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https://www.readbyqxmd.com/read/27911260/population-scale-mapping-of-transposable-element-diversity-reveals-links-to-gene-regulation-and-epigenomic-variation
#1
Tim Stuart, Steven Eichten, Jonathan Cahn, Yuliya Karpievitch, Justin Borevitz, Ryan Lister
Variation in the presence or absence of transposable elements (TEs) is a major source of genetic variation between individuals. Here, we identified 23,095 TE presence/absence variants between 216 Arabidopsis accessions. Most TE variants were rare, and we find these rare variants associated with local extremes of gene expression and DNA methylation levels within the population. Of the common alleles identified, two thirds were not in linkage disequilibrium with nearby SNPs, implicating these variants as a source of novel genetic diversity...
December 2, 2016: ELife
https://www.readbyqxmd.com/read/27909926/metals-as-chemical-tracers-to-discriminate-ecological-populations-of-threatened-franciscana-dolphins-pontoporia-blainvillei-from-argentina
#2
M B Romero, P Polizzi, L Chiodi, A Robles, K Das, M Gerpe
Franciscana dolphins are the most impacted small cetacean in the Southwestern Atlantic Ocean, classified as Vulnerable A3d by IUCN. Essential (Fe, Mo, Mn, Cr, Ni, Co) and non-essential (Ag, Pb, Sn) trace elements (TEs) were measured in liver, kidney, and brain samples of by-catch Franciscana dolphins that were living in estuarine (n = 21) and marine (n = 21) habitats (1) to assess whether TEs posed a threat and (2) to evaluate the suitability of TEs for discriminating ecological populations of this species in Argentinean waters...
December 1, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27900322/patterns-of-transposable-element-expression-and-insertion-in-cancer
#3
Evan A Clayton, Lu Wang, Lavanya Rishishwar, Jianrong Wang, John F McDonald, I King Jordan
Human transposable element (TE) activity in somatic tissues causes mutations that can contribute to tumorigenesis. Indeed, TE insertion mutations have been implicated in the etiology of a number of different cancer types. Nevertheless, the full extent of somatic TE activity, along with its relationship to tumorigenesis, have yet to be fully explored. Recent developments in bioinformatics software make it possible to analyze TE expression levels and TE insertional activity directly from transcriptome (RNA-seq) and whole genome (DNA-seq) next-generation sequence data...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27899997/testin-tes-as-a-candidate-tumour-suppressor-and-prognostic-marker-in-human-astrocytoma
#4
Giedrius Steponaitis, Arunas Kazlauskas, Daina Skiriute, Indre Valiulyte, Kestutis Skauminas, Arimantas Tamasauskas, Paulina Vaitkiene
Astrocytomas are one of the most common brain tumours; however, the current methods used to characterize these tumours are inadequate. The establishment of molecular markers may identify variables required to improve tumour characterization and subtyping, and may aid to specify targets for improved treatment with essential prognostic value for patient survival. One such candidate is testin (TES), which was reported to have prognostic value for glioblastoma patients. However, the role of TES protein in gliomagenesis is currently unknown...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27898760/exploiting-the-repetitive-fraction-of-the-wheat-genome-for-high-throughput-single-nucleotide-polymorphism-discovery-and-genotyping
#5
Nelly Cubizolles, Elodie Rey, Frédéric Choulet, Hélène Rimbert, Christel Laugier, François Balfourier, Jacques Bordes, Charles Poncet, Peter Jack, Chris James, Jan Gielen, Odile Argillier, Jean-Pierre Jaubertie, Jérôme Auzanneau, Antje Rohde, Pieter B F Ouwerkerk, Viktor Korzun, Sonja Kollers, Laurent Guerreiro, Delphine Hourcade, Olivier Robert, Pierre Devaux, Anna-Maria Mastrangelo, Catherine Feuillet, Pierre Sourdille, Etienne Paux
Transposable elements (TEs) account for more than 80% of the wheat genome. Although they represent a major obstacle for genomic studies, TEs are also a source of polymorphism and consequently of molecular markers such as insertion site-based polymorphism (ISBP) markers. Insertion site-based polymorphisms have been found to be a great source of genome-specific single-nucleotide polymorphism (SNPs) in the hexaploid wheat ( L.) genome. Here, we report on the development of a high-throughput SNP discovery approach based on sequence capture of ISBP markers...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27895926/non-invasive-brain-stimulation-as-a-tool-to-study-cerebellar-m1-interactions-in-humans
#6
REVIEW
Sara Tremblay, Duncan Austin, Ricci Hannah, John C Rothwell
The recent development of non-invasive brain stimulation techniques such as transcranial magnetic stimulation (TMS) has allowed the non-invasive assessment of cerebellar function in humans. Early studies showed that cerebellar activity, as reflected in the excitability of the dentate-thalamo-cortical pathway, can be assessed with paired stimulation of the cerebellum and the primary motor cortex (M1) (cerebellar inhibition of motor cortex, CBI). Following this, many attempts have been made, using techniques such as repetitive TMS and transcranial electrical stimulation (TES), to modulate the activity of the cerebellum and the dentate-thalamo-cortical output, and measure their impact on M1 activity...
