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https://www.readbyqxmd.com/read/28320126/gab2-rs2373115-variant-contributes-to-alzheimer-s-disease-risk-specifically-in-european-population
#1
Yang Hu, Likun Zheng, Liang Cheng, Ying Zhang, Weiyang Bai, Wenyang Zhou, Tao Wang, Zhifa Han, Jian Zong, Shuilin Jin, Jun Zhang, Guiyou Liu, Qinghua Jiang
A genome-wide association study identified GAB2 rs2373115 to be associated with Alzheimer's disease (AD) risk in European population. However, inconsistent results are reported in East Asian population. Here, we performed an updated analysis using 65,704 samples including 20,982 AD cases and 44,722 controls. First, we investigated the GAB2 rs2373115 variant in Asian population using 3974 AD cases and 7568 controls. To further evaluate the effect of rs2373115 in different populations, we selected 17,008 AD cases and 37,154 controls in European population...
April 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28319896/a-dynamic-sandwich-assay-on-magnetic-beads-for-selective-detection-of-single-nucleotide-mutations-at-room-temperature
#2
Junxiu Wang, Guoliang Xiong, Liang Ma, Shihui Wang, Xu Zhou, Lei Wang, Lehui Xiao, Xin Su, Changyuan Yu
Single-nucleotide mutation (SNM) has proven to be associated with a variety of human diseases. Development of reliable methods for the detection of SNM is crucial for molecular diagnosis and personalized medicine. The sandwich assays are widely used tools for detecting nucleic acid biomarkers due to their low cost and rapid signaling. However, the poor hybridization specificity of signal probe at room temperature hampers the discrimination of mutant and wild type. Here, we demonstrate a dynamic sandwich assay on magnetic beads for SNM detection based on the transient binding between signal probe and target...
March 12, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28319850/methylation-of-hpa-axis-related-genes-in-men-with-hypersexual-disorder
#3
Jussi Jokinen, Adrian E Boström, Andreas Chatzittofis, Diana M Ciuculete, Katarina Görts Öberg, John N Flanagan, Stefan Arver, Helgi B Schiöth
Hypersexual Disorder (HD) defined as non-paraphilic sexual desire disorder with components of compulsivity, impulsivity and behavioral addiction, and proposed as a diagnosis in the DSM 5, shares some overlapping features with substance use disorder including common neurotransmitter systems and dysregulated hypothalamic-pituitary-adrenal (HPA) axis function. In this study, comprising 67 HD male patients and 39 male healthy volunteers, we aimed to identify HPA-axis coupled CpG-sites, in which modifications of the epigenetic profile are associated with hypersexuality...
March 10, 2017: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/28319736/structural-variants-in-snca-gene-and-the-implication-to-synucleinopathies
#4
REVIEW
Ornit Chiba-Falek
Synucleinopathies are a group of neurodegenerative diseases that share a common pathological lesion of intracellular protein inclusions largely composed of aggregates of alpha-synuclein protein. Accumulating evidence, including genome-wide association studies, has implicated the alpha-synuclein (SNCA) gene in the etiology of synucleinopathies and it has been suggested that SNCA expression levels are critical for the development of these diseases. This review focuses on genetic variants from the class of structural variants (SVs), including multiplication of large genomic segments and short (<50bp) genomic variants such as simple sequence repeats (SSRs), within the SNCA locus...
March 2, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28319371/expression-of-heterologous-sigma-factor-expands-the-searchable-space-for-biofuel-tolerance-mechanisms
#5
Timothy A Tomko, Mary J Dunlop
Microorganisms can produce hydrocarbons that can serve as replacements or additions to conventional liquid fuels for use in the transportation sector. However, a common problem in the microbial synthesis of biofuels is that these compounds often have toxic effects on the cell. In this study, we focused on mitigating the toxicity of the bio-jet fuel precursor pinene on Escherichia coli. We used genomic DNA from Pseudomonas putida KT2440, which has innate solvent-tolerance properties, to create transgenic libraries in an E...
