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https://www.readbyqxmd.com/read/27933714/development-of-chemical-tools-to-monitor-and-control-isoaspartyl-peptide-methyltransferase-activity
#1
Yusuke Kimura, Toru Komatsu, Kouichi Yanagi, Kenjiro Hanaoka, Tasuku Ueno, Takuya Terai, Hirotatsu Kojima, Takayoshi Okabe, Tetsuo Nagano, Yasuteru Urano
We have established a coupled assay system targeting protein l-isoaspartyl methyltransferase (PIMT), a key enzyme in the metabolism of isoaspartyl peptides and proteins. The system utilizes a fluorogenic peptide probe containing an isoaspartyl residue at the P1' position of the caspase-3 recognition sequence. Following PIMT-catalyzed methyl transfer reaction, the methylated probe is specifically cleaved by caspase-3 to give fluorescence activation. High-throughput screening of our chemical library with this assay system identified PIMT inhibitors that may be useful as leads in the design of chemical probes for controlling PIMT activity...
December 9, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27933661/mutations-in-the-neb-gene-cause-fetal-akinesia-arthrogryposis-multiplex-congenita
#2
Michal Feingold-Zadok, David Chitayat, Karen Chong, Marie Injeyan, Patrick Shannon, Daphne Chapmann, Ron Maymon, Nir Pillar, Orit Reish
OBJECTIVE: We studied a series of patients with fetal akinesia deformation sequence (FADS)/arthrogryposis multiplex congenita (AMC), with nemaline bodies on muscle specimens, that revealed mutations in the NEB gene. METHOD: We pathologically assessed seven cases from three families, who presented with AMC/FADS. Targeted genetic analysis for Ashkenazi Jewish (AJ) mutation (in relevant patients) was followed by next generation sequencing and Multiplex Ligation-dependent Probe Amplification...
December 9, 2016: Prenatal Diagnosis
https://www.readbyqxmd.com/read/27933533/systems-genetics-as-a-tool-to-identify-master-genetic-regulators-in-complex-disease
#3
Aida Moreno-Moral, Francesco Pesce, Jacques Behmoaras, Enrico Petretto
Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933525/expression-qtls-mapping-and-analysis-a-bayesian-perspective
#4
Martha Imprialou, Enrico Petretto, Leonardo Bottolo
The aim of expression Quantitative Trait Locus (eQTL) mapping is the identification of DNA sequence variants that explain variation in gene expression. Given the recent yield of trait-associated genetic variants identified by large-scale genome-wide association analyses (GWAS), eQTL mapping has become a useful tool to understand the functional context where these variants operate and eventually narrow down functional gene targets for disease. Despite its extensive application to complex (polygenic) traits and disease, the majority of eQTL studies still rely on univariate data modeling strategies, i...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933313/genetic-engineering-of-chimeric-antigen-receptors-using-lamprey-derived-variable-lymphocyte-receptors
#5
Robert Moot, Sunil S Raikar, Lauren Fleischer, Melissa Querrey, Daniel E Tylawsky, Hirotomo Nakahara, Christopher B Doering, H Trent Spencer
Chimeric antigen receptors (CARs) are used to redirect effector cell specificity to selected cell surface antigens. Using CARs, antitumor activity can be initiated in patients with no prior tumor specific immunity. Although CARs have shown promising clinical results, the technology remains limited by the availability of specific cognate cell target antigens. To increase the repertoire of targetable tumor cell antigens we utilized the immune system of the sea lamprey to generate directed variable lymphocyte receptors (VLRs)...
2016: Molecular Therapy Oncolytics
https://www.readbyqxmd.com/read/27933214/integrating-next-generation-sequencing-into-clinical-oncology-strategies-promises-and-pitfalls
#6
REVIEW
Peter Horak, Stefan Fröhling, Hanno Glimm
We live in an era of genomic medicine. The past five years brought about many significant achievements in the field of cancer genetics, driven by rapidly evolving technologies and plummeting costs of next-generation sequencing (NGS). The official completion of the Cancer Genome Project in 2014 led many to envision the clinical implementation of cancer genomic data as the next logical step in cancer therapy. Stemming from this vision, the term 'precision oncology' was coined to illustrate the novelty of this individualised approach...
2016: ESMO Open
https://www.readbyqxmd.com/read/27933110/profiling-lung-adenocarcinoma-by-liquid-biopsy-can-one-size-fit-all
#7
Harry W Clifford, Amy P Cassidy, Courtney Vaughn, Evaline S Tsai, Bianka Seres, Nirmesh Patel, Hannah L O'Neill, Emil Hewage, John W Cassidy
BACKGROUND: Cancer is first and foremost a disease of the genome. Specific genetic signatures within a tumour are prognostic of disease outcome, reflect subclonal architecture and intratumour heterogeneity, inform treatment choices and predict the emergence of resistance to targeted therapies. Minimally invasive liquid biopsies can give temporal resolution to a tumour's genetic profile and allow the monitoring of treatment response through levels of circulating tumour DNA (ctDNA). However, the detection of ctDNA in repeated liquid biopsies is currently limited by economic and time constraints associated with targeted sequencing...
