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epigenetics and weight

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https://www.readbyqxmd.com/read/28100166/smite-an-r-bioconductor-package-that-identifies-network-modules-by-integrating-genomic-and-epigenomic-information
#1
N Ari Wijetunga, Andrew D Johnston, Ryo Maekawa, Fabien Delahaye, Netha Ulahannan, Kami Kim, John M Greally
BACKGROUND: The molecular assays that test gene expression, transcriptional, and epigenetic regulation are increasingly diverse and numerous. The information generated by each type of assay individually gives an insight into the state of the cells tested. What should be possible is to add the information derived from separate, complementary assays to gain higher-confidence insights into cellular states. At present, the analysis of multi-dimensional, massive genome-wide data requires an initial pruning step to create manageable subsets of observations that are then used for integration, which decreases the sizes of the intersecting data sets and the potential for biological insights...
January 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28092570/identifying-epigenetic-biomarkers-using-maximal-relevance-and-minimal-redundancy-based-feature-selection-for-multi-omics-data
#2
Saurav Mallik, Tapas Bhadra, Ujjwal Maulik
Epigenetic Biomarker discovery is an important task in bioinformatics. In this article, we develop a new framework of identifying statistically significant epigenetic biomarkers using maximal-relevance and minimal-redundancy criterion based feature (gene) selection for multi-omics dataset. Firstly, we determine the genes that have both expression as well as methylation values, and follow normal distribution. Similarly, we identify the genes which consist of both expression and methylation values, but do not follow normal distribution...
January 9, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28090638/late-gestational-intermittent-hypoxia-induces-metabolic-and-epigenetic-changes-in-male-adult-offspring-mice
#3
Abdelnaby Khalyfa, Rene Cortese, Zhuanhong Qiao, Honggang Ye, Riyue Bao, Jorge Andrade, David Gozal
Pregnancy, particularly late gestation, has been associated with a relatively high prevalence of obstructive sleep apnea (OSA). Intermittent hypoxia (IH), a hallmark of OSA, could impose significant long-term effects on somatic growth, energy homeostasis, and metabolic function in offspring. We hypothesized that IH during late pregnancy (LG-IH) may increase the propensity for metabolic dysregulation and obesity in adult offspring via epigenetic modifications. Time-pregnant female C57BL/6 mice were exposed to LG-IH or room air (LG-RA) during days 13-18 of gestation...
January 15, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28089957/the-epigenetic-clock-and-physical-development-during-childhood-and-adolescence-longitudinal-analysis-from-a-uk-birth-cohort
#4
Andrew J Simpkin, Laura D Howe, Kate Tilling, Tom R Gaunt, Oliver Lyttleton, Wendy L McArdle, Susan M Ring, Steve Horvath, George Davey Smith, Caroline L Relton
BACKGROUND: Statistical models that use an individual's DNA methylation levels to estimate their age (known as epigenetic clocks) have recently been developed, with 96% correlation found between epigenetic and chronological age. We postulate that differences between estimated and actual age [age acceleration (AA)] can be used as a measure of developmental age in early life. METHODS: We obtained DNA methylation measures at three time points (birth, age 7 years and age 17 years) in 1018 children from the Avon Longitudinal Study of Parents and Children (ALSPAC)...
January 15, 2017: International Journal of Epidemiology
https://www.readbyqxmd.com/read/28089486/molecular-genetics-of-human-obesity-a-comprehensive-review
#5
Rajan Kumar Singh, Permendra Kumar, Kulandaivelu Mahalingam
Obesity and its related health complications is a major problem worldwide. Hypothalamus and their signalling molecules play a critical role in the intervening and coordination with energy balance and homeostasis. Genetic factors play a crucial role in determining an individual's predisposition to the weight gain and being obese. In the past few years, several genetic variants were identified as monogenic forms of human obesity having success over common polygenic forms. In the context of molecular genetics, genome-wide association studies (GWAS) approach and their findings signified a number of genetic variants predisposing to obesity...
