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Frontiers in Genetics

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https://www.readbyqxmd.com/read/30237808/epigenome-wide-analyses-identify-two-novel-associations-with-recurrent-stroke-in-the-vitamin-intervention-for-stroke-prevention-clinical-trial
#1
Nicole M Davis Armstrong, Wei-Min Chen, Michael S Brewer, Stephen R Williams, Michèle M Sale, Bradford B Worrall, Keith L Keene
DNA methylation, a well-characterized epigenetic modification that is influenced by both environment and genetic variation, has previously been implicated in a number of complex diseases, including cardiovascular disease and stroke. The goal of this study was to evaluate epigenome-wide associations with recurrent stroke and the folate one-carbon metabolism-related trait, plasma homocysteine (hcy). Differential methylation analyses were performed on 473,864 autosomal CpG loci, using Illumina HumanMethylation 450K array data in 180 ischemic stroke cases from the Vitamin Intervention for Stroke Prevention (VISP) clinical trial...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30233648/williams-beuren-syndrome-as-a-potential-risk-factor-for-burkitt-lymphoma
#2
Ryo Kimura, Yuko Ishii, Kiyotaka Tomiwa, Tomonari Awaya, Masatoshi Nakata, Takeo Kato, Shin Okazaki, Toshio Heike, Masatoshi Hagiwara
Williams-Beuren syndrome (WBS) is a multisystemic neurodevelopmental disorder caused by a hemizygous deletion on chromosome 7q11.23. Though at present there is a limited number of reports on WBS patients with tumors, most cases are related to blood cancer in children with WBS. We describe a case of Burkitt lymphoma in a 21-year-old man with WBS. In addition to providing a summary of published reports describing tumors observed in patients with WBS, we present a hypothesis about a possible mechanism of oncogenesis...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30233647/computational-tools-for-splicing-defect-prediction-in-breast-ovarian-cancer-genes-how-efficient-are-they-at-predicting-rna-alterations
#3
Alejandro Moles-Fernández, Laura Duran-Lozano, Gemma Montalban, Sandra Bonache, Irene López-Perolio, Mireia Menéndez, Marta Santamariña, Raquel Behar, Ana Blanco, Estela Carrasco, Adrià López-Fernández, Neda Stjepanovic, Judith Balmaña, Gabriel Capellá, Marta Pineda, Ana Vega, Conxi Lázaro, Miguel de la Hoya, Orland Diez, Sara Gutiérrez-Enríquez
In silico tools for splicing defect prediction have a key role to assess the impact of variants of uncertain significance. Our aim was to evaluate the performance of a set of commonly used splicing in silico tools comparing the predictions against RNA in vitro results. This was done for natural splice sites of clinically relevant genes in hereditary breast/ovarian cancer (HBOC) and Lynch syndrome. A study divided into two stages was used to evaluate SSF-like, MaxEntScan, NNSplice, HSF, SPANR, and dbscSNV tools...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30233646/genomic-prediction-of-complex-phenotypes-using-genic-similarity-based-relatedness-matrix
#4
Ning Gao, Jinyan Teng, Shaopan Ye, Xiaolong Yuan, Shuwen Huang, Hao Zhang, Xiquan Zhang, Jiaqi Li, Zhe Zhang
In the last years, a series of methods for genomic prediction (GP) have been established, and the advantages of GP over pedigree best linear unbiased prediction (BLUP) have been reported. However, the majority of previously proposed GP models are purely based on mathematical considerations while seldom take the abundant biological knowledge into account. Prediction ability of those models largely depends on the consistency between the statistical assumptions and the underlying genetic architectures of traits of interest...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30233645/genome-editing-of-pigs-for-agriculture-and-biomedicine
#5
REVIEW
Huaqiang Yang, Zhenfang Wu
Pigs serve as an important agricultural resource and animal model in biomedical studies. Efficient and precise modification of pig genome by using recently developed gene editing tools has significantly broadened the application of pig models in various research areas. The three types of site-specific nucleases, namely, zinc-finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein, are the main gene editing tools that can efficiently introduce predetermined modifications, including knockouts and knockins, into the pig genome...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30233644/identification-of-hyper-methylated-tumor-suppressor-genes-based-diagnostic-panel-for-esophageal-squamous-cell-carcinoma-escc-in-a-chinese-han-population