2016: Cancer Nanotechnology
https://www.readbyqxmd.com/read/27933100/genome-and-methylome-of-the-oleaginous-diatom-cyclotella-cryptica-reveal-genetic-flexibility-toward-a-high-lipid-phenotype
#8
Jesse C Traller, Shawn J Cokus, David A Lopez, Olga Gaidarenko, Sarah R Smith, John P McCrow, Sean D Gallaher, Sheila Podell, Michael Thompson, Orna Cook, Marco Morselli, Artur Jaroszewicz, Eric E Allen, Andrew E Allen, Sabeeha S Merchant, Matteo Pellegrini, Mark Hildebrand
BACKGROUND: Improvement in the performance of eukaryotic microalgae for biofuel and bioproduct production is largely dependent on characterization of metabolic mechanisms within the cell. The marine diatom Cyclotella cryptica, which was originally identified in the Aquatic Species Program, is a promising strain of microalgae for large-scale production of biofuel and bioproducts, such as omega-3 fatty acids. RESULTS: We sequenced the nuclear genome and methylome of this oleaginous diatom to identify the genetic traits that enable substantial accumulation of triacylglycerol...
2016: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/27933097/molecular-mechanisms-of-hpv-mediated-neoplastic-progression
#9
REVIEW
Rashmirani Senapati, Nihar Nalini Senapati, Bhagirathi Dwibedi
Human Papillomavirus is the major etiological agent in the development of cervical cancer but not a sufficient cause. Despite significant research, the underlying mechanisms of progression from a low-grade squamous intraepithelial lesion to high grade squamous intraepithelial lesion are yet to be understood. Deregulation of viral gene expression and host genomic instability play a central role in virus-mediated carcinogenesis. Key events such as viral integration and epigenetic modifications may lead to the deregulation of viral and host gene expression...
2016: Infectious Agents and Cancer
https://www.readbyqxmd.com/read/27933087/revisiting-vitis-vinifera-subtilase-gene-family-a-possible-role-in-grapevine-resistance-against-plasmopara-viticola
#10
Joana Figueiredo, Gonçalo J Costa, Marisa Maia, Octávio S Paulo, Rui Malhó, Marta Sousa Silva, Andreia Figueiredo
Subtilisin-like proteases, also known as subtilases, are a very diverse family of serine peptidases present in many organisms. In grapevine, there are hints of the involvement of subtilases in defense mechanisms, but their role is not yet understood. The first characterization of the subtilase gene family was performed in 2014. However, simultaneously, the grapevine genome was re-annotated and several sequences were re-annotated or retrieved. We have performed a re-characterization of this family in grapevine and identified 82 genes coding for 97 putative proteins, as result of alternative splicing...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27933051/short-interfering-rna-inhibits-rift-valley-fever-virus-replication-and-degradation-of-protein-kinase-r-in-human-cells
#11
Bonto Faburay, Juergen A Richt
Rift Valley fever virus (RVFV) is a mosquito-borne zoonotic pathogen causing severe outbreaks in humans and livestock in sub-Saharan Africa and the Arabian Peninsula. Human infections are characterized by fever, sometimes leading to encephalitis, retinitis, hemorrhagic fever, and occasionally death. There are currently no fully licensed vaccines or effective therapies for human use. Gene silencing mediated by double-stranded short interfering RNA (siRNA) is a sequence-specific, highly conserved mechanism in eukaryotes, which serves as an antiviral defense mechanism...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27933049/high-diversity-of-genogroup-i-picobirnaviruses-in-mammals
#12
Patrick C Y Woo, Jade L L Teng, Ru Bai, Annette Y P Wong, Paolo Martelli, Suk-Wai Hui, Alan K L Tsang, Candy C Y Lau, Syed S Ahmed, Cyril C Y Yip, Garnet K Y Choi, Kenneth S M Li, Carol S F Lam, Susanna K P Lau, Kwok-Yung Yuen
In a molecular epidemiology study using 791 fecal samples collected from different terrestrial and marine mammals in Hong Kong, genogroup I picobirnaviruses (PBVs) were positive by RT-PCR targeting the partial RdRp gene in specimens from five cattle, six monkeys, 17 horses, nine pigs, one rabbit, one dog, and 12 California sea lions, with 11, 9, 23, 17, 1, 1, and 15 sequence types in the positive specimens from the corresponding animals, respectively. Phylogenetic analysis showed that the PBV sequences from each kind of animal were widely distributed in the whole tree with high diversity, sharing 47...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27933047/diazotroph-diversity-in-the-sea-ice-melt-ponds-and-surface-waters-of-the-eurasian-basin-of-the-central-arctic-ocean
#13
Mar Fernández-Méndez, Kendra A Turk-Kubo, Pier L Buttigieg, Josephine Z Rapp, Thomas Krumpen, Jonathan P Zehr, Antje Boetius
The Eurasian basin of the Central Arctic Ocean is nitrogen limited, but little is known about the presence and role of nitrogen-fixing bacteria. Recent studies have indicated the occurrence of diazotrophs in Arctic coastal waters potentially of riverine origin. Here, we investigated the presence of diazotrophs in ice and surface waters of the Central Arctic Ocean in the summer of 2012. We identified diverse communities of putative diazotrophs through targeted analysis of the nifH gene, which encodes the iron protein of the nitrogenase enzyme...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27933036/functional-analysis-of-the-nitrogen-metabolite-repression-regulator-gene-nmra-in-aspergillus-flavus