January 12, 2017: Comptes Rendus Biologies
https://www.readbyqxmd.com/read/28088786/ezh2-inhibition-suppresses-endometrial-cancer-progression-via-mir-361-twist-axis
#6
Kei Ihira, Peixin Dong, Ying Xiong, Hidemichi Watari, Yosuke Konno, Sharon Jb Hanley, Masayuki Noguchi, Noriyuki Hirata, Futoshi Suizu, Takahiro Yamada, Masataka Kudo, Noriaki Sakuragi
EZH2 inhibition and reactivation of tumor suppressor microRNAs (miRNAs) represent attractive anti-cancer therapeutic strategies. We found that EZH2-suppressed let 7b and miR-361, two likely tumor suppressors, inhibited endometrial cancer (EC) cell proliferation and invasion, and abrogated cancer stem cell-like properties. In EC cells, EZH2 induced and functioned together with YY1 to epigenetically suppress miR-361, which upregulated Twist, a direct target of miR-361. Treating EC cells with GSK343, a specific EZH2 inhibitor, mimicked the effects of siRNA-mediated EZH2 knockdown, upregulating miR-361 and downregulating Twist expression...
January 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28077626/low-dose-or-low-dose-rate-ionizing-radiation-induced-bioeffects-in-animal-models
#7
REVIEW
Feng Ru Tang, Weng Keong Loke, Boo Cheong Khoo
Animal experimental studies indicate that acute or chronic low-dose ionizing radiation (LDIR) (≤100 mSv) or low-dose-rate ionizing radiation (LDRIR) (<6 mSv/h) exposures may be harmful. It induces genetic and epigenetic changes and is associated with a range of physiological disturbances that includes altered immune system, abnormal brain development with resultant cognitive impairment, cataractogenesis, abnormal embryonic development, circulatory diseases, weight gain, premature menopause in female animals, tumorigenesis and shortened lifespan...
January 10, 2017: Journal of Radiation Research
https://www.readbyqxmd.com/read/28076749/epigenetic-changes-of-hepatic-glucocorticoid-receptor-in-sheep-male-offspring-undernourished-in-utero
#8
Stella Chadio, Basiliki Kotsampasi, Stylliani Taka, Emmanouil Liandris, Nikolaos Papadopoulos, Elias Plakokefalos
The aim of this study was to characterise the effects of maternal undernutrition during gestation on hepatic gluconeogenic enzyme gene expression and to determine whether such effects are mediated through epigenetic changes in the glucocorticoid receptor (GR). Pregnant ewes were fed a 50% nutrient-restricted diet from Day 0 to 30 (R1) or from Day 31 to 100 of gestation (R2) or a 100% diet throughout gestation (Control). After parturition lambs were fed to appetite. At 10 months of age offspring were euthanised and livers were removed...
January 12, 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/28071704/high-fat-diet-induced-changes-of-mouse-hepatic-transcription-and-enhancer-activity-can-be-reversed-by-subsequent-weight-loss
#9
Majken Siersbæk, Lyuba Varticovski, Shutong Yang, Songjoon Baek, Ronni Nielsen, Susanne Mandrup, Gordon L Hager, Jay H Chung, Lars Grøntved
Epigenetic factors have been suggested to play an important role in metabolic memory by trapping and maintaining initial metabolic changes within the transcriptional regulatory machinery. In this study we fed mice a high fat diet (HFD) for seven weeks followed by additional five weeks of chow, to identify HFD-mediated changes to the hepatic transcriptional program that may persist after weight loss. Mice fed a HFD displayed increased fasting insulin levels, hepatosteatosis and major changes in hepatic gene transcription associated with modulation of H3K27Ac at enhancers, but no significant changes in chromatin accessibility, indicating that HFD-regulated gene transcription is primarily controlled by modulating the activity of pre-established enhancers...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28068899/maternal-bmi-as-a-predictor-of-methylation-of-obesity-related-genes-in-saliva-samples-from-preschool-age-hispanic-children-at-risk-for-obesity
#10
Kathryn Tully Oelsner, Yan Guo, Sophie Bao-Chieu To, Amy L Non, Shari L Barkin
BACKGROUND: The study of epigenetic processes and mechanisms present a dynamic approach to assess complex individual variation in obesity susceptibility. However, few studies have examined epigenetic patterns in preschool-age children at-risk for obesity despite the relevance of this developmental stage to trajectories of weight gain. We hypothesized that salivary DNA methylation patterns of key obesogenic genes in Hispanic children would 1) correlate with maternal BMI and 2) allow for identification of pathways associated with children at-risk for obesity...