#6
Chenji Wang, Weilin Pu, Dunmei Zhao, Yinghui Zhou, Ting Lu, Sidi Chen, Zhenglei He, Xulong Feng, Ying Wang, Caihua Li, Shilin Li, Li Jin, Shicheng Guo, Jiucun Wang, Minghua Wang
DNA methylation-based biomarkers were suggested to be promising for early cancer diagnosis. However, DNA methylation-based biomarkers for esophageal squamous cell carcinoma (ESCC), especially in Chinese Han populations have not been identified and evaluated quantitatively. Candidate tumor suppressor genes ( N = 65) were selected through literature searching and four public high-throughput DNA methylation microarray datasets including 136 samples totally were collected for initial confirmation. Targeted bisulfite sequencing was applied in an independent cohort of 94 pairs of ESCC and normal tissues from a Chinese Han population for eventual validation...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30233643/the-lysine-demethylase-dkdm2-is-non-essential-for-viability-but-regulates-circadian-rhythms-in-drosophila
#7
Yani Zheng, Yongbo Xue, Xingjie Ren, Mengmeng Liu, Xiao Li, Yu Jia, Ye Niu, Jian-Quan Ni, Yong Zhang, Jun-Yuan Ji
Post-translational modification of histones, such as histone methylation controlled by specific methyltransferases and demethylases, play critical roles in modulating chromatin dynamics and transcription in eukaryotes. Misregulation of histone methylation can lead to aberrant gene expression, thereby contributing to abnormal development and diseases such as cancer. As such, the mammalian lysine-specific demethylase 2 (KDM2) homologs, KDM2A and KDM2B, are either oncogenic or tumor suppressive depending on specific pathological contexts...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30233642/early-onset-multiple-primary-tumors-in-atypical-presentation-of-cowden-syndrome-identified-by-whole-exome-sequencing
#8
Mathias Cavaillé, Flora Ponelle-Chachuat, Nancy Uhrhammer, Sandrine Viala, Mathilde Gay-Bellile, Maud Privat, Yannick Bidet, Yves-Jean Bignon
A family with an aggregation of rare early onset multiple primary tumors has been managed in our oncogenetics department: the proband developed four early onset carcinomas between ages 31 and 33 years, including acral melanoma, bilateral clear cell renal carcinoma (RC), and follicular variant of papillary thyroid carcinoma. The proband's parent developed orbital lymphoma and small intestine mucosa-associated lymphoid tissue (MALT) lymphoma between 40 and 50 years old. Whole-exome-sequencing (WES) of the nuclear family (proband, parents, and sibling) identified in the proband a de novo deleterious heterozygous mutation c...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30233641/sensory-difficulties-in-children-with-an-fmr1-premutation
#9
Melissa Raspa, Amanda Wylie, Anne C Wheeler, Jacek Kolacz, Anne Edwards, Keri Heilman, Stephen W Porges
Abnormal sensory processing is one of the core characteristics of the fragile X phenotype. Studies of young children with fragile X syndrome (FXS) and the FMR1 premutation have shown sensory challenges as early as infancy and into early childhood. This study sought to examine differences in sensory difficulties in children with an FMR1 premutation compared with children with FXS and typically developing children. We conducted an online survey of 176 parents of affected children (FXS or FMR1 premutation). Most respondents were mothers who are Caucasian (86%), have a 4-year college or graduate degree (68%), and are married (92%)...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30233640/rare-genetic-blood-disease-modeling-in-zebrafish
#10
REVIEW
Alberto Rissone, Shawn M Burgess
Hematopoiesis results in the correct formation of all the different blood cell types. In mammals, it starts from specific hematopoietic stem and precursor cells residing in the bone marrow. Mature blood cells are responsible for supplying oxygen to every cell of the organism and for the protection against pathogens. Therefore, inherited or de novo genetic mutations affecting blood cell formation or the regulation of their activity are responsible for numerous diseases including anemia, immunodeficiency, autoimmunity, hyper- or hypo-inflammation, and cancer...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30233639/bivariate-causal-discovery-and-its-applications-to-gene-expression-and-imaging-data-analysis
