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https://www.readbyqxmd.com/read/29792937/a-reliable-targeted-next-generation-sequencing-strategy-for-diagnosis-of-myopathies-and-muscular-dystrophies-especially-for-the-giant-titin-and-nebulin-genes
#1
Reda Zenagui, Delphine Lacourt, Henri Pegeot, Kevin Yauy, Raul Juntas Morales, Corine Theze, François Rivier, Claude Cances, Guilhem Sole, Dimitri Renard, Ulrike Walther-Louvier, Xavier Ferrer-Monasterio, Caroline Espil, Marie-Christine Arné-Bes, Pascal Cintas, Emmanuelle Uro-Coste, Marie-Laure Martin Negrier, Valérie Rigau, Eric Bieth, Cyril Goizet, Mireille Claustres, Michel Koenig, Mireille Cossée
Myopathies and muscular dystrophies (M-MDs) are genetically heterogeneous diseases, with more than 100 identified genes, including the giant and complex titin (TTN) and nebulin (NEB) genes. Next-generation sequencing technology revolutionized M-MD diagnosis and revealed high frequency of TTN and NEB variants. We developed a next-generation sequencing diagnostic strategy targeted on the coding sequences of 135 M-MD genes. Comparison of two targeted capture technologies (SeqCap EZ Choice library capture kit (Roche-Nimblegen) and Nextera Rapid Capture Custom Enrichment kit (Illumina)) and of two whole exome sequencing kits (SureSelect V5 (Agilent) and TruSeq RapidExome capture (Illumina)) revealed best coverage with the SeqCap EZ Choice protocol...
May 21, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29792936/efficient-detection-of-copy-number-mutations-in-pms2-exons-with-close-homologs-detection-of-copy-number-variants-in-3-pms2-exons
#2
Daniel S Herman, Christina Smith, Chang Liu, Cecily P Vaughn, Selvi Palaniappan, Colin C Pritchard, Brian H Shirts
Detection of 3' PMS2 copy number mutations that cause Lynch syndrome is difficult, because of highly homologous pseudogenes. To improve the accuracy and efficiency of clinical screening for these mutations, we developed a new method to analyze standard capture-based, next-generation sequencing data to identify deletions and duplications in PMS2 exons 9 to 15. The approach captures sequence reads using PMS2 targets, maps sequences randomly amongst regions with equal mapping quality, counts reads aligned to homologous exons and introns, and flags read count ratios outside of empirically derived reference ranges...
May 21, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29792514/a-flow-procedure-for-linearization-of-genome-sequence-graphs
#3
David Haussler, Maciej Smuga-Otto, Jordan M Eizenga, Benedict Paten, Adam M Novak, Sergei Nikitin, Maria Zueva, Dmitrii Miagkov
Efforts to incorporate human genetic variation into the reference human genome have converged on the idea of a graph representation of genetic variation within a species, a genome sequence graph. A sequence graph represents a set of individual haploid reference genomes as paths in a single graph. When that set of reference genomes is sufficiently diverse, the sequence graph implicitly contains all frequent human genetic variations, including translocations, inversions, deletions, and insertions. In representing a set of genomes as a sequence graph, one encounters certain challenges...
May 24, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29792392/hemizygous-fabry-disease-associated-with-membranous-nephropathy-a-rare-case-report
#4
Wenyan Zhou, Zhaohui Ni, Minfang Zhang
BACKGROUND: Fabry disease may coexist with various glomerular diseases, including IgA nephropathy, focal segmental glomerulosclerosis, etc. In this study, we report a rare case of Fabry disease associated with membranous nephropathy (MN). CASE PRESENTATION: A 30-year-old man with nephrotic proteinuria, normal renal function, and no other extrarenal manifestations underwent a renal biopsy in February 2017. Light microscopy and immunofluorescence indicated MN (stage 1)...
May 24, 2018: Clinical Nephrology
https://www.readbyqxmd.com/read/29792161/a-website-to-identify-shared-genes-in-saccharomyces-cerevisiae-homozygous-deletion-library-screens
#5
Mark D Temple
BACKGROUND: The homozygous yeast deletion library includes approximately 4800 diploid strains each containing one deleted non-essential gene. Hundreds of publications have arisen through experimentation using this genome-wide biological resource. As part of this work over 677 genesets have been collated from these experiments representing the phenotypic responses of the library to a diverse set of chemical and physical challenges. DESCRIPTION: A website called the Saccharomyces cerevisiae Homozygous Deletion Library Tools (ScHo DeLiTo-96) has been developed with the primary goal of browsing and identifying genes shared between these responsive phenotypes (available at yeastdb...