January 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28068485/obesity-in-low-and-middle-income-countries-burden-drivers-and-emerging-challenges
#11
Nicole D Ford, Shivani A Patel, K M Venkat Narayan
We have reviewed the distinctive features of excess weight, its causes, and related prevention and management efforts, as well as data gaps and recommendations for future research in low- and middle-income countries (LMICs). Obesity is rising in every region of the world, and no country has been successful at reversing the epidemic once it has begun. In LMICs, overweight is higher in women compared with men, in urban compared with rural settings, and in older compared with younger individuals; however, the urban-rural overweight differential is shrinking in many countries...
December 23, 2016: Annual Review of Public Health
https://www.readbyqxmd.com/read/28061846/map4k4-and-il-6-th17-cells-play-important-roles-in-non-obese-type-2-diabetes
#12
REVIEW
Huai-Chia Chuang, Tse-Hua Tan
Obesity is a causal factor of type 2 diabetes (T2D); however, people without obesity (including lean, normal weight, or overweight) may still develop T2D. Non-obese T2D is prevalent in Asia and also frequently occurs in Europe. Recently, multiple evidences oppose the notion that either obesity or central obesity (visceral fat accumulation) promotes non-obese T2D. Several factors such as inflammation and environmental factors contribute to non-obese T2D. According to the data derived from gene knockout mice and T2D clinical samples in Asia and Europe, the pathogenesis of non-obese T2D has been unveiled recently...
January 7, 2017: Journal of Biomedical Science
https://www.readbyqxmd.com/read/28052772/placental-mitochondrial-dna-and-cyp1a1-gene-methylation-as-molecular-signatures-for-tobacco-smoke-exposure-in-pregnant-women-and-the-relevance-for-birth-weight
#13
Bram G Janssen, Wilfried Gyselaers, Hyang-Min Byun, Harry A Roels, Ann Cuypers, Andrea A Baccarelli, Tim S Nawrot
BACKGROUND: Maternal smoking during pregnancy results in an increased risk of low birth weight through perturbations in the utero-placental exchange. Epigenetics and mitochondrial function in fetal tissues might be molecular signatures responsive to in utero tobacco smoke exposure. METHODS: In the framework of the ENVIRONAGE birth cohort, we investigated the effect of self-reported tobacco smoke exposure during pregnancy on birth weight and the relation with placental tissue markers such as, (1) relative mitochondrial DNA (mtDNA) content as determined by real-time quantitative PCR, (2) DNA methylation of specific loci of mtDNA (D-loop and MT-RNR1), and (3) DNA methylation of the biotransformation gene CYP1A1 (the last two determined by bisulfite-pyrosequencing)...
January 4, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28050331/placental-microrna-expression-is-not-altered-by-maternal-obesity-and-fetal-overgrowth
#14
Neda Ghaffari, Samuel Parry, Michal A Elovitz, Celeste P Durnwald
Objective The epigenetic mechanisms underlying fetal metabolic programming are poorly understood. We studied whether obesity is associated with alterations in placental miRNA expression. Study Design A cross-sectional study was performed, including (1) normal-weight women (BMI 20-24.9 kg/m(2)) and normal-birth-weight (BW) infants (2,700-3,500 g) (n = 20), (2) normal-weight and macrosomic infants (BW ≥ 4,000 g) (n = 10), (3) obese (BMI ≥ 35 kg/m(2)) and normal BW infants (n = 16), and (4) obese and macrosomic infants (n = 10)...
October 2016: American Journal of Perinatology Reports
https://www.readbyqxmd.com/read/28045465/methylomic-profiling-of-cortex-samples-from-completed-suicide-cases-implicates-a-role-for-psors1c3-in-major-depression-and-suicide
#15
T M Murphy, B Crawford, E L Dempster, E Hannon, J Burrage, G Turecki, Z Kaminsky, J Mill
Major depressive disorder (MDD) represents a major social and economic health issue and constitutes a major risk factor for suicide. The molecular pathology of suicidal depression remains poorly understood, although it has been hypothesised that regulatory genomic processes are involved in the pathology of both MDD and suicidality. In this study, genome-wide patterns of DNA methylation were assessed in depressed suicide completers (n=20) and compared with non-psychiatric, sudden-death controls (n=20) using tissue from two cortical brain regions (Brodmann Area 11 (BA11) and Brodmann Area 25 (BA25))...
