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Gene-environment interaction

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https://www.readbyqxmd.com/read/28634433/the-draft-genome-of-the-non-host-associated-methanobrevibacter-arboriphilus-strain-dh1-encodes-a-large-repertoire-of-adhesin-like-proteins
#1
Anja Poehlein, Rolf Daniel, Henning Seedorf
Methanobrevibacter arboriphilus strain DH1 is an autotrophic methanogen that was isolated from the wetwood of methane-emitting trees. This species has been of considerable interest for its unusual oxygen tolerance and has been studied as a model organism for more than four decades. Strain DH1 is closely related to other host-associated Methanobrevibacter species from intestinal tracts of animals and the rumen, making this strain an interesting candidate for comparative analysis to identify factors important for colonizing intestinal environments...
2017: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28633471/development-of-a-chicken-ileal-explant-culture-model-for-measurement-of-gut-inflammation-induced-by-lipopolysaccharide
#2
Qian Zhang, Susan D Eicher, Kolapo M Ajuwon, Todd J Applegate
Gut mucosa holds a single layer of epithelial cells and the largest mass of lymphoid tissue in the body. Although the epithelial cell culture model is widely used to assess intestinal barrier function, it has limitations for studying cellular interactions, in particular those of the immune system. In this study, a chicken ileal explant culture model was developed for investigating short-term gut inflammatory and secretory responses in an ex vivo environment. Initially, ileal explants from broilers at 21 d of age were cultured ex vivo up to 6 h...
June 16, 2017: Poultry Science
https://www.readbyqxmd.com/read/28633381/robust-tests-for-additive-gene-environment-interaction-in-case-control-studies-using-gene-environment-independence
#3
Gang Liu, Seunggeun Lee, Alice W Lee, Anna H Wu, Elisa V Bandera, Allan Jensen, Mary Anne Rossing, Kirsten B Moysich, Jenny Chang-Claude, Jennifer Doherty, Aleksandra Gentry-Maharaj, Lambertus Kiemeney, Simon A Gayther, Francesmary Modugno, Leon Massuger, Ellen L Goode, Brooke Fridley, Kathryn L Terry, Daniel W Cramer, Susan J Ramus, Hoda Anton-Culver, Argyrios Ziogas, Jonathan P Tyrer, Joellen M Schildkraut, Susanne K Kjaer, Penelope M Webb, Roberta B Ness, Usha Menon, Andrew Berchuck, Paul D Pharoah, Harvey Risch, Celeste Leigh Pearce, Bhramar Mukherjee
There have been recent proposals advocating the use of additive gene-environment interaction instead of the widely used multiplicative scale, as a more relevant public health measure. Using gene-environment independence enhances the power for testing multiplicative interaction in case-control studies. However, under departure from this assumption, substantial bias in the estimates and inflated Type I error in the corresponding tests can occur. This paper extends the empirical Bayes (EB) approach previously developed for multiplicative interaction that trades off between bias and efficiency in a data-adaptive way, to the additive scale...
June 14, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28632790/diversity-structure-of-culturable-bacteria-isolated-from-the-fildes-peninsula-king-george-island-antarctica-a-phylogenetic-analysis-perspective
#4
Gerardo González-Rocha, Gabriel Muñoz-Cartes, Cristian B Canales-Aguirre, Celia A Lima, Mariana Domínguez-Yévenes, Helia Bello-Toledo, Cristián E Hernández
It has been proposed that Antarctic environments select microorganisms with unique biochemical adaptations, based on the tenet 'Everything is everywhere, but, the environment selects' by Baas-Becking. However, this is a hypothesis that has not been extensively evaluated. This study evaluated the fundamental prediction contained in this hypothesis-in the sense that species are structured in the landscape according to their local habitats-, using as study model the phylogenetic diversity of the culturable bacteria of Fildes Peninsula (King George Island, Antarctica)...
2017: PloS One
https://www.readbyqxmd.com/read/28632173/gene-expression-profiling-reveals-potential-players-of-left-right-asymmetry-in-female-chicken-gonads
#5
Zhiyi Wan, Yanan Lu, Lei Rui, Xiaoxue Yu, Fang Yang, Chengfang Tu, Zandong Li
Most female birds develop only a left ovary, whereas males develop bilateral testes. The mechanism underlying this process is still not completely understood. Here, we provide a comprehensive transcriptional analysis of female chicken gonads and identify novel candidate side-biased genes. RNA-Seq analysis was carried out on total RNA harvested from the left and right gonads on embryonic day 6 (E6), E12, and post-hatching day 1 (D1). By comparing the gene expression profiles between the left and right gonads, 347 differentially expressed genes (DEGs) were obtained on E6, 3730 were obtained on E12, and 2787 were obtained on D1...
June 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28629460/interaction-between-pasteurella-multocida-b-2-and-its-derivatives-with-bovine-aortic-endothelial-cell-baec
#6
Nuriqmaliza M Kamal, M Zamri-Saad, Mas Jaffri Masarudin, Sarah Othman
BACKGROUND: Pasteurella multocida B:2 causes bovine haemorrhagic septicaemia (HS), leading to rapid fatalities in cattle and buffaloes. An attenuated derivative of P. multocida B:2 GDH7, was previously constructed through mutation of the gdhA gene and proved to be an effective live attenuated vaccine for HS. Currently, only two potential live attenuated vaccine candidates for HS are being reported; P. multocida B:2 GDH7 and P. multocida B:2 JRMT12. This study primarily aims to investigate the potential of P...
June 19, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28627812/genetics-of-alcohol-consumption-in-drosophila-melanogaster
#7
Sophia Fochler, Tatiana V Morozova, Morgan R Davis, Alexander W Gearhart, Wen Huang, Trudy F C Mackay, Robert R H Anholt
Individual variation in alcohol consumption in human populations is determined by genetic, environmental, social and cultural factors. In contrast to humans, genetic contributions to complex behavioral phenotypes can be readily dissected in Drosophila, where both the genetic background and environment can be controlled and behaviors quantified through simple high-throughput assays. Here, we measured voluntary consumption of ethanol in ~3,000 individuals of each sex from an advanced intercross population derived from 37 lines of the Drosophila melanogaster Genetic Reference Panel...
June 19, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/28626565/site-specific-azide-acetyllysine-photochemistry-on-epigenetic-readers-for-interactome-profiling
#8
Babu Sudhamalla, Debasis Dey, Megan Breski, Tiffany Nguyen, Kabirul Islam
Chemical modifications on DNA, RNA and histones are recognized by an array of 'reader' modules to regulate transcriptional programming and cell fate. However, identification of reader-specific interacting partners in a dynamic cellular environment remains a significant challenge. Herein, we report a chemoproteomic approach termed 'interaction-based protein profiling' (IBPP) to characterize novel interacting partners of potentially any reader protein. IBPP harnesses a photosensitive amino acid introduced into the hydrophobic pocket of a reader module to crosslink and enrich transient interacting partners that are inaccessible to traditional methods...
June 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28626066/cytoplasmic-form-of-carlr-lncrna-facilitates-inflammatory-gene-expression-upon-nf-%C3%AE%C2%BAb-activation
#9
Ainara Castellanos-Rubio, Radomir Kratchmarov, Maialen Sebastian, Koldo Garcia-Etxebarria, Liher Garcia, Iñaki Irastorza, Sankar Ghosh
Long noncoding RNAs (lncRNAs) have emerged as critical regulators of inflammation. To further understand the interaction between inflammatory signaling pathways and lncRNAs, we characterized the function of cardiac and apoptosis-related lncRNA (Carlr), an lncRNA expressed in both mouse and human cells of diverse tissues. Carlr expression is increased following NF-κB signaling in macrophages, with concomitant translocation to, and enrichment of, the transcript in the cytoplasm. Knockdown of Carlr results in impaired expression of NF-κB pathway genes and influences the interaction between macrophages and intestinal cells in an inflammatory environment...
June 16, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28625682/are-circadian-rhythms-new-pathways-to-understand-autism-spectrum-disorder
#10
M-M Geoffray, A Nicolas, M Speranza, N Georgieff
Autism Spectrum Disorder (ASD) is a frequent neurodevelopmental disorder. ASD is probably the result of intricate interactions between genes and environment altering progressively the development of brain structures and functions. Circadian rhythms are a complex intrinsic timing system composed of almost as many clocks as there are body cells. They regulate a variety of physiological and behavioral processes such as the sleep- wake rhythm. ASD is often associated with sleep disorders and low levels of melatonin...
June 15, 2017: Journal of Physiology, Paris
https://www.readbyqxmd.com/read/28625324/esr2-genetic-variants-and-combined-oral-contraceptive-use-associated-with-the-risk-of-stroke
#11
Zhenlin Xu, Ying Li, Xiaoping Huang, Wei Shen, Jianling Bai, Chong Shen, Yang Zhao
BACKGROUND AND AIM: There is accumulating evidence suggesting an important role of estrogen receptor-β in the development of cardiovascular disease. The present study aims to investigate the relationship of estrogen receptor β gene (ESR2) polymorphisms with stroke risk in Chinese women, and further evaluate the gene-environment interaction of ESR2 and combined oral contraceptive (COC) use on stroke risk. METHODS: A case-control study was conducted with 446 first-ever stroke patients and 864 control subjects recruited from our prospective female cohort...
February 2017: Archives of Medical Research
https://www.readbyqxmd.com/read/28624939/additive-effect-of-calcium-depletion-and-low-resource-quality-on-gammarus-fossarum-crustacea-amphipoda-life-history-traits
#12
Marc Rollin, Romain Coulaud, Michael Danger, Bénédicte Sohm, Justine Flayac, Alexandre Bec, Arnaud Chaumot, Olivier Geffard, Vincent Felten
Gammarus fossarum is an often-abundant crustacean detritivore that contributes importantly to leaf litter breakdown in oligotrophic, mainly heterotrophic, headwater streams. This species requires large amounts of Ca to moult, thus allowing growth and reproduction. Because resource quality is tightly coupled to the organism's growth and physiological status, we hypothesised that low Ca concentration [Ca] and low food resource quality (low phosphorus [P] and/or reduced highly unsaturated fatty acid [HUFA] contents) would interactively impair molecular responses (gene expression) and reproduction of G...
June 17, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28623160/basic-concepts-in-molecular-biology-related-to-genetics-and-epigenetics
#13
Dolores Corella, Jose M Ordovas
The observation that "one size does not fit all" for the prevention and treatment of cardiovascular disease, among other diseases, has driven the concept of precision medicine. The goal of precision medicine is to provide the best-targeted interventions tailored to an individual's genome. The human genome is composed of billions of sequence arrangements containing a code that controls how genes are expressed. This code depends on other nonstatic regulators that surround the DNA and constitute the epigenome...
June 13, 2017: Revista Española de Cardiología
https://www.readbyqxmd.com/read/28622698/interactions-between-acyp2-genetic-polymorphisms-and-environment-factors-with-susceptibility-to-ischemic-stroke-in-a-han-chinese-population
#14
Qiong Cheng, Yong-Kun Li, Feng Lu, Lianhua Yin, Yin-Zhou Wang, Wen Wei, Qian Lin
AIMS: To investigate the association of several single nucleotide polymorphisms (SNPs) within ACYP2 gene and additional gene- environment interaction with ischemic stroke (IS) risk in a Chinese population. RESULTS: IS risk was significantly higher in carriers with the G allele of rs11896604 than those with CC genotype (CG or GG versus CC), adjusted OR (95%CI) =1.60 (1.18-2.20), and higher in carriers with the A allele of rs12615793 than those with GG genotype (GA or AA versus GG), adjusted OR (95%CI) = 1...
June 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28621426/foxd1-protein-interacts-with-wnt-and-bmp-signaling-to-differentially-pattern-mesoderm-and-neural-tissue
#15
Hanna Polevoy, Anastasia Malyarova, Yuri Fonar, Sara Elias, Dale Frank
The foxd1 gene (previously known as Brain Factor 2/BF2) is expressed during early Xenopus laevis development. At gastrula stages, foxd1 is expressed in dorsal mesoderm regions fated for muscle and notochord, while at neurula stages, foxd1 is expressed in the forebrain region. Previous studies in the neural plate showed that FoxD1 protein acts as transcriptional repressor downstream of BMP antagonism, neuralizing the embryo to control anterior neural cell fates. FoxD1 mesoderm function was not rigorously analyzed, but ectopic FoxD1 levels increased muscle marker expression in embryos...
2017: International Journal of Developmental Biology
https://www.readbyqxmd.com/read/28620608/a-path-to-implement-precision-child-health-cardiovascular-medicine
#16
REVIEW
Marlin Touma, Brian Reemtsen, Nancy Halnon, Juan Alejos, J Paul Finn, Stanley F Nelson, Yibin Wang
Congenital heart defects (CHDs) affect approximately 1% of live births and are a major source of childhood morbidity and mortality even in countries with advanced healthcare systems. Along with phenotypic heterogeneity, the underlying etiology of CHDs is multifactorial, involving genetic, epigenetic, and/or environmental contributors. Clear dissection of the underlying mechanism is a powerful step to establish individualized therapies. However, the majority of CHDs are yet to be clearly diagnosed for the underlying genetic and environmental factors, and even less with effective therapies...
2017: Frontiers in Cardiovascular Medicine
https://www.readbyqxmd.com/read/28620589/transcriptomic-profiling-of-high-density-giardia-foci-encysting-in-the-murine-proximal-intestine
#17
Jonathan K Pham, Christopher Nosala, Erica Y Scott, Kristofer F Nguyen, Kari D Hagen, Hannah N Starcevich, Scott C Dawson
Giardia is a highly prevalent, understudied protistan parasite causing significant diarrheal disease worldwide. Its life cycle consists of two stages: infectious cysts ingested from contaminated food or water sources, and motile trophozoites that colonize and attach to the gut epithelium, later encysting to form new cysts that are excreted into the environment. Current understanding of parasite physiology in the host is largely inferred from transcriptomic studies using Giardia grown axenically or in co-culture with mammalian cell lines...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28620587/a-dual-luciferase-reporter-system-for-b-burgdorferi-measures-transcriptional-activity-during-tick-pathogen-interactions
#18
Philip P Adams, Carlos Flores Avile, Mollie W Jewett
Knowledge of the transcriptional responses of vector-borne pathogens at the vector-pathogen interface is critical for understanding disease transmission. Borrelia (Borreliella) burgdorferi, the causative agent of Lyme disease in the United States, is transmitted by the bite of infected Ixodes sp. ticks. It is known that B. burgdorferi has altered patterns of gene expression during tick acquisition, persistence and transmission. Recently, we and others have discovered in vitro expression of RNAs found internal, overlapping, and antisense to annotated open reading frames in the B...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28620159/main-and-epistatic-loci-studies-in-soybean-for-sclerotinia-sclerotiorum-resistance-reveal-multiple-modes-of-resistance-in-multi-environments
#19
Tara C Moellers, Arti Singh, Jiaoping Zhang, Jae Brungardt, Mehdi Kabbage, Daren S Mueller, Craig R Grau, Ashish Ranjan, Damon L Smith, R V Chowda-Reddy, Asheesh K Singh
Genome-wide association (GWAS) and epistatic (GWES) studies along with expression studies in soybean [Glycine max (L.) Merr.] were leveraged to dissect the genetics of Sclerotinia stem rot (SSR) [caused by Sclerotinia sclerotiorum (Lib.) de Bary], a significant fungal disease causing yield and quality losses. A large association panel of 466 diverse plant introduction accessions were phenotyped in multiple field and controlled environments to: (1) discover sources of resistance, (2) identify SNPs associated with resistance, and (3) determine putative candidate genes to elucidate the mode of resistance...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28620071/multiancestry-study-of-gene-lifestyle-interactions-for-cardiovascular-traits-in-610-475-individuals-from-124-cohorts-design-and-rationale
#20
D C Rao, Yun J Sung, Thomas W Winkler, Karen Schwander, Ingrid Borecki, L Adrienne Cupples, W James Gauderman, Kenneth Rice, Patricia B Munroe, Bruce M Psaty
BACKGROUND: Several consortia have pursued genome-wide association studies for identifying novel genetic loci for blood pressure, lipids, hypertension, etc. They demonstrated the power of collaborative research through meta-analysis of study-specific results. METHODS AND RESULTS: The Gene-Lifestyle Interactions Working Group was formed to facilitate the first large, concerted, multiancestry study to systematically evaluate gene-lifestyle interactions. In stage 1, genome-wide interaction analysis is performed in 53 cohorts with a total of 149 684 individuals from multiple ancestries...
June 2017: Circulation. Cardiovascular Genetics
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