2016: Cerebellum & Ataxias
https://www.readbyqxmd.com/read/27893459/extended-t2-ivim-model-for-correction-of-te-dependence-of-pseudo-diffusion-volume-fraction-in-clinical-diffusion-weighted-magnetic-resonance-imaging
#7
N P Jerome, J A d'Arcy, T Feiweier, D-M Koh, M O Leach, D J Collins, M R Orton
The bi-exponential intravoxel-incoherent-motion (IVIM) model for diffusion-weighted MRI (DWI) fails to account for differential T 2 s in the model compartments, resulting in overestimation of pseudodiffusion fraction f. An extended model, T2-IVIM, allows removal of the confounding echo-time (TE) dependence of f, and provides direct compartment T 2 estimates. Two consented healthy volunteer cohorts (n  =  5, 6) underwent DWI comprising multiple TE/b-value combinations (Protocol 1: TE  =  62-102 ms, b  =  0-250 mm(-2)s, 30 combinations...
December 21, 2016: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/27888135/antihypertensive-effects-of-androgens-in-conscious-spontaneously-hypertensive-rats
#8
Mercedes Perusquía, Nieves Herrera, Mercedes Ferrer, John N Stallone
Androgens are vasoactive steroids that induce acute vasodilation in a number of isolated vascular beds from different species, but the effects of these hormones on systemic blood pressure (BP) have been studied little. Although it has been reported that androgens exert systemic hypotensive effects through peripheral vasodilation in normotensive rats, there have not been any reports of systemic hypotensive effects of androgens in animals with hypertension. This study was designed to evaluate the acute effects of testosterone (TES) and its 5-reduced metabolites on systemic BP in hypertensive rats and to test the hypothesis that hypotestosteronemia may be involved in the pathogenesis of hypertension...
November 23, 2016: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/27886419/functional-characterization-of-a-novel-loss-of-function-mutation-of-prps1-related-to-early-onset-progressive-nonsyndromic-hearing-loss-in-koreans-dfnx1-potential-implications-on-future-therapeutic-intervention
#9
So Young Kim, Ah Reum Kim, Nayoung K D Kim, Chung Lee, Jin Hee Han, Min Young Kim, Eun-Hee Jeon, Woong-Yang Park, Rahul Mittal, Denise Yan, Xue Zhong Liu, Byung Yoon Choi
BACKGROUND: The symptoms of phosphoribosyl pyrophosphate synthetase 1 (PRPS1) deficiency diseases have been reported to be alleviated by medication. Herein, we report biochemical data to favor PRPS1 deficiency-related hearing loss as a potential target for pharmaceutical treatment. METHODS: We recruited 42 probands from subjects under the age of 15 years with a moderate degree of nonsyndromic autosomal-recessive or sporadic sensorineural hearing loss (SNHL) in at least one side...
November 25, 2016: Journal of Gene Medicine
https://www.readbyqxmd.com/read/27875251/the-impact-of-transposable-elements-on-mammalian-development
#10
REVIEW
Jose L Garcia-Perez, Thomas J Widmann, Ian R Adams
Despite often being classified as selfish or junk DNA, transposable elements (TEs) are a group of abundant genetic sequences that have a significant impact on mammalian development and genome regulation. In recent years, our understanding of how pre-existing TEs affect genome architecture, gene regulatory networks and protein function during mammalian embryogenesis has dramatically expanded. In addition, the mobilization of active TEs in selected cell types has been shown to generate genetic variation during development and in fully differentiated tissues...
