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https://www.readbyqxmd.com/read/28545234/validation-of-splicing-events-in-transcriptome-sequencing-data
#1
Wolfgang Kaisers, Johannes Ptok, Holger Schwender, Heiner Schaal
Genomic alignments of sequenced cellular messenger RNA contain gapped alignments which are interpreted as consequence of intron removal. The resulting gap-sites, genomic locations of alignment gaps, are landmarks representing potential splice-sites. As alignment algorithms report gap-sites with a considerable false discovery rate, validations are required. We describe two quality scores, gap quality score (gqs) and weighted gap information score (wgis), developed for validation of putative splicing events: While gqs solely relies on alignment data wgis additionally considers information from the genomic sequence...
May 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28545146/transcriptomics-technologies
#2
Rohan Lowe, Neil Shirley, Mark Bleackley, Stephen Dolan, Thomas Shafee
Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst noncoding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. The first attempts to study the whole transcriptome began in the early 1990s, and technological advances since the late 1990s have made transcriptomics a widespread discipline...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28544663/from-song-dialects-to-speciation-in-white-crowned-sparrows
#3
David P L Toews
The behavioural signals used in mate selection are a key component in the evolution of premating isolating barriers and, subsequently, the formation of new species. The importance of mating signals has a long tradition of study in songbirds, where many species differ in their song characteristics. In oscine songbirds, individual birds usually learn their songs from a tutor. Mistakes during learning can help generate geographic dialects, akin to those within human language groups. In songbirds, dialect differences can often be substantial and there is an intuitive connection between the evolution of song amongst populations at a small scale, and the more substantive song differences between bird species and presumably used in species recognition...
June 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28544650/diverse-application-of-mri-for-mouse-phenotyping
#4
REVIEW
Yijen L Wu, Cecilia W Lo
Small animal models, particularly mouse models, of human diseases are becoming an indispensable tool for biomedical research. Studies in animal models have provided important insights into the etiology of diseases and accelerated the development of therapeutic strategies. Detailed phenotypic characterization is essential, both for the development of such animal models and mechanistic studies into disease pathogenesis and testing the efficacy of experimental therapeutics. MRI is a versatile and noninvasive imaging modality with excellent penetration depth, tissue coverage, and soft tissue contrast...
May 22, 2017: Birth Defects Res
https://www.readbyqxmd.com/read/28544620/phenotyping-cardiac-and-structural-birth-defects-in-fetal-and-newborn-mice
#5
REVIEW
Xiaoqin Liu, Andrew J Kim, William Reynolds, Yijen Wu, Cecilia W Lo
Mouse models are invaluable for investigating the developmental etiology and molecular pathogenesis of structural birth defects. While this has been deployed for studying a wide spectrum of birth defects, mice are particularly valuable for modeling congenital heart disease, given they have the same four-chamber cardiac anatomy as in humans. We have developed the use of noninvasive fetal ultrasound together with micro-computed tomography (micro-CT) imaging for high throughput phenotyping of mice for congenital heart defects (CHD) and other developmental anomalies...
May 22, 2017: Birth Defects Res
https://www.readbyqxmd.com/read/28544272/ensemble-variant-interpretation-methods-to-predict-enzyme-activity-and-assign-pathogenicity-in-the-cagi4-naglu-human-n-acetyl-glucosaminidase-and-ube2i-human-sumo-ligase-challenges
#6
Yizhou Yin, Kunal Kundu, Lipika R Pal, John Moult
CAGI (Critical Assessment of Genome Interpretation) conducts community experiments to determine the state of the art in relating genotype to phenotype. Here we report results obtained using newly-developed ensemble methods to address two CAGI4 challenges: enzyme activity for population missense variants found in NAGLU (Human N-acetyl-glucosaminidase) and random missense mutations in Human UBE2I (Human SUMO E2 ligase), assayed in a high throughput competitive yeast complementation procedure. The ensemble methods are effective, ranked 2(nd) for SUMO-ligase and 3(rd) for NAGLU, according to the CAGI independent assessors...