May 23, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29792160/nextsv-a-meta-caller-for-structural-variants-from-low-coverage-long-read-sequencing-data
#6
Li Fang, Jiang Hu, Depeng Wang, Kai Wang
BACKGROUND: Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively high cost of long-read sequencing, it is unclear what coverage is needed and how to optimally use the aligners and SV callers. RESULTS: In this study, we developed NextSV, a meta-caller to perform SV calling from low coverage long-read sequencing data...
May 23, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29792159/on-the-possibility-of-death-of-new-genes-evidence-from-the-deletion-of-de-novo-micrornas
#7
Guang-An Lu, Yixin Zhao, Zhongqi Liufu, Chung-I Wu
BACKGROUND: New genes are constantly formed, sometimes from non-genic sequences, creating what is referred to as de novo genes. Since the total number of genes remains relatively steady, gene deaths likely balance out new births. In metazoan genomes, microRNAs (miRs) genes, small and non-coding, account for the bulk of functional de novo genes and are particularly suited to the investigation of gene death. RESULTS: In this study, we discover a Drosophila-specific de novo miRNA (mir-977) that may be facing impending death...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29791873/rhoa-rock-signaling-regulates-smooth-muscle-phenotypic-modulation-and-vascular-remodeling-via-the-jnk-pathway-and-vimentin-cytoskeleton
#8
Lian Tang, Fan Dai, Yan Liu, Xiaoqiang Yu, Chao Huang, Yuqin Wang, Wenjuan Yao
The RhoA/ROCK signaling pathway regulates cell morphology, adhesion, proliferation, and migration. In this study, we investigated the regulatory role of RhoA/ROCK signaling on PDGF-BB-mediated smooth muscle phenotypic modulation and vascular remodeling and clarified the molecular mechanisms behind these effects. PDGF-BB treatment induced the activation of RhoA, ROCK, PDGF-Rβ, and the expression of PDGF-Rβ in HA-VSMCs (human aortic vascular smooth muscle cells). PDGF-Rβ inhibition and RhoA suppression blocked PDGF-BB-induced RhoA activation and ROCK induction...
May 20, 2018: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/29791846/myosin-iia-promotes-antibody-responses-by-regulating-b-cell-activation-acquisition-of-antigen-and-proliferation
#9
Robbert Hoogeboom, Elizabeth M Natkanski, Carla R Nowosad, Dessislava Malinova, Rajesh P Menon, Antonio Casal, Pavel Tolar
B cell responses are regulated by antigen acquisition, processing, and presentation to helper T cells. These functions are thought to depend on contractile activity of non-muscle myosin IIa. Here, we show that B cell-specific deletion of the myosin IIa heavy chain reduced the numbers of bone marrow B cell precursors and splenic marginal zone, peritoneal B1b, and germinal center B cells. In addition, myosin IIa-deficient follicular B cells acquired an activated phenotype and were less efficient in chemokinesis and extraction of membrane-presented antigens...
May 22, 2018: Cell Reports
https://www.readbyqxmd.com/read/29791844/regulation-of-pathogenic-t-helper-17-cell-differentiation-by-steroid-receptor-coactivator-3
#10
Kentaro Tanaka, Gustavo J Martinez, Xiaowei Yan, Weiwen Long, Kenji Ichiyama, Xinxin Chi, Byung-Seok Kim, Joseph M Reynolds, Yeonseok Chung, Shinya Tanaka, Lan Liao, Yoichi Nakanishi, Akihiko Yoshimura, Pan Zheng, Xiaohu Wang, Qiang Tian, Jianming Xu, Bert W O'Malley, Chen Dong
T helper 17 (Th17) cell development is programmed by the orphan nuclear receptor RORγt, but the underlying mechanism is not well understood. Nuclear receptor-mediated transcriptional activation depends on coactivators. Here, we show that steroid receptor coactivator-3 (SRC-3) critically regulates Th17 cell differentiation. Reduced incidence of experimental autoimmune encephalitis (EAE) associated with decreased Th17 cell generation in vivo was observed in mice with SRC-3 deletion specifically in T cells...