March 20, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28319194/genome-wide-analysis-of-brain-and-gonad-transcripts-reveals-changes-of-key-sex-reversal-related-genes-expression-and-signaling-pathways-in-three-stages-of-monopterus-albus
#6
Wei Chi, Yu Gao, Qing Hu, Wei Guo, Dapeng Li
BACKGROUND: The natural sex reversal severely affects the sex ratio and thus decreases the productivity of the rice field eel (Monopterus albus). How to understand and manipulate this process is one of the major issues for the rice field eel stocking. So far the genomics and transcriptomics data available for this species are still scarce. Here we provide a comprehensive study of transcriptomes of brain and gonad tissue in three sex stages (female, intersex and male) from the rice field eel to investigate changes in transcriptional level during the sex reversal process...
2017: PloS One
https://www.readbyqxmd.com/read/28319091/whole-genome-sequencing-identifies-rare-genotypes-in-comp-and-chadl-associated-with-high-risk-of-hip-osteoarthritis
#7
Unnur Styrkarsdottir, Hannes Helgason, Asgeir Sigurdsson, Gudmundur L Norddahl, Arna B Agustsdottir, Louise N Reynard, Amanda Villalvilla, Gisli H Halldorsson, Aslaug Jonasdottir, Audur Magnusdottir, Asmundur Oddson, Gerald Sulem, Florian Zink, Gardar Sveinbjornsson, Agnar Helgason, Hrefna S Johannsdottir, Anna Helgadottir, Hreinn Stefansson, Solveig Gretarsdottir, Thorunn Rafnar, Ina S Almdahl, Anne Brækhus, Tormod Fladby, Geir Selbæk, Farhad Hosseinpanah, Fereidoun Azizi, Jung Min Koh, Nelson L S Tang, Maryams Danesphour, Jose I Mayordomo, Corrine Welt, Peter S Braund, Nilesh J Samani, Lambertus A Kiemeney, L Stefan Lohmander, Claus Christiansen, Ole A Andreassen, Olafur Magnusson, Gisli Masson, Augustine Kong, Ingileif Jonsdottir, Daniel Gudbjartsson, Patrick Sulem, Helgi Jonsson, John Loughlin, Thorvaldur Ingvarsson, Unnur Thorsteinsdottir, Kari Stefansson
We performed a genome-wide association study of total hip replacements, based on variants identified through whole-genome sequencing, which included 4,657 Icelandic patients and 207,514 population controls. We discovered two rare signals that strongly associate with osteoarthritis total hip replacement: a missense variant, c.1141G>C (p.Asp369His), in the COMP gene (allelic frequency = 0.026%, P = 4.0 × 10(-12), odds ratio (OR) = 16.7) and a frameshift mutation, rs532464664 (p.Val330Glyfs*106), in the CHADL gene that associates through a recessive mode of inheritance (homozygote frequency = 0...
March 20, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28319011/resequencing-helminth-genomes-for-population-and-genetic-studies
#8
REVIEW
Janneke Wit, John S Gilleard
Next-generation sequencing has become increasingly accessible and economical, making genome-wide studies routine for many species, including humans, model organisms, and domestic livestock. However, in the case of helminth parasites, there are still major practical challenges to the application of these approaches for genetic and population studies. Dozens to hundreds of individual parasites from multiple populations may need to be re-sequenced which, together with the relatively large size of helminth genomes, can still make whole-genome resequencing of individual parasites unfeasible for many studies...
March 16, 2017: Trends in Parasitology
https://www.readbyqxmd.com/read/28318978/the-mitochondrial-dna-polymerase-promotes-elimination-of-paternal-mitochondrial-genomes
#9
Zhongsheng Yu, Patrick H O'Farrell, Nikita Yakubovich, Steven Z DeLuca
Mitochondrial DNA (mtDNA) is typically inherited from only one parent [1-3]. In animals, this is usually the mother. Maternal inheritance is often presented as the passive outcome of the difference in cytoplasmic content of egg and sperm; however, active programs enforce uniparental inheritance at two levels, eliminating paternal mitochondrial genomes or destroying mitochondria delivered to the zygote by the sperm [4-13]. Both levels operate in Drosophila [8, 12, 13]. As sperm formation begins, hundreds of doomed mitochondrial genomes are visualized within the two huge mitochondria of each spermatid...