May 24, 2017: Human Mutation
https://www.readbyqxmd.com/read/28544218/genome-wide-mediation-analysis-of-psychiatric-and-cognitive-traits-through-imaging-phenotypes
#7
Xuan Bi, Liuqing Yang, Tengfei Li, Baisong Wang, Hongtu Zhu, Heping Zhang
Heritability is well documented for psychiatric disorders and cognitive abilities which are, however, complex, involving both genetic and environmental factors. Hence, it remains challenging to discover which and how genetic variations contribute to such complex traits. In this article, they propose to use mediation analysis to bridge this gap, where neuroimaging phenotypes were utilized as intermediate variables. The Philadelphia Neurodevelopmental Cohort was investigated using genome-wide association studies (GWAS) and mediation analyses...
May 22, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28543951/determination-of-genetic-relatedness-from-low-coverage-human-genome-sequences-using-pedigree-simulations
#8
Michael D Martin, Flora Jay, Sergi Castellano, Montgomery Slatkin
We develop and evaluate methods for inferring relatedness among individuals from low-coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate, and the presence of contamination from present-day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present-day contamination, and sequencing error...
May 25, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28542881/genetic-susceptibility-in-cervical-cancer-from-bench-to-bedside
#9
Afsane Bahrami, Malihe Hasanzadeh, Soodabeh Shahidsales, Marjaneh Farazestanian, Seyed Mahdi Hassanian, Mehrdad Ahmadi, Mina Maftouh, Masoumeh Gharib, Zohre Yousefi, Sima Kadkhodayan, Gordon A Ferns, Amir Avan
Cervical cancer (CC) is the third most common malignancy in women globally, and persistent infection with the oncogenic human papillomaviruses (HPV) is recognized as the major risk factor. The pathogenesis of CC relies on the interplay between the tumorigenic properties of the HPV and host factors. Host-related genetic factors, including the presence of susceptibility loci for cervix tumor is substantial importance. Preclinical and genome-wide association studies (GWAS) have reported the associations of genetic variations in several susceptibility loci for the development of cervical cancer...
May 19, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28542603/a-conformational-switch-high-throughput-screening-assay-and-allosteric-inhibition-of-the-flavivirus-ns2b-ns3-protease
#10
Matthew Brecher, Zhong Li, Binbin Liu, Jing Zhang, Cheri A Koetzner, Adham Alifarag, Susan A Jones, Qishan Lin, Laura D Kramer, Hongmin Li
The flavivirus genome encodes a single polyprotein precursor requiring multiple cleavages by host and viral proteases in order to produce the individual proteins that constitute an infectious virion. Previous studies have revealed that the NS2B cofactor of the viral NS2B-NS3 heterocomplex protease displays a conformational dynamic between active and inactive states. Here, we developed a conformational switch assay based on split luciferase complementation (SLC) to monitor the conformational change of NS2B and to characterize candidate allosteric inhibitors...
May 25, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28542600/snp-in-human-arhgef3-promoter-is-associated-with-dnase-hypersensitivity-transcript-level-and-platelet-function-and-arhgef3-ko-mice-have-increased-mean-platelet-volume
#11
Siying Zou, Alexandra M Teixeira, Myrto Kostadima, William J Astle, Aparna Radhakrishnan, Lukas Mikolaj Simon, Lucy Truman, Jennifer S Fang, John Hwa, Ping-Xia Zhang, Pim van der Harst, Paul F Bray, Willem H Ouwehand, Mattia Frontini, Diane S Krause
Genome-wide association studies have identified a genetic variant at 3p14.3 (SNP rs1354034) that strongly associates with platelet number and mean platelet volume in humans. While originally proposed to be intronic, analysis of mRNA expression in primary human hematopoietic subpopulations reveals that this SNP is located directly upstream of the predominantly expressed ARHGEF3 isoform in megakaryocytes (MK). We found that ARHGEF3, which encodes a Rho guanine exchange factor, is dramatically upregulated during both human and murine MK maturation...