May 22, 2018: Cell Reports
https://www.readbyqxmd.com/read/29791841/functional-genomic-screening-reveals-core-modulators-of-echinocandin-stress-responses-in-candida-albicans
#11
Tavia Caplan, Elizabeth J Polvi, Jinglin L Xie, Shoshana Buckhalter, Michelle D Leach, Nicole Robbins, Leah E Cowen
Candida albicans is a leading cause of death due to fungal infection. Treatment of systemic candidiasis often relies on echinocandins, which disrupt cell wall synthesis. Resistance is readily acquired via mutations in the drug target gene, FKS1. Both basal tolerance and resistance to echinocandins require cellular stress responses. We performed a systematic analysis of 3,030 C. albicans mutants to define circuitry governing cellular responses to echinocandins. We identified 16 genes for which deletion or transcriptional repression enhanced echinocandin susceptibility, including components of the Pkc1-MAPK signaling cascade...
May 22, 2018: Cell Reports
https://www.readbyqxmd.com/read/29791811/the-putative-transient-receptor-potential-trp-channel-protein-encoded-by-the-orf19-4805-is-involved-in-cation-sensitivity-antifungal-tolerance-and-filamentation-in-candida-albicans
#12
Linghuo Jiang, Yi Yang
The ancient family of cation channels, transient receptor potential (TRP) channels, is highly conserved in eukaryotes and plays various physiological functions from sensation of ion homeostasis to reception of pain and vision. Calcium-permeable TRP channels have been identified from the plant Arabidopsis thaliana (AtCsc1) and the budding yeast Saccharomyces cerevisiae (ScCsc1), respectively. In this study, we have characterized the functions of the Csc1 homolog, the orf19.4805, in Candida albicans. The orf19...
May 23, 2018: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/29791617/speech-perception-task-with-pseudowords
#13
Mariana Martins Appezzato, Maria Mercedes Saraiva Hackerott, Clara Regina Brandão de Avila
Purpose Prepare a list of pseudowords in Brazilian Portuguese to assess the auditory discrimination ability of schoolchildren and investigate the internal consistency of test items and the effect of school grade on discrimination performance. Methods Study participants were 60 schoolchildren (60% female) enrolled in the 3rd (n=14), 4th (n=24) and 5th (n=22) grades of an elementary school in the city of Sao Paulo, Brazil, aged between eight years and two months and 11 years and eight months (99 to 136 months; mean=120...
2018: CoDAS
https://www.readbyqxmd.com/read/29791178/-rare-combination-of-turner-syndrome-and-congenital-adrenal-hyperplasia-with-21-hydroxylase-deficiency-case-report
#14
Ivana Ságová, Matej Stančík, Dušan Pavai, Daniela Kantárová, Anton Vaňuga, Peter Vaňuga
Combination of Turner syndrome (TS) and classic congenital adrenal hyperplasia (CAH) is rare. Globally, the incidence of CAH, autosomal recessive disorder caused by enzyme defect of steroidogenic pathway, is very low (1 : 10 000-16 000). 90 % of CAH cases are caused by 21-hydroxylase gene mutation (CYP21A2). Globally, the incidencie of Turner syndrome reaches 1 : 2 500. Phenotypically, females with TS may render wide spectrum of clinical features. Dominant symptoms are lowered terminal height and gonadal dysgenesia, ultimately leading to absence of puberty and infertility...
2018: Vnitr̆ní Lékar̆ství
https://www.readbyqxmd.com/read/29790873/diversity-of-genetic-events-associated-with-mlh1-promoter-methylation-in-lynch-syndrome-families-with-heritable-constitutional-epimutation
#15
Julie Leclerc, Cathy Flament, Tonio Lovecchio, Lucie Delattre, Emilie Ait Yahya, Stéphanie Baert-Desurmont, Nelly Burnichon, Myriam Bronner, Odile Cabaret, Sophie Lejeune, Rosine Guimbaud, Gilles Morin, Jacques Mauillon, Philippe Jonveaux, Pierre Laurent-Puig, Thierry Frébourg, Nicole Porchet, Marie-Pierre Buisine
PurposeConstitutional epimutations are an alternative to genetic mutations in the etiology of genetic diseases. Some of these epimutations, termed secondary, correspond to the epigenetic effects of cis-acting genetic defects transmitted to the offspring following a Mendelian inheritance pattern. In Lynch syndrome, a few families with such apparently heritable MLH1 epimutations have been reported so far.MethodsWe designed a long-range polymerase chain reaction next-generation sequencing strategy to screen MLH1 entire gene and applied it to 4 French families with heritable epimutations and 10 additional patients with no proven transmission of their epimutations...
