR-complemented mutant (ΔphaR/phaR)...
March 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28339467/a-non-canonical-rna-degradation-pathway-suppresses-rnai-dependent-epimutations-in-the-human-fungal-pathogen-mucor-circinelloides
#5
Silvia Calo, Francisco E Nicolás, Soo Chan Lee, Ana Vila, Maria Cervantes, Santiago Torres-Martinez, Rosa M Ruiz-Vazquez, Maria E Cardenas, Joseph Heitman
Mucorales are a group of basal fungi that includes the casual agents of the human emerging disease mucormycosis. Recent studies revealed that these pathogens activate an RNAi-based pathway to rapidly generate drug-resistant epimutant strains when exposed to stressful compounds such as the antifungal drug FK506. To elucidate the molecular mechanism of this epimutation pathway, we performed a genetic analysis in Mucor circinelloides that revealed an inhibitory role for the non-canonical RdRP-dependent Dicer-independent silencing pathway, which is an RNAi-based mechanism involved in mRNA degradation that was recently identified...
March 24, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28339466/in-silico-search-for-modifier-genes-associated-with-pancreatic-and-liver-disease-in-cystic-fibrosis
#6
Pascal Trouvé, Emmanuelle Génin, Claude Férec
Cystic Fibrosis is the most common lethal autosomal recessive disorder in the white population, affecting among other organs, the lung, the pancreas and the liver. Whereas Cystic Fibrosis is a monogenic disease, many studies reveal a very complex relationship between genotype and clinical phenotype. Indeed, the broad phenotypic spectrum observed in Cystic Fibrosis is far from being explained by obvious genotype-phenotype correlations and it is admitted that Cystic Fibrosis disease is the result of multiple factors, including effects of the environment as well as modifier genes...
2017: PloS One
https://www.readbyqxmd.com/read/28338722/dissecting-the-transcriptional-patterns-of-social-dominance-across-teleosts
#7
Suzy C P Renn, Cynthia F O'Rourke, Nadia Aubin-Horth, Eleanor J Fraser, Hans A Hofmann
In many species, under varying ecological conditions, social interactions among individuals result in the formation of dominance hierarchies. Despite general similarities, there are robust differences among dominance hierarchies across species, populations, environments, life stages, sexes, and individuals. Understanding the proximate mechanisms underlying the variation is an important step toward understanding the evolution of social behavior. However, physiological changes associated with dominance, such as gonadal maturation and somatic growth, often complicate efforts to identify the specific underlying mechanisms...
December 16, 2016: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/28338224/adolescent-externalizing-behaviour-psychological-control-and-peer-rejection-transactional-links-and-dopaminergic-moderation
#8
Annelies Janssens, Wim Van Den Noortgate, Luc Goossens, Karine Verschueren, Hilde Colpin, Stephan Claes, Martijn Van Heel, Karla Van Leeuwen
This study investigated (1) reciprocal links among parental psychological control, peer rejection, and adolescent externalizing (aggressive and rule-breaking behaviour), and (2) the moderating effect of an adolescent genetic factor (biologically informed polygenic score for dopamine signalling). Three-year longitudinal data from 1,116 adolescents (51% boys; M age = 13.79) and their parents included psychological measures (adolescent-reported psychological control, peer-reported rejection, and parent-reported aggressive and rule-breaking behaviour)...
March 24, 2017: British Journal of Developmental Psychology
https://www.readbyqxmd.com/read/28337153/defense-responses-to-short-term-hypoxia-and-seawater-acidification-in-the-thick-shell-mussel-mytilus-coruscus
#9
Yanming Sui, Yimeng Liu, Xin Zhao, Sam Dupont, Menghong Hu, Fangli Wu, Xizhi Huang, Jiale Li, Weiqun Lu, Youji Wang
The rising anthropogenic atmospheric CO2 results in the reduction of seawater pH, namely ocean acidification (OA). In East China Sea, the largest coastal hypoxic zone was observed in the world. This region is also strongly impacted by ocean acidification as receiving much nutrient from Changjiang and Qiantangjiang, and organisms can experience great short-term natural variability of DO and pH in this area. In order to evaluate the defense responses of marine mussels under this scenario, the thick shell mussel Mytilus coruscus were exposed to three pH/pCO2 levels (7...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28336271/helminth-secretomes-reflect-different-lifestyles-and-parasitized-hosts
#10
Yesid Cuesta-Astroz, Francislon Silva de Oliveira, Laila Alves Nahum, Guilherme Oliveira
Helminths cause a number of medical and agricultural problems and are a major cause of parasitic infections in humans, animals and plants. Comparative analysis of helminth genes and genomes are important to understand the genomic biodiversity and evolution of parasites and their hosts in terms of different selective pressures in their habitats. The interactions between the infective organisms and their hosts are mediated in large part by secreted proteins, known collectively as the "secretome". Proteins secreted by parasites are able to modify a host's environment and modulate their immune system...