November 15, 2016: Development
https://www.readbyqxmd.com/read/27873340/adequacy-of-physician-documentation-and-correlation-with-assessment-of-transfusion-appropriateness-a-follow-up-study-in-the-setting-of-prospective-audits-and-patient-blood-management
#11
Emilio Madrigal, Shyam Prajapati, Vaidehi Avadhani, Kyle Annen, Mark T Friedman
BACKGROUND: A previous study in our hospitals correlated suboptimal documentation and failure to justify transfusions. In light of implemented blood-conservation strategies, including patient blood management (PBM) and prospective audits (PAs), we performed a follow-up study. STUDY DESIGN AND METHODS: We reviewed prospectively audited red blood cell (RBC) transfusions received by adult patients from January to July 2014. Survey forms were used to assess the level of documentation and to classify documentation as adequate, intermediate, or inadequate...
November 21, 2016: Transfusion
https://www.readbyqxmd.com/read/27867194/regulatory-activities-of-transposable-elements-from-conflicts-to-benefits
#12
Edward B Chuong, Nels C Elde, Cédric Feschotte
Transposable elements (TEs) are a prolific source of tightly regulated, biochemically active non-coding elements, such as transcription factor-binding sites and non-coding RNAs. Many recent studies reinvigorate the idea that these elements are pervasively co-opted for the regulation of host genes. We argue that the inherent genetic properties of TEs and the conflicting relationships with their hosts facilitate their recruitment for regulatory functions in diverse genomes. We review recent findings supporting the long-standing hypothesis that the waves of TE invasions endured by organisms for eons have catalysed the evolution of gene-regulatory networks...
November 21, 2016: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/27863519/tet-dependent-regulation-of-retrotransposable-elements-in-mouse-embryonic-stem-cells
#13
Lorenzo de la Rica, Özgen Deniz, Kevin C L Cheng, Christopher D Todd, Cristina Cruz, Jonathan Houseley, Miguel R Branco
BACKGROUND: Ten-eleven translocation (TET) enzymes oxidise DNA methylation as part of an active demethylation pathway. Despite extensive research into the role of TETs in genome regulation, little is known about their effect on transposable elements (TEs), which make up nearly half of the mouse and human genomes. Epigenetic mechanisms controlling TEs have the potential to affect their mobility and to drive the co-adoption of TEs for the benefit of the host. RESULTS: We performed a detailed investigation of the role of TET enzymes in the regulation of TEs in mouse embryonic stem cells (ESCs)...
November 18, 2016: Genome Biology
https://www.readbyqxmd.com/read/27851806/5-hydroxymethylcytosine-precedes-loss-of-cpg-methylation-in-enhancers-and-genes-undergoing-activation-in-cardiomyocyte-maturation
#14
David K Kranzhöfer, Ralf Gilsbach, Björn A Grüning, Rolf Backofen, Thomas G Nührenberg, Lutz Hein
BACKGROUND: Cardiomyocytes undergo major changes in DNA methylation during maturation and transition to a non-proliferative state after birth. 5'-hydroxylation of methylated cytosines (5hmC) is not only involved in DNA loss of CpG methylation but is also thought to be an epigenetic mark with unique distribution and functions. Here, we sought to get insight into the dynamics of 5'-hydroxymethylcytosine in newborn and adult cardiomyocytes. METHODS: Cardiomyocyte nuclei from newborn and adult C57BL/6 mice were purified by flow cytometric sorting...
2016: PloS One
https://www.readbyqxmd.com/read/27836342/influence-of-fireworks-displays-on-the-chemical-characteristics-of-pm2-5-in-rural-and-suburban-areas-in-central-and-east-china
#15
Junmei Zhang, Lingxiao Yang, Jianmin Chen, Abdelwahid Mellouki, Pan Jiang, Ying Gao, Yanyan Li, Yumeng Yang, Wenxing Wang
To explore the spatial and chemical characteristics of PM2.5 pollution and the influence of fireworks displays on PM2.5 and its chemical components in rural areas in Central and East China, PM2.5 samples were collected at three rural sites and one suburban site in Henan and Shandong provinces during the 2016 Chinese New Year, and the chemical composition of PM2.5, including water-soluble inorganic ions (WSIIs), organic carbon (OC), elemental carbon (EC), water-soluble organic carbon (WSOC) and trace elements (TEs) was analysed...