#11
Rong Jiao, Nan Lin, Zixin Hu, David A Bennett, Li Jin, Momiao Xiong
The mainstream of research in genetics, epigenetics, and imaging data analysis focuses on statistical association or exploring statistical dependence between variables. Despite their significant progresses in genetic research, understanding the etiology and mechanism of complex phenotypes remains elusive. Using association analysis as a major analytical platform for the complex data analysis is a key issue that hampers the theoretic development of genomic science and its application in practice. Causal inference is an essential component for the discovery of mechanical relationships among complex phenotypes...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30233638/integrative-analyses-of-transcriptome-sequencing-identify-functional-mirnas-in-the-chicken-embryo-fibroblasts-cells-infected-with-reticuloendotheliosis-virus
#12
Jie Zhai, Chang Gao, Lisheng Fu, Long Jing, Shengyuan Dang, Shimin Zheng
In this study, we found a much higher proportion of reticuloendotheliosis virus (REV) infected chicken embryo fibroblasts (CEF) were in active cell division phase than that of control cells which indicated that REV can affect the fate of CEF. So, we performed high-throughput sequencing and transcriptomic analysis to identify functional miRNAs, in order to figure out the possible mechanism in the interaction of REV with CEF. In total, 50 differentially expressed miRNAs (DEmiRNAs) were identified. Then target genes of DEmiRNAs were predicted and identified by transcriptome profile results...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30233637/bioinformatics-analysis-identifies-p53-as-a-candidate-prognostic-biomarker-for-neuropathic-pain
#13
Yibo Gao, Na Sun, Lieju Wang, Ying Wu, Longfei Ma, Juncong Hong, Jinxuan Ren, Bin Zhu, Lina Yu, Min Yan
Neuropathic pain (NP) is a type of chronic pain that is different from the common type of pain. The mechanisms of NP are still poorly understood. Exploring the key genes and neurobiological changes in NP could provide important diagnostic and treatment tools for clinicians. GSE24982 is an mRNA-seq dataset that we downloaded from the Gene Expression Omnibus database to identify key genes in NP. Differentially expressed genes (DEGs) were identified using the BRB-ArrayTools software and R. Functional and pathway enrichment analyses of the DEGs were performed using Metascape...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30214456/stable-histone-methylation-changes-at-proteoglycan-network-genes-following-ethanol-exposure
#14
David P Gavin, Joel G Hashimoto, Nathan H Lazar, Lucia Carbone, John C Crabbe, Marina Guizzetti
Alcohol use disorder (AUD) is a chronic mental illness in which patients often achieve protracted periods of abstinence prior to relapse. Epigenetic mechanisms may provide an explanation for the persisting gene expression changes that can be observed even after long periods of abstinence and may contribute to relapse. In this study, we examined two histone modifications, histone 3 lysine 4 tri-methylation (H3K4me3) and histone 3 lysine 27 tri-methylation (H3K27me3), in the prefrontal cortex of Withdrawal Seizure Resistant (WSR) mice 21 days after 72 h of ethanol vapor exposure...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30214455/identification-and-analysis-of-blood-gene-expression-signature-for-osteoarthritis-with-advanced-feature-selection-methods
#15
Jing Li, Chun-Na Lan, Ying Kong, Song-Shan Feng, Tao Huang
Osteoarthritis (OA) is a complex disease that affects articular joints and may cause disability. The incidence of OA is extremely high. Most elderly people have the symptoms of osteoarthritis. The physiotherapy of OA is time consuming, and the chances of full recovery from OA are very minimal. The most effective way of fighting OA is early diagnosis and early intervention. Liquid biopsy has become a popular noninvasive test. To find the blood gene expression signature for OA, we reanalyzed the publicly available blood gene expression profiles of 106 patients with OA and 33 control samples using an automatic computational pipeline based on advanced feature selection methods...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30210532/-sinorhizobium-meliloti-rnase-iii-catalytic-features-and-impact-on-symbiosis