March 20, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28334351/effects-of-antenatal-maternal-depressive-symptoms-and-socio-economic-status-on-neonatal-brain-development-are-modulated-by-genetic-risk
#11
Anqi Qiu, Mojun Shen, Claudia Buss, Yap-Seng Chong, Kenneth Kwek, Seang-Mei Saw, Peter D Gluckman, Pathik D Wadhwa, Sonja Entringer, Martin Styner, Neerja Karnani, Christine M Heim, Kieran J O'Donnell, Joanna D Holbrook, Marielle V Fortier, Michael J Meaney
This study included 168 and 85 mother-infant dyads from Asian and United States of America cohorts to examine whether a genomic profile risk score for major depressive disorder (GPRSMDD) moderates the association between antenatal maternal depressive symptoms (or socio-economic status, SES) and fetal neurodevelopment, and to identify candidate biological processes underlying such association. Both cohorts showed a significant interaction between antenatal maternal depressive symptoms and infant GPRSMDD on the right amygdala volume...
March 18, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28333316/convergent-balancing-selection-on-the-mu-opioid-receptor-in-primates
#12
Carolyn G Sweeney, Juliette M Rando, Helen N Panas, Gregory M Miller, Donna M Platt, Eric J Vallender
The mu opioid receptor is involved in many natural processes including stress response, pleasure, and pain. Mutations in the gene also have been associated with opiate and alcohol addictions as well as with responsivity to medication targeting these disorders. Two common and mutually exclusive polymorphisms have been identified in humans, A118G (N40D), found commonly in non-African populations, and C17T (V6A), found almost exclusively in African populations. While A118G has been studied extensively for associations and in functional assays, C17T is much less well understood...
March 15, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28333262/selection-in-europeans-on-fatty-acid-desaturases-associated-with-dietary-changes
#13
Matthew T Buckley, Fernando Racimo, Morten E Allentoft, Majken K Jensen, Anna Jonsson, Hongyan Huang, Farhad Hormozdiari, Martin Sikora, Davide Marnetto, Eleazar Eskin, Marit E Jørgensen, Niels Grarup, Oluf Pedersen, Torben Hansen, Peter Kraft, Eske Willerslev, Rasmus Nielsen
FADS genes encode fatty acid desaturases that are important for the conversion of short chain polyunsaturated fatty acids (PUFAs) to long chain fatty acids. Prior studies indicate that the FADS genes have been subjected to strong positive selection in Africa, South Asia, Greenland, and Europe. By comparing FADS sequencing data from present-day and Bronze Age (5-3k years ago) Europeans, we identify possible targets of selection in the European population, which suggest that selection has targeted different alleles in the FADS genes in Europe than it has in South Asia or Greenland...
March 16, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28332559/the-immunogenetics-of-narcolepsy-associated-with-a-h1n1-pdm09-vaccination-pandemrix-supports-a-potent-gene-environment-interaction
#14
I L Bomfim, F Lamb, K Fink, A Szakács, A Silveira, L Franzén, V Azhary, M Maeurer, N Feltelius, N Darin, T Hallböök, L Arnheim-Dahlström, I Kockum, T Olsson
The influenza A(H1N1)pdm09 vaccination campaign from 2009 to 2010 was associated with a sudden increase in the incidence of narcolepsy in several countries. Narcolepsy with cataplexy is strongly associated with the human leukocyte antigen (HLA) class II DQB1*06:02 allele, and protective associations with the DQB1*06:03 allele have been reported. Several non-HLA gene loci are also associated, such as common variants of the T-cell receptor-α (TRA), the purinergic receptor P2RY11, cathepsin H (CTSH) and TNFSF4/OX40L/CD252...
March 23, 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28330911/pcsk9-variant-long-chain-n-3-pufas-and-risk-of-nonfatal-myocardial-infarction-in-costa-rican-hispanics
#15
Zhi Yu, Tao Huang, Yan Zheng, Tiange Wang, Yoriko Heianza, Dianjianyi Sun, Hannia Campos, Lu Qi
Background: Previous studies have indicated that the cardioprotective effects of long-chain (LC) n-3 (ω-3) polyunsaturated fatty acids (PUFAs) may vary across various ethnic populations. Emerging evidence has suggested that the gene-environment interaction may partly explain such variations. Proprotein convertase subtilisin/kexin type 9 (PCSK9) was shown to have a mutually regulating relation with LC n-3 PUFAs and also to reduce the risk of cardiovascular diseases (CVDs). Therefore, we hypothesized that certain PCSK9 genetic variants may modify the association between LC n-3 PUFA intake and CVD risk...