March 11, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28318822/genome-wide-analysis-of-rna-polymerase-ii-termination-at-protein-coding-genes
#10
Carlo Baejen, Jessica Andreani, Phillipp Torkler, Sofia Battaglia, Bjoern Schwalb, Michael Lidschreiber, Kerstin C Maier, Andrea Boltendahl, Petra Rus, Stephanie Esslinger, Johannes Söding, Patrick Cramer
At the end of protein-coding genes, RNA polymerase (Pol) II undergoes a concerted transition that involves 3'-processing of the pre-mRNA and transcription termination. Here, we present a genome-wide analysis of the 3'-transition in budding yeast. We find that the 3'-transition globally requires the Pol II elongation factor Spt5 and factors involved in the recognition of the polyadenylation (pA) site and in endonucleolytic RNA cleavage. Pol II release from DNA occurs in a narrow termination window downstream of the pA site and requires the "torpedo" exonuclease Rat1 (XRN2 in human)...
March 6, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28318412/effects-of-lithium-and-2-4-dichlorophenol-on-zebrafish-circadian-rhythm-disorder-and-molecular-effects
#11
Bo Xiao, Li-Qiang Cui, Cheng Ding, Han Wang
The aim of this study was to investigate lithium and 2,4-dichlorophenol (2,4-DCP)-induced circadian rhythm disorder and their genome-wide effects in zebrafish. Zebrafish larvae were exposed to 250 ppm LiCl (n = 40) or 20 ppm 2,4-DCP. RNA was subsequently extracted and determined quantitatively. The mRNA levels of circadian clock-related genes, including clock1a, bmal1b, per2, and per1b, were determined. Microarray datasets were generated and the differentially expressed genes (DEGs) were identified. The mRNA levels of some upregulated and downregulated DEGs were examined by quantitative real-time polymerase chain reaction (RT-PCR)...
March 20, 2017: Zebrafish
https://www.readbyqxmd.com/read/28318110/on-the-association-analysis-of-genome-sequencing-data-a-spatial-clustering-approach-for-partitioning-the-entire-genome-into-nonoverlapping-windows
#12
Heide Loehlein Fier, Dmitry Prokopenko, Julian Hecker, Michael H Cho, Edwin K Silverman, Scott T Weiss, Rudolph E Tanzi, Christoph Lange
For the association analysis of whole-genome sequencing (WGS) studies, we propose an efficient and fast spatial-clustering algorithm. Compared to existing analysis approaches for WGS data, that define the tested regions either by sliding or consecutive windows of fixed sizes along variants, a meaningful grouping of nearby variants into consecutive regions has the advantage that, compared to sliding window approaches, the number of tested regions is likely to be smaller. In comparison to consecutive, fixed-window approaches, our approach is likely to group nearby variants together...
March 20, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28317850/maternally-expressed-nlrp2-links-the-subcortical-maternal-complex-scmc-to-fertility-embryogenesis-and-epigenetic-reprogramming
#13
Sangeetha Mahadevan, Varsha Sathappan, Budi Utama, Isabel Lorenzo, Khalied Kaskar, Ignatia B Van den Veyver
Mammalian parental genomes contribute differently to early embryonic development. Before activation of the zygotic genome, the maternal genome provides all transcripts and proteins required for the transition from a highly specialized oocyte to a pluripotent embryo. Depletion of these maternally-encoded transcripts frequently results in failure of preimplantation embryonic development, but their functions in this process are incompletely understood. We found that female mice lacking NLRP2 are subfertile because of early embryonic loss and the production of fewer offspring that have a wide array of developmental phenotypes and abnormal DNA methylation at imprinted loci...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28317342/genetic-determinants-of-adiponectin-regulation-revealed-by-pregnancy
#14
Marie-France Hivert, Denise M Scholtens, Catherine Allard, Michael Nodzenski, Luigi Bouchard, Diane Brisson, Lynn P Lowe, Ian McDowell, Tim Reddy, Zari Dastani, J Brent Richards, M Geoffrey Hayes, William L Lowe
OBJECTIVE: This study investigated genetic determinants of adiponectin during pregnancy to reveal novel biology of adipocyte regulation. METHODS: A genome-wide association study was conducted in 1,322 pregnant women from the Hyperglycemia and Adverse Pregnancy Outcome Study with adiponectin measured at ∼28 weeks of gestation. Variants reaching P < 5×10(-5) for de novo genotyping in two replication cohorts (Genetics of Glycemic regulation in Gestation and Growth N = 522; ECOGENE-21 N = 174) were selected...