2017: PloS One
https://www.readbyqxmd.com/read/28542550/a-spatio-temporal-assessment-of-simian-human-immunodeficiency-virus-shiv-evolution-reveals-a-highly-dynamic-process-within-the-host
#12
Alison F Feder, Christopher Kline, Patricia Polacino, Mackenzie Cottrell, Angela D M Kashuba, Brandon F Keele, Shiu-Lok Hu, Dmitri A Petrov, Pleuni S Pennings, Zandrea Ambrose
The process by which drug-resistant HIV-1 arises and spreads spatially within an infected individual is poorly understood. Studies have found variable results relating how HIV-1 in the blood differs from virus sampled in tissues, offering conflicting findings about whether HIV-1 throughout the body is homogeneously distributed. However, most of these studies sample only two compartments and few have data from multiple time points. To directly measure how drug resistance spreads within a host and to assess how spatial structure impacts its emergence, we examined serial sequences from four macaques infected with RT-SHIVmne027, a simian immunodeficiency virus encoding HIV-1 reverse transcriptase (RT), and treated with RT inhibitors...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28542463/insights-into-reston-virus-spillovers-and-adaption-from-virus-whole-genome-sequences
#13
César G Albariño, Lisa Wiggleton Guerrero, Harley M Jenks, Ayan K Chakrabarti, Thomas G Ksiazek, Pierre E Rollin, Stuart T Nichol
Reston virus (family Filoviridae) is unique among the viruses of the Ebolavirus genus in that it is considered non-pathogenic in humans, in contrast to the other members which are highly virulent. The virus has however, been associated with several outbreaks of highly lethal hemorrhagic fever in non-human primates (NHPs), specifically cynomolgus monkeys (Macaca fascicularis) originating in the Philippines. In addition, Reston virus has been isolated from domestic pigs in the Philippines. To better understand virus spillover events and potential adaption to new hosts, the whole genome sequences of representative Reston virus isolates were obtained using a next generation sequencing (NGS) approach and comparative genomic analysis and virus fitness analyses were performed...
2017: PloS One
https://www.readbyqxmd.com/read/28542390/analysis-of-early-mesothelial-cell-responses-to-staphylococcus-epidermidis-isolated-from-patients-with-peritoneal-dialysis-associated-peritonitis
#14
Amanda L McGuire, Kieran T Mulroney, Christine F Carson, Ramesh Ram, Grant Morahan, Aron Chakera
The major complication of peritoneal dialysis (PD) is the development of peritonitis, an infection within the abdominal cavity, primarily caused by bacteria. PD peritonitis is associated with significant morbidity, mortality and health care costs. Staphylococcus epidermidis is the most frequently isolated cause of PD-associated peritonitis. Mesothelial cells are integral to the host response to peritonitis, and subsequent clinical outcomes, yet the effects of infection on mesothelial cells are not well characterised...
2017: PloS One
https://www.readbyqxmd.com/read/28542388/targeted-dna-methylation-in-pericentromeres-with-genome-editing-based-artificial-dna-methyltransferase
#15
Taiga Yamazaki, Yu Hatano, Tetsuya Handa, Sakiko Kato, Kensuke Hoida, Rui Yamamura, Takashi Fukuyama, Takayuki Uematsu, Noritada Kobayashi, Hiroshi Kimura, Kazuo Yamagata
To study the impact of epigenetic changes on biological functions, the ability to manipulate the epigenetic status of certain genomic regions artificially could be an indispensable technology. "Epigenome editing" techniques have gradually emerged that apply TALE or CRISPR/Cas9 technologies with various effector domains isolated from epigenetic code writers or erasers such as DNA methyltransferase, 5-methylcytosine oxidase, and histone modification enzymes. Here we demonstrate that a TALE recognizing a major satellite, consisting of a repeated sequence in pericentromeres, could be fused with the bacterial CpG methyltransferase, SssI...