March 22, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28327890/draft-genome-of-the-honey-bee-ectoparasitic-mite-tropilaelaps-mercedesae-is-shaped-by-the-parasitic-life-history
#16
Xiaofeng Dong, Stuart D Armstrong, Dong Xia, Benjamin L Makepeace, Alistair C Darby, Tatsuhiko Kadowaki
Background: The number of managed honey bee colonies has considerably decreased in many developed countries in recent years and ectoparasitic mites are considered as major threats to honey bee colonies and health. However, their general biology remains poorly understood. Results: We sequenced the genome of Tropilaelaps mercedesae , the prevalent ectoparasitic mite infesting honey bees in Asia and predicted 15,190 protein-coding genes which were well supported by the mite transcriptomes and proteomic data...
February 22, 2017: GigaScience
https://www.readbyqxmd.com/read/28326758/genetic-determinants-of-low-birth-weight
#17
Theresa Mallia, Alexia Grech, Abigail Hili, Jean Calleja Agius, Nikolai P Pace
Birth weight depends on the elaborate interaction between maternal and foetal genotypes, placental function, maternal nutrition and lifestyle and their effect on epigenetic regulators ofgene activity. The maternal environment in which the foetus develops is a critical factor indetermining birth weight. This review provides an overview of the effect of several geneticvariants leading to intrauterine growth restriction and low birth weight. Irrespective of theexact cause of genetic variations of foetal genes, intrauterine growth restriction is most likelydue to alteration in the growth hormone and insulin like growth factor axis with distinctchanges in the growth factors and their interaction with corresponding receptors...
March 21, 2017: Minerva Ginecologica
https://www.readbyqxmd.com/read/28326484/genome-wide-transcriptional-analysis-of-cardiovascular-related-genes-and-pathways-induced-by-pm2-5-in-human-myocardial-cells
#18
Lin Feng, Xiaozhe Yang, Collins Otieno Asweto, Jing Wu, Yannan Zhang, Hejing Hu, Yanfeng Shi, Junchao Duan, Zhiwei Sun
Air pollution has been a major environment-related health threat. Most of the studies on PM2.5 toxicity have verified on the cardiovascular system and endothelial cells. However, researches on PM2.5-induced myocardial-related toxicity are limited. This study aims to fully understand the toxic effects of PM2.5 on human myocardial cell (AC16) and explore its molecular mechanism based on microarray analysis and bioinformatics analysis. Microarray data analysis manifested that PM2.5-induced toxicity affected expression of 472 genes compared with the control group, including 166 upregulated genes and 306 downregulated genes in human myocardial (AC16) cells...
March 22, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28324352/the-six-tomato-yellow-leaf-curl-virus-genes-expressed-individually-in-tomato-induce-different-levels-of-plant-stress-response-attenuation
#19
Rena Gorovits, Adi Moshe, Linoy Amrani, Rotem Kleinberger, Ghandi Anfoka, Henryk Czosnek
Tomato yellow leaf curl virus (TYLCV) is a begomovirus infecting tomato plants worldwide. TYLCV needs a healthy host environment to ensure a successful infection cycle for long periods. Hence, TYLCV restrains its destructive effect and induces neither a hypersensitive response nor cell death in infected tomatoes. On the contrary, TYLCV counteracts cell death induced by other factors, such as inactivation of HSP90 functionality. Suppression of plant death is associated with the inhibition of the ubiquitin 26S proteasome degradation and with a deactivation of the heat shock transcription factor HSFA2 pathways (including decreased HSP17 levels)...
March 21, 2017: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/28321184/the-role-of-early-growth-response-1-egr1-in-brain-plasticity-and-neuropsychiatric-disorders
#20
REVIEW
Florian Duclot, Mohamed Kabbaj
It is now clearly established that complex interactions between genes and environment are involved in multiple aspects of neuropsychiatric disorders, from determining an individual's vulnerability to onset, to influencing its response to therapeutic intervention. In this perspective, it appears crucial to better understand how the organism reacts to environmental stimuli and provide a coordinated and adapted response. In the central nervous system, neuronal plasticity and neurotransmission are among the major processes integrating such complex interactions between genes and environmental stimuli...
2017: Frontiers in Behavioral Neuroscience
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