#16
Margarida Saramago, Marta Robledo, Rute G Matos, José I Jiménez-Zurdo, Cecília M Arraiano
Members of the ribonuclease (RNase) III family of enzymes are metal-dependent double-strand specific endoribonucleases. They are ubiquitously found and eukaryotic RNase III-like enzymes include Dicer and Drosha, involved in RNA processing and RNA interference. In this work, we have addressed the primary characterization of RNase III from the symbiotic nitrogen-fixing α-proteobacterium Sinorhizobium meliloti . The S. meliloti rnc gene does encode an RNase III-like protein ( Sm RNase III), with recognizable catalytic and double-stranded RNA (dsRNA)-binding domains that clusters in a branch with its α-proteobacterial counterparts...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30210531/the-telomerase-complex-directly-controls-hematopoietic-stem-cell-differentiation-and-senescence-in-an-induced-pluripotent-stem-cell-model-of-telomeropathy
#17
Shyam Sushama Jose, Federico Tidu, Petra Burilova, Tomas Kepak, Kamila Bendickova, Jan Fric
Telomeropathies are rare disorders associated with impaired telomere length control mechanisms that frequently result from genetic mutations in the telomerase complex. Dyskeratosis congenita is a congenital progressive telomeropathy in which mutation in the telomerase RNA component ( TERC ) impairs telomere maintenance leading to accelerated cellular senescence and clinical outcomes resembling premature aging. The most severe clinical feature is perturbed hematopoiesis and bone-marrow failure, but the underlying mechanisms are not fully understood...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30210530/epigenetic-mechanisms-link-maternal-diets-and-gut-microbiome-to-obesity-in-the-offspring
#18
REVIEW
Yuanyuan Li
Nutrition is the most important environmental factor that can influence early developmental processes through regulation of epigenetic mechanisms during pregnancy and neonatal periods. Maternal diets or nutritional compositions contribute to the establishment of the epigenetic profiles in the fetus that have a profound impact on individual susceptibility to certain diseases or disorders in the offspring later in life. Obesity is considered a global epidemic that impairs human life quality and also increases risk of development of many human diseases such as diabetes and cardiovascular diseases...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30210529/impact-of-fmr1-premutation-on-neurobehavior-and-bioenergetics-in-young-monozygotic-twins
#19
Eleonora Napoli, Andrea Schneider, Randi Hagerman, Gyu Song, Sarah Wong, Flora Tassone, Cecilia Giulivi
Mitochondrial dysfunction (MD) has been identified in lymphocytes, fibroblasts and brain samples from adults carrying a 55-200 CGG expansion in the fragile X mental retardation 1 ( FMR1 ) gene (premutation; PM); however, limited data are available on the bioenergetics of pediatric carriers. Here we discuss a case report of three PM carriers: two monozygotic twins (aged 8 years) harboring an FMR1 allele with 150-180 CGG repeats, with no cognitive or intellectual issues but diagnosed with depression, mood instability and ADHD, and their mother (asymptomatic carrier with 78 CGG repeats)...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30210528/qtl-mapping-and-marker-identification-for-sex-determining-indicating-xy-sex-determination-system-in-the-swimming-crab-portunus-trituberculatus
#20
Jianjian Lv, Dongfang Sun, Pengpeng Huan, Liu Song, Ping Liu, Jian Li
Sex determination is an important area of research, which has always had an intriguing aspect in evolutionary and developmental biology. Quantitative trait locus (QTL) mapping for sex will be helpful in clarifying the sex determination system. In this study, the sex QTL mapping of the swimming crab ( Portunus trituberculatus ) was performed based on a high-density linkage map, and a highly significant QTL specifically mapped on a single linkage group (LG) was firstly identified (LG24, LOD > 14). Twenty markers in the QTL region showed significant associations with sex by association analysis, of which heterogametic genotypes in males supported the XY sex determination mechanism...
2018: Frontiers in Genetics
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