November 8, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/27830735/the-use-of-targeted-exome-sequencing-in-genetic-diagnosis-of-young-patients-with-severe-hypercholesterolemia
#16
Long Jiang, Wen-Feng Wu, Li-Yuan Sun, Pan-Pan Chen, Wei Wang, Asier Benito-Vicente, Fan Zhang, Xiao-Dong Pan, Wei Cui, Shi-Wei Yang, Yu-Jie Zhou, Cesar Martin, Lu-Ya Wang
Familial hypercholesterolemia (FH) is an autosomal dominant disorder. Although genetic testing is an important tool for detecting FH-causing mutations in patients, diagnostic methods for young patients with severe hypercholesterolemia are understudied. This study compares the target exome sequencing (TES) technique with the DNA resequencing array technique on young patients with severe hypercholesterolemia. A total of 20 unrelated patients (mean age 14.8 years) with total cholesterol > 10 mmol/L were included...
November 10, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27821059/recent-and-dynamic-transposable-elements-contribute-to-genomic-divergence-under-asexuality
#17
Julie Ferreira de Carvalho, Victor de Jager, Thomas P van Gurp, Niels C A M Wagemaker, Koen J F Verhoeven
BACKGROUND: Transposable elements (TEs) are mobile pieces of genetic information with high mutagenic potential for the host genome. Transposition is often neutral or deleterious but may also generate potentially adaptive genetic variation. This additional source of variation could be especially relevant in non-recombining species reproducing asexually. However, evidence is lacking to determine the relevance of TEs in plant asexual genome evolution and their associated effects. Here, we characterize the repetitive fraction of the genome of the common dandelion, Taraxacum officinale and compare it between five accessions from the same apomictic lineage...
November 7, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27812277/a-bioinformatics-approach-for-detecting-repetitive-nested-motifs-using-pattern-matching
#18
José R Romero, Jessica A Carballido, Ingrid Garbus, Viviana C Echenique, Ignacio Ponzoni
The identification of nested motifs in genomic sequences is a complex computational problem. The detection of these patterns is important to allow the discovery of transposable element (TE) insertions, incomplete reverse transcripts, deletions, and/or mutations. In this study, a de novo strategy for detecting patterns that represent nested motifs was designed based on exhaustive searches for pairs of motifs and combinatorial pattern analysis. These patterns can be grouped into three categories, motifs within other motifs, motifs flanked by other motifs, and motifs of large size...
2016: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/27809537/comprehensive-proteomics-analysis-reveals-metabolic-reprogramming-of-tumor-associated-macrophages-stimulated-by-the-tumor-microenvironment
#19
Di Liu, Cheng Chang, Ning Lu, Xing Wang, Qian Lu, Xiaojie Ren, Peng Ren, Dianyuan Zhao, Lijing Wang, Yunping Zhu, Fuchu He, Li Tang
Tumor-associated macrophages (TAMs) are major components of the tumor microenvironment. Although a role for TAMs in promoting tumor progression has been revealed, the differentiation mechanisms and intrinsic signals of TAMs regulated by the tumor microenvironment remain unclear. Here we constructed an in vitro TAMs cell model, TES-TAMs, which is from tumor-extract-stimulated bone-marrow-derived macrophages. We performed a comparative proteomics analysis of bone-marrow-derived macrophages and TES-TAMs, which indicated that TES-TAMs possessed characteristic molecular expression of TAMs...
November 3, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27809350/clinical-usefulness-of-western-blotting-and-elisa-avidity-for-the-diagnosis-of-human-toxocariasis
#20
Monika Rudzińska, Beata Kowalewska, Katarzyna Sikorska
The serodiagnosis of human toxocariasis is difficult. Specific IgGs detected routinely with ELISA based on Toxocara excretory-secretory (TES) antigens often persist for years at an elevated level, which does not allow either the differentiation between an active and persistent infection or monitoring the effect of treatment. Additionally, false positive results may occur in co-infections with other helminths due to cross-reactions. We evaluated the usefulness of an IgG avidity index (AI) and a Western blotting (WB) IgG in the diagnosis of patients suspected of Toxocara infection...
November 3, 2016: Parasite Immunology
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