2017: PloS One
https://www.readbyqxmd.com/read/28542387/lncrna-af113014-promotes-the-expression-of-egr2-by-interaction-with-mir-20a-to-inhibit-proliferation-of-hepatocellular-carcinoma-cells
#16
Tao Zeng, Dan Wang, Juan Chen, Yuanyuan Tian, Xuefei Cai, Hong Peng, Liying Zhu, Ailong Huang, Hua Tang
Long non-coding RNAs (lncRNAs), tentatively identified as non-protein coding RNA, are transcripts more than 200nt in length and accounting for 98% of the whole genome of human being. Accumulating evidence showed aberrant expressions of lncRNAs are strongly correlated to the development of cancers. In this study, AF113014 is a new lncRNA identified from Microarray. We found AF113014 is differentially expressed between HCC cell lines and normal hepatocytes. Functionally, AF113014 inhibited proliferation of HCC cells both in vitro and in vivo, whereas the opposite effect was observed when AF113014 knockdown...
2017: PloS One
https://www.readbyqxmd.com/read/28542306/gene-signature-associated-with-benign-neurofibroma-transformation-to-malignant-peripheral-nerve-sheath-tumors
#17
Marta Martínez, Carlos O S Sorzano, Alberto Pascual-Montano, Jose M Carazo
Benign neurofibromas, the main phenotypic manifestations of the rare neurological disorder neurofibromatosis type 1, degenerate to malignant tumors associated to poor prognosis in about 10% of patients. Despite efforts in the field of (epi)genomics, the lack of prognostic biomarkers with which to predict disease evolution frustrates the adoption of appropriate early therapeutic measures. To identify potential biomarkers of malignant neurofibroma transformation, we integrated four human experimental studies and one for mouse, using a gene score-based meta-analysis method, from which we obtained a score-ranked signature of 579 genes...
2017: PloS One
https://www.readbyqxmd.com/read/28542303/differential-dna-methylation-of-msi2-and-its-correlation-with-diabetic-traits
#18
Jae-Pil Jeon, In-Uk Koh, Nak-Hyun Choi, Bong-Jo Kim, Bok-Ghee Han, Suman Lee
Differential DNA methylation with hyperglycemia is significantly associated with Type 2 Diabetes (T2D). Longtime extended exposure to high blood glucose levels can affect the epigenetic signatures in all organs. However, the relevance of the differential DNA methylation changes with hyperglycemia in blood with pancreatic islets remains unclear. We investigated differential DNA methylation in relation to glucose homeostasis based on the Oral Glucose Tolerance Test (OGTT) in a population-based cohort. We found a total of 382 differential methylation sites from blood DNA in hyperglycemia and type 2 diabetes subgroups using a longitudinal and cross-sectional approach...
2017: PloS One
https://www.readbyqxmd.com/read/28542292/development-of-a-versatile-oncolytic-virus-platform-for-local-intra-tumoural-expression-of-therapeutic-transgenes
#19
Nalini Marino, Sam Illingworth, Prithvi Kodialbail, Ashvin Patel, Hugo Calderon, Rochelle Lear, Kerry D Fisher, Brian R Champion, Alice C N Brown
Oncolytic viruses which infect and kill tumour cells can also be genetically modified to express therapeutic genes that augment their anti-cancer activities. Modifying oncolytic viruses to produce effective cancer therapies is challenging as encoding transgenes often attenuates virus activity or prevents systemic delivery in patients due to the risk of off-target expression of transgenes in healthy tissues. To overcome these issues we aimed to generate a readily modifiable virus platform using the oncolytic adenovirus, enadenotucirev...
2017: PloS One
https://www.readbyqxmd.com/read/28542229/thermodynamic-framework-to-assess-low-abundance-dna-mutation-detection-by-hybridization
#20
Hanny Willems, An Jacobs, Wahyu Wijaya Hadiwikarta, Tom Venken, Dirk Valkenborg, Nadine Van Roy, Jo Vandesompele, Jef Hooyberghs
The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform...
2017: PloS One
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