April 12, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29790428/multi-ethnic-sult1a1-copy-number-profiling-with-multiplex-ligation-dependent-probe-amplification
#16
Raymon Vijzelaar, Mariana R Botton, Lisette Stolk, Suparna Martis, Robert J Desnick, Stuart A Scott
AIM: To develop a SULT1A1 multiplex ligation-dependent probe amplification assay and to investigate multi-ethnic copy number variant frequencies. METHODS: A novel multiplex ligation-dependent probe amplification assay was developed and tested on 472 African-American, Asian, Caucasian, Hispanic and Ashkenazi Jewish individuals. RESULTS: The frequencies of atypical total copy number (i.e., greater or less than two) were 38.7% for Hispanics, 38...
May 23, 2018: Pharmacogenomics
https://www.readbyqxmd.com/read/29790390/collecting-duct-principal-but-not-intercalated-cell-prorenin-receptor-regulates-renal-sodium-and-water-excretion
#17
Nirupama Ramkumar, Deborah Stuart, Elena Mironova, Nikita Abraham, Yang Gao, Shuping Wang, Jayalakshmi Lakshmipathi, James D Stockand, Donald E Kohan
The collecting duct is the predominant nephron site of prorenin and prorenin receptor (PRR) expression. We previously demonstrated that the collecting duct PRR regulates epithelial Na+ channel (ENaC) activity and water transport; however, which cell type is involved remains unclear. Herein, we examined the effects of principal cell (PC) or intercalated cell (IC) PRR deletion on renal Na+ and water handling. PC or IC PRR KO mice were obtained by crossing floxed PRR mice with mice harboring Cre recombinase under the control of the AQP2 or B-1 subunit of the H+ ATPase promoters, respectively...
May 23, 2018: American Journal of Physiology. Renal Physiology
https://www.readbyqxmd.com/read/29790350/glutaredoxin-deletion-shortens-chronological-life-span-in-saccharomyces-cerevisiae-via-ros-mediated-ras-pka-activation
#18
Yan Liu, Fan Yang, Siying Li, Junbiao Dai, Haiteng Deng
Glutaredoxins (GRXs), small redox proteins that use reduced glutathione (GSH) as an electron donor, are key components of the cellular antioxidant system. In this study, we used Saccharomyces cerevisiae as a model system to investigate the effects of GRX deletion on yeast chronological life span (CLS). Deletion of either Grx1 or Grx2 shortened yeast CLS. Quantitative proteomics revealed that GRX deletion decreased expression of stress-response proteins, leading to increased cellular reactive oxygen species (ROS) accumulation and, subsequently, intracellular acidification...
May 23, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29789941/new-variants-of-porcine-epidemic-diarrhea-virus-with-large-deletions-in-the-spike-protein-identified-in-the-united-states-2016-2017
#19
Yunfang Su, Yixuan Hou, Melanie Prarat, Yan Zhang, Qiuhong Wang
Four types of porcine epidemic diarrhea virus (PEDV) variants with a large deletion in the spike protein were detected, together with the original US PEDV, from pig fecal and oral fluid samples collected during 2016-2017 in the US. Two of the variants are similar to those identified in Japan: one contains a 194-aa deletion, the same as PEDV variant TTR-2/JPN/2014, while the other contains a 204-aa deletion, the same as PEDV variant JKa-292/CS1de204. Two new S1 NTD-del PEDV variants were found: one contains a 201-aa deletion located at residues 30-230 and the other contains a 202-aa deletion located at residues 24-225 of the S protein...
May 22, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29789886/gcttca-as-a-novel-motif-for-regulating-mesocarp-specific-expression-of-the-oil-palm-elaeis-guineensis-jacq-stearoyl-acp-desaturase-gene
#20
Farah Hanan Abu Hanifiah, Siti Nor Akmar Abdullah, Ashida Othman, Noor Azmi Shaharuddin, Halimi Mohd Saud, Hasnul Abdul Hakim Hasnulhadi, Umaiyal Munusamy
TAAAAT and a novel motif, GCTTCA found in the oil palm stearoyl-ACP desaturase (SAD1) promoter are involved in regulating mesocarp-specific expression. Two key fatty acid biosynthetic genes, stearoyl-ACP desaturase (SAD1), and acyl-carrier protein (ACP3) in Elaeis guineensis (oil palm) showed high level of expression during the period of oil synthesis in the mesocarp [12-19 weeks after anthesis (w.a.a.)] and kernel (12-15 w.a.a.). Both genes are expressed in spear leaves at much lower levels and the expression increased by 1...
May 22, 2018: Plant Cell Reports
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