March 20, 2017: Obesity
https://www.readbyqxmd.com/read/28317148/bortezomib-induced-peripheral-neuropathy-a-genome-wide-association-study-on-multiple-myeloma-patients
#15
Chiara Campo, Miguel Inacio da Silva Filho, Niels Weinhold, Seyed Hamidreza Mahmoudpour, Hartmut Goldschmidt, Kari Hemminki, Maximilian Merz, Asta Försti
The proteasome-inhibitor bortezomib was introduced into the treatment of multiple myeloma more than a decade ago. It is clinically beneficial, but peripheral neuropathy (PNP) is a side effect that may limit its use in some patients. To examine the possible genetic predisposing factors to PNP, we performed a genome-wide association study on 646 bortezomib-treated German multiple myeloma patients. Our aim was to identify genetic risk variants associated with the development of PNP as a serious side effect of the treatment...
March 20, 2017: Hematological Oncology
https://www.readbyqxmd.com/read/28317033/returning-genome-sequences-to-research-participants-policy-and-practice
#16
Caroline F Wright, Anna Middleton, Jeffrey C Barrett, Helen V Firth, David R FitzPatrick, Matthew E Hurles, Michael Parker
Despite advances in genomic science stimulating an explosion of literature around returning health-related findings, the possibility of returning entire genome sequences to individual research participants has not been widely considered. Through direct involvement in large-scale translational genomics studies, we have identified a number of logistical challenges that would need to be overcome prior to returning individual genome sequence data, including verifying that the data belong to the requestor and providing appropriate informatics support...
February 24, 2017: Wellcome Open Res
https://www.readbyqxmd.com/read/28316879/a-preliminary-study-of-genetic-variation-in-the-dopaminergic-and-serotonergic-systems-and-genome-wide-additive-genetic-effects-on-depression-severity-and-treatment-response
#17
Rohan H C Palmer, Christopher G Beevers, John E McGeary, Leslie A Brick, Valerie S Knopik
No abstract text is available yet for this article.
January 2017: Clinical Psychological Science
https://www.readbyqxmd.com/read/28316371/znf395-is-an-activator-of-a-subset-of-ifn-stimulated-genes
#18
Linda Schroeder, Christine Herwartz, Darko Jordanovski, Gertrud Steger
Activation of the interferon (IFN) pathway in response to infection with pathogens results in the induction of IFN-stimulated genes (ISGs) including proinflammatory cytokines, which mount the proper antiviral immune response. However, aberrant expression of these genes is pathogenic to the host. In addition to IFN-induced transcription factors non-IFN-regulated factors contribute to the transcriptional control of ISGs. Here, we show by genome wide expression analysis, siRNA-mediated suppression and Doxycycline-induced overexpression that the cellular transcription factor ZNF395 activates a subset of ISGs including the chemokines CXCL10 and CXCL11 in keratinocytes...
2017: Mediators of Inflammation
https://www.readbyqxmd.com/read/28316365/extracting-databases-from-dark-data-with-deepdive
#19
Ce Zhang, Jaeho Shin, Christopher Ré, Michael Cafarella, Feng Niu
DeepDive is a system for extracting relational databases from dark data: the mass of text, tables, and images that are widely collected and stored but which cannot be exploited by standard relational tools. If the information in dark data - scientific papers, Web classified ads, customer service notes, and so on - were instead in a relational database, it would give analysts a massive and valuable new set of "big data." DeepDive is distinctive when compared to previous information extraction systems in its ability to obtain very high precision and recall at reasonable engineering cost; in a number of applications, we have used DeepDive to create databases with accuracy that meets that of human annotators...
June 2016: Proceedings
https://www.readbyqxmd.com/read/28316214/-expression-of-tyrosine-and-threonine-protein-kinase-in-carcinogenic-process-of-colorectal-cancer-and-its-relationship-with-prognosis
#20
X L Zhang, W X Han, Y M Ma, H W Y Baohan, X H Zhao, H Y Wang
Objective: To investigate the expression of TTK (tyrosine and threonine protein kinase) in the process of colorectal cancer (CRC) development and its relationship to prognosis in CRC patients. Methods: Colitis-associated colon cancer model was induced by azoxymethane (AOM) and dextran sulfate sodium (DSS) in C57BL/6 mice. Mice at four different stages of colon cancer development were obtained, named AD1 (inflammation of the recovery), AD2 (mild dysplasia), AD3 (adenoma) and AD4 (adenocarcinoma), as well as negative control (no treatment)...
March 23, 2017: Zhonghua Zhong Liu za Zhi [Chinese Journal of Oncology]
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