January 3, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28035374/activation-of-oncogenic-pathways-in-classical-hodgkin-lymphoma-by-decitabine-a-rationale-for-combination-with-small-molecular-weight-inhibitors
#16
Tatjana Maria Swerev, Thomas Wirth, Alexey Ushmorov
DNA methylation is an epigenetic control mechanism that contributes to the specific phenotype and to the oncogenic program of virtually all tumor entities. Although efficacy of demethylating agents in classical Hodgkin lymphoma (cHL) was not specifically tested, a case of regression of relapsed metastatic cHL was described as a fortunate side‑effect of the demethylating agent 5‑azacytidine in a patient with myelodysplastic syndrome. We investigated molecular mechanisms of decitabine (5‑Aza‑dC) antitumor activity in cHL using gene expression profiling followed by gene set enrichment analysis...
February 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28031523/protective-effects-of-resveratrol-against-mancozeb-induced-apoptosis-damage-in-mouse-oocytes
#17
Yu Liu, Ya-Long Wang, Shu-Wen He, Ming-Huang Chen, Zhen Zhang, Xian-Pei Fu, Bin-Bin Fu, Bao-Qiong Liao, Yan-Hong Lin, Zhong-Quan Qi, Hai-Long Wang
Mancozeb, a mixture of ethylene-bis-dithiocarbamate manganese and zinc salts, is one of the most widely used fungicides in agriculture. Mancozeb could lead to mitochondria dysfunction, cellular anti-oxidation enzymes depletion and apoptotic pathways activation. Previous studies indicated the exposure of mancozeb through mother would lead to irregular estrous cycles, decreased progesterone levels, reduced litter sizes, and more frequent delivery of dead fetuses. In this study, we investigated mancozeb inducing reproductive toxicity, especially focusing on its apoptotic effect and epigenetic modifications...
December 21, 2016: Oncotarget
https://www.readbyqxmd.com/read/28031460/inhibitory-role-of-%C3%AE-2-6-sialylation-in-adipogenesis
#18
Tomoko Kaburagi, Yasuhiko Kizuka, Shinobu Kitazume, Naoyuki Taniguchi
Adipose tissue plays critical roles in obesity and related diseases such as diabetes and cardiovascular diseases. Previous reports suggest that glycans, the most common post-translational modifications, are involved in obesity-related diseases, but what type of glycan regulates adipogenesis during obesity remains unclear. In this study, we first quantified the mRNA levels of 167 genes (encoding 144 glycosyltransferases and 23 related enzymes) in visceral adipose tissues (VATs) from control mice and high fat diet (HFD)-induced obese mice...
December 28, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28030376/the-effect-of-obesity-weight-gain-and-weight-loss-on-asthma-inception-and-control
#19
Erick Forno, Juan C Celedón
PURPOSE OF REVIEW: There is ample and growing evidence that obesity increases the risk of asthma and morbidity from asthma. Here, we review recent clinical evidence supporting a causal link between obesity and asthma, and the mechanisms that may lead to 'obese asthma'. RECENT FINDINGS: Although in some children obesity and asthma simply co-occur, those with 'obese asthma' have increased asthma severity, lower quality of life, and reduced medication response. Underlying mechanistic pathways may include anatomical changes of the airways such as obstruction and dysanapsis, systemic inflammation, production of adipokines, impaired glucose-insulin metabolism, altered nutrient levels, genetic and epigenetic changes, and alterations in the airway and/or gut microbiome...
December 24, 2016: Current Opinion in Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28026884/making-a-queen-an-epigenetic-analysis-of-the-robustness-of-the-honey-bee-apis-mellifera-queen-developmental-pathway
#20
Xu Jiang He, Lin Bin Zhou, Qi Zhong Pan, Andrew B Barron, Wei Yu Yan, Zhi Jiang Zeng
Specialised castes are considered a key reason for the evolutionary and ecological success of the social insect lifestyle. The most essential caste distinction is between the fertile queen and the sterile workers. Honey bee (Apis mellifera) workers and queens are not genetically distinct, rather these different phenotypes are the result of epigenetically regulated divergent developmental pathways. This is an important phenomenon in understanding the evolution of social insect societies. Here we studied the genomic regulation of the worker and queen developmental pathways, and the robustness of the pathways by transplanting eggs or young larvae to queen cells...
December 27, 2016: Molecular Ecology
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