#14
Xiaoyun Han, Mengguang Qiu, Bin Wang, Wen-Bing Yin, Xinyi Nie, Qiuping Qin, Silin Ren, Kunlong Yang, Feng Zhang, Zhenhong Zhuang, Shihua Wang
In Aspergillus nidulans, the nitrogen metabolite repression (NMR) regulator NmrA plays a major role in regulating the activity of the GATA transcription factor AreA during nitrogen metabolism. However, the function of nmrA in A. flavus has not been previously studied. Here, we report the identification and functional analysis of nmrA in A. flavus. Our work showed that the amino acid sequences of NmrA are highly conserved among Aspergillus species and that A. flavus NmrA protein contains a canonical Rossmann fold motif...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27933016/task-irrelevant-expectation-violations-in-sequential-manual-actions-evidence-for-a-check-after-surprise-mode-of-visual-attention-and-eye-hand-decoupling
#15
Rebecca M Foerster
When performing sequential manual actions (e.g., cooking), visual information is prioritized according to the task determining where and when to attend, look, and act. In well-practiced sequential actions, long-term memory (LTM)-based expectations specify which action targets might be found where and when. We have previously demonstrated (Foerster and Schneider, 2015b) that violations of such expectations that are task-relevant (e.g., target location change) cause a regression from a memory-based mode of attentional selection to visual search...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27932582/translational-safety-genetics-leveraging-genetic-variation-for-enhanced-safety-assessment
#16
Priyasma Bhoumik, Alberto Del Rio-Espinola, Florian Hahne, Jonathan Moggs, Olivier Grenet
The emerging field of translational safety genetics is providing new opportunities to enhance drug discovery and development. Genetic variation in therapeutic drug targets, off-target interactors and relevant drug metabolism/disposition pathways can contribute to diverse drug pharmacologic and toxicologic responses between different animal species, strains and geographic origins. Recent advances in the sequencing of rodent, canine, nonhuman primate, and minipig genomes have dramatically improved the ability to select the most appropriate animal species for preclinical drug toxicity studies based on genotypic characterization of drug targets/pathways and drug metabolism and/or disposition, thus avoiding inconclusive or misleading animal studies, consistent with the principles of the 3Rs (replacement, reduction and refinement)...
December 8, 2016: Toxicologic Pathology
https://www.readbyqxmd.com/read/27932494/loss-of-a-doublecortin-dcx-domain-protein-causes-structural-defects-in-a-tubulin-based-organelle-of-toxoplasma-gondii-and-impairs-host-cell-invasion
#17
Eiji Nagayasu, Yu-Chen Hwang, Jun Liu, John M Murray, Ke Hu
The ∼6000 species in phylum Apicomplexa are single-celled obligate intracellular parasites. Their defining characteristic is the "apical complex", membranous and cytoskeletal elements at the apical end of the cell that participate in host-cell invasion. The apical complex of Toxoplasma gondii and some other apicomplexans includes a cone-shaped assembly, the "conoid", which (in T. gondii) comprises 14 spirally arranged fibers that are non-tubular polymers of tubulin. The tubulin dimers of the conoid fibers make canonical microtubules elsewhere in the same cell, suggesting that non-tubulin protein dictates their special arrangement in the conoid fibers...
December 8, 2016: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/27932423/integrated-genomic-analysis-of-survival-outliers-in-glioblastoma
#18
Sen Peng, Harshil Dhurv, Brock Armstrong, Bodour Salhia, Christophe Legendre, Jeffrey Kiefer, Julianna Parks, Selene Virk, Andrew E Sloan, Quinn T Ostrom, Jill S Barnholtz-Sloan, Nhan L Tran, Michael E Berens
BACKGROUND: To elucidate molecular features associated with disproportionate survival of glioblastoma (GB) patients, we conducted deep genomic comparative analysis of a cohort of patients receiving standard therapy (surgery plus concurrent radiation and temozolomide); "GB outliers" were identified: long-term survivor of 33 months (LTS; n = 8) versus short-term survivor of 7 months (STS; n = 10). METHODS: We implemented exome, RNA, whole genome sequencing, and DNA methylation for collection of deep genomic data from STS and LTS GB patients...
December 8, 2016: Neuro-oncology
https://www.readbyqxmd.com/read/27932415/targeted-next-generation-sequencing-for-diagnostics-and-forensics
#19
Timothy D Minogue, Jeffery W Koehler, David A Norwood
No abstract text is available yet for this article.
December 8, 2016: Clinical Chemistry
https://www.readbyqxmd.com/read/27932412/universal-haplotype-based-noninvasive-prenatal-testing-for-single-gene-diseases
#20
Winnie W I Hui, Peiyong Jiang, Yu K Tong, Wing-Shan Lee, Yvonne K