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Gene-environment interaction

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https://www.readbyqxmd.com/read/28724080/qtls-associated-with-crown-root-angle-stomatal-conductance-and-maturity-in-sorghum
#1
Jose R Lopez, John E Erickson, Patricio Munoz, Ana Saballos, Terry J Felderhoff, Wilfred Vermerris
Three factors that directly affect the water inputs in cropping systems are root architecture, length of the growing season, and stomatal conductance to water vapor (). Deeper-rooted cultivars will perform better under water-limited conditions because they can access water stored deeper in the soil profile. Reduced limits transpiration rate () and thus throughout the vegetative phase conserves water that may be used during grain filling in water-limited environments. Additionally, growing early-maturing varieties in regions that rely on soil-stored water is a key water management strategy...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28723619/a-novel-sharpin-prmt5-h3r2me1-axis-is-essential-for-lung-cancer-cell-invasion
#2
Tingxiong Fu, Xiuwei Lv, Qingzhi Kong, Changjing Yuan
SHARPIN (Shank-associated RH domain interacting protein) is the main component of the linear ubiquitin chain activation complex (LUBAC). SHARPIN is involved in regulating inflammation and cancer progression. However, whether SHARPIN plays an important role in lung cancer metastasis and the potential underlying mechanism are still unknown. Here, for the first time, we reported that SHARPIN expression is closely related to lung cancer progression. Moreover, SHARPIN plays a central role in controlling lung cancer cell metastasis...
July 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28721594/exome-analysis-in-an-estonian-multiplex-family-with-neural-tube-defects-a-case-report
#3
Liina Pappa, Mart Kals, Paula Ann Kivistik, Andres Metspalu, Ann Paal, Tiit Nikopensius
INTRODUCTION: Neural tube defects (NTDs) are a group of common and severe congenital birth defects that occur during early embryonic development due to incomplete closure of the neural tube. The genetic architecture of human NTDs, including spina bifida and hydrocephalus, is highly heterogeneous, with multiple genes/loci and both gene-gene and gene-environment interactions involved. Hence, the variation in outcomes also most likely relates to a combination of the severity of different variants in multiple genes and genetic modifiers affecting the biochemical traits...
July 18, 2017: Child's Nervous System: ChNS: Official Journal of the International Society for Pediatric Neurosurgery
https://www.readbyqxmd.com/read/28720731/an-in-vitro-chicken-gut-model-demonstrates-transfer-of-a-multidrug-resistance-plasmid-from-salmonella-to-commensal-escherichia-coli
#4
Roderick M Card, Shaun A Cawthraw, Javier Nunez-Garcia, Richard J Ellis, Gemma Kay, Mark J Pallen, Martin J Woodward, Muna F Anjum
The chicken gastrointestinal tract is richly populated by commensal bacteria that fulfill various beneficial roles for the host, including helping to resist colonization by pathogens. It can also facilitate the conjugative transfer of multidrug resistance (MDR) plasmids between commensal and pathogenic bacteria which is a significant public and animal health concern as it may affect our ability to treat bacterial infections. We used an in vitro chemostat system to approximate the chicken cecal microbiota, simulate colonization by an MDR Salmonella pathogen, and examine the dynamics of transfer of its MDR plasmid harboring several genes, including the extended-spectrum beta-lactamase blaCTX-M1 We also evaluated the impact of cefotaxime administration on plasmid transfer and microbial diversity...
July 18, 2017: MBio
https://www.readbyqxmd.com/read/28720431/biological-responses-to-immobilized-microscale-and-nanoscale-surface-topographies
#5
REVIEW
Shelby A Skoog, Girish Kumar, Roger J Narayan, Peter L Goering
Cellular responses are highly influenced by biochemical and biomechanical interactions with the extracellular matrix (ECM). Due to the impact of the ECM architecture on cellular responses, significant research has been dedicated towards developing biomaterials that mimic the physiological environment for design of improved medical devices. Surface topographies with microscale and nanoscale features have demonstrated an effect on numerous cellular responses including cell adhesion, migration, proliferation, gene expression, protein production, and differentiation; however, determining relationships between biological responses and surface topographies are difficult to establish due to differences in cell types and biomaterial surface properties...
July 15, 2017: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28720099/association-between-genome-wide-copy-number-variation-and-arsenic-induced-skin-lesions-a-prospective-study
#6
Muhammad G Kibriya, Farzana Jasmine, Faruque Parvez, Maria Argos, Shantanu Roy, Rachelle Paul-Brutus, Tariqul Islam, Alauddin Ahmed, Muhammad Rakibuz-Zaman, Justin Shinkle, Vesna Slavkovich, Joseph H Graziano, Habibul Ahsan
BACKGROUND: Exposure to arsenic in drinking water is a global health problem and arsenic-induced skin lesions are hallmark of chronic arsenic toxicity. We and others have reported germline genetic variations as risk factors for such skin lesions. The role of copy number variation (CNV) in the germline DNA in this regard is unknown. METHODS: From a large prospectively followed-up cohort, exposed to arsenic, we randomly selected 2171 subjects without arsenic-induced skin lesions at enrollment and genotyped their whole blood DNA samples on Illumina Cyto12v2...
July 18, 2017: Environmental Health: a Global Access Science Source
https://www.readbyqxmd.com/read/28716044/type-2-diabetes-is-associated-with-an-increased-prevalence-of-respiratory-symptoms-as-compared-to-the-general-population
#7
F De Santi, G Zoppini, F Locatelli, E Finocchio, V Cappa, M Dauriz, G Verlato
BACKGROUND: To estimate the prevalence of respiratory symptoms in individuals with type 2 diabetes, as compared to the general population. METHODS: Between 2007 and 2010 the screening questionnaire of GEIRD (Gene Environment Interactions in Respiratory Diseases) study was administered to two samples of Verona general population, aged respectively 45-64 years and 65-84 years, and to a convenience sample of individuals with type 2 diabetes, consequently recruited at the local Diabetes Centre...
July 17, 2017: BMC Pulmonary Medicine
https://www.readbyqxmd.com/read/28715420/blood-vessel-tortuosity-selects-against-evolution-of-aggressive-tumor-cells-in-confined-tissue-environments-a-modeling-approach
#8
András Szabó, Roeland M H Merks
Cancer is a disease of cellular regulation, often initiated by genetic mutation within cells, and leading to a heterogeneous cell population within tissues. In the competition for nutrients and growth space within the tumors the phenotype of each cell determines its success. Selection in this process is imposed by both the microenvironment (neighboring cells, extracellular matrix, and diffusing substances), and the whole of the organism through for example the blood supply. In this view, the development of tumor cells is in close interaction with their increasingly changing environment: the more cells can change, the more their environment will change...
July 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28714190/polymorphisms-of-xenobiotic-metabolizing-genes-and-colorectal-cancer-risk-in-patients-with-lynch-syndrome-a-retrospective-cohort-study-in-taiwan
#9
Abram Bunya Kamiza, Jeng-Fu You, Wen-Chang Wang, Reiping Tang, Chun-Yu Chang, Huei-Tzu Chien, Chih-Hsiung Lai, Li-Ling Chiu, Tsai-Ping Lo, Kuan-Yi Hung, Chao A Hsiung, Chih-Ching Yeh
Cytochrome P450 (CYP), glutathione-S-transferase (GST), and N-acetyltransferase (NAT) are crucial for metabolism and clearance of xenobiotics. This study investigated whether CYP, GST, and NAT single nucleotide polymorphisms (SNPs) are associated with colorectal cancer (CRC) in patients with Lynch syndrome. The interaction between these SNPs and cigarette smoking or meat consumption was also explored. We identified 270 patients with Lynch syndrome from the Taiwan Hereditary Nonpolyposis Colorectal Cancer Consortium...
July 17, 2017: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/28713862/metabolic-surgery-gastric-bypass-for-the-treatment-of-type-2-diabetes-mellitus
#10
REVIEW
Maria Del Pilar Quevedo, Mariano Palermo, Edgardo Serra, Marianela A Ackermann
Type 2 diabetes mellitus (T2DM) is one of the largest health emergencies of the 21st century given the worldwide increase of obesity during the last decades and its close association. T2DM is an inherited, polygenic and chronic disease caused by the interaction between several genetic variants in genes and the environment. The continuous search for new and more effective tools to achieve appropriate glycemic control became imperative in order to reduce long-term complications and mortality rates related to T2DM...
2017: Translational Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28713358/aquarium-viromes-viromes-of-human-managed-aquatic-systems
#11
Yiseul Kim, William Van Bonn, Tiong G Aw, Joan B Rose
An aquarium ecosystem is home to many animal species providing conditions similar to native aquatic habitats but under highly controlled management. With a growing interest in understanding the interaction of microbiomes and resident animal health within aquarium environments, we undertook a metagenomic survey of viromes in seven aquarium systems with differing physicochemical and resident animal profiles. Our results show that a diverse array of viruses was represented in aquarium viromes, many of which were widespread in different aquarium systems (27 common viral families in all of the aquarium systems)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28712705/engineering-of-global-regulators-and-cell-surface-properties-toward-enhancing-stress-tolerance-in-saccharomyces-cerevisiae
#12
REVIEW
Kouichi Kuroda, Mitsuyoshi Ueda
Microbial cell factories are subject to various stresses, leading to the reductions of metabolic activity and bioproduction efficiency. Therefore, the development of stress-tolerant microorganisms is important for improving bio-production efficiency. Recently, modifications of cell surface properties and master regulators have been shown to be effective approaches for enhancing stress tolerance. The cell surface is an attractive target owing to its interactions with the environment and its role in transmitting environmental information...
July 13, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28709615/transcriptional-profiling-of-rickettsia-prowazekii-coding-and-non-coding-transcripts-during-in-vitro-host-pathogen-and-vector-pathogen-interactions
#13
Casey L C Schroeder, Hema P Narra, Abha Sahni, Kamil Khanipov, Jignesh Patel, Yuriy Fofanov, Sanjeev K Sahni
Natural pathogen transmission of Rickettsia prowazekii, the etiologic agent of epidemic typhus, to humans is associated with arthropods, including human body lice, ticks, and ectoparasites of eastern flying squirrel. Recently, we have documented the presence of small RNAs in Rickettsia species and expression of R. prowazekii sRNAs during infection of cultured human microvascular endothelial cells (HMECs), which represent the primary target cells during human infections. Bacterial noncoding transcripts are now well established as critical post-transcriptional regulators of virulence and adaptation mechanisms in varying host environments...
June 29, 2017: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/28707299/detection-of-gene-environment-interactions-in-a-family-based-population-using-scad
#14
Gwangsu Kim, Chao-Qiang Lai, Donna K Arnett, Laurence D Parnell, Jose M Ordovas, Yongdai Kim, Joungyoun Kim
Gene-environment interaction (GxE) is emphasized as one potential source of missing genetic variation on disease traits, and the ultimate goal of GxE research is prediction of individual risk and prevention of complex diseases. However, there are various challenges in statistical analysis of GxE. In this paper, we focus on the three methodological challenges: (i) the high dimensions of genes; (ii) the hierarchical structure between interaction effects and their corresponding main effects; and (iii) the correlation among subjects from family-based population studies...
July 13, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28707126/estrogen-receptor-alpha-gene-esr1-polymorphism-and-its-interaction-with-smoking-and-drinking-contribute-to-susceptibility-of-systemic-lupus-erythematosus
#15
Aihong Zhou, Xin Liu, Tao Xia, Fang Li, Jibo Wang, Jun Li
The aim of this study is to investigate the association of estrogen receptor alpha gene (ESR1) polymorphisms, additional gene-gene, and gene-environment interaction with systemic lupus erythematosus (SLE) risk. SNPStats (available online at http://bioinfo.iconcologia.net/SNPstats ) was used to investigate the Hardy-Weinberg equilibrium (HWE) in controls and association between SNP and SLE risk. Generalized multifactor dimensionality reduction (GMDR) was used to screen the interactions among SNPs and environmental risk factors; SLE risk was significantly higher in carriers of rs2234693 C allele than those with TT (TC + CC versus TT), adjusted OR (95%CI) = 1...
July 13, 2017: Immunologic Research
https://www.readbyqxmd.com/read/28706906/mesothelioma-recent-highlights
#16
REVIEW
Michele Carbone, Haining Yang
Recent discoveries have elucidated some of the mechanisms responsible for the development of mesothelioma. These discoveries are: (I) the critical role of chronic inflammation in promoting mesothelioma growth, driven by the release of high mobility group box protein-1 (HMGB1) following asbestos deposition in tissues and its potential role as a biomarker to identify asbestos exposed individuals and mesothelioma patients; (II) the discovery that inherited heterozygous germline mutations of the deubiquitylase BRCA-associated protein 1 (BAP1) cause a high incidence of mesothelioma in some families; and that (III) germline BAP1 mutations lower the threshold of asbestos required to cause mesothelioma in mice, evidence of gene X environment interaction...
June 2017: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28702378/thioredoxin-a-is-essential-for-motility-and-contributes-to-host-infection-of-listeria-monocytogenes-via-redox-interactions
#17
Changyong Cheng, Zhimei Dong, Xiao Han, Hang Wang, Li Jiang, Jing Sun, Yongchun Yang, Tiantian Ma, Chunyan Shao, Xiaodu Wang, Zhongwei Chen, Weihuan Fang, Nancy E Freitag, Huarong Huang, Houhui Song
Microbes employ the thioredoxin system to defend against oxidative stress and ensure correct disulfide bonding to maintain protein function. Listeria monocytogenes has been shown to encode a putative thioredoxin, TrxA, but its biological roles and underlying mechanisms remain unknown. Here, we showed that expression of L. monocytogenes TrxA is significantly induced in bacteria treated with the thiol-specific oxidizing agent, diamide. Deletion of trxA markedly compromised tolerance of the pathogen to diamide, and mainly impaired early stages of infection in human intestinal epithelial Caco-2 cells...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28702035/the-soybean-basic-helix-loop-helix-transcription-factor-org3-like-enhances-cadmium-tolerance-via-increased-iron-and-reduced-cadmium-uptake-and-transport-from-roots-to-shoots
#18
Zhaolong Xu, Xiaoqing Liu, Xiaolan He, Ling Xu, Yihong Huang, Hongbo Shao, Dayong Zhang, Boping Tang, Hongxiang Ma
Cadmium (Cd) is one of the most dangerous heavy metal pollutants in the environment and is toxic to animal and plant cells. On the other hand, iron (Fe) is an essential element for plant growth and development. The chlorosis of plant leaves under cadmium stress is similar to the typical symptom of iron deficiency. Recently, several Arabidopsis basic/helix-loop-helix (bHLH) transcription factors have been identified that are involved in the interactions between Cd and Fe. In the present study, over-expression the ORG3-like gene GmORG3, a bHLH transcription factor OBP3-responsive gene (ORG), enhanced Cd tolerance and stabilized Fe homeostasis...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28701815/next-generation-crop-models-a-modular-approach-to-model-early-vegetative-and-reproductive-development-of-the-common-bean-phaseolus-vulgaris-l
#19
C Hwang, M J Correll, S A Gezan, L Zhang, M S Bhakta, C E Vallejos, K J Boote, J A Clavijo-Michelangeli, J W Jones
The next generation of gene-based crop models offers the potential of predicting crop vegetative and reproductive development based on genotype and weather data as inputs. Here, we illustrate an approach for developing a dynamic modular gene-based model to simulate changes in main stem node numbers, time to first anthesis, and final node number on the main stem of common bean (Phaseolus vulgaris L.). In the modules, these crop characteristics are functions of relevant genes (quantitative trait loci (QTL)), the environment (E), and QTL × E interactions...
July 2017: Agricultural Systems
https://www.readbyqxmd.com/read/28701235/analyses-of-reaction-norms-reveal-new-chromosome-regions-associated-with-tick-resistance-in-cattle
#20
R R Mota, F F Silva, P S Lopes, R J Tempelman, B P Sollero, I Aguilar, F F Cardoso
Despite single nucleotide polymorphism (SNP) availability and frequent cost reduction has allowed genome-wide association studies even in complex traits as tick resistance, the use of this information source in SNP by environment interaction context is unknown for many economically important traits in cattle. We aimed at identifying putative genomic regions explaining differences in tick resistance in Hereford and Braford cattle under SNP by environment point of view as well as to identify candidate genes derived from outliers/significant markers...
July 13, 2017: Animal: An International Journal of Animal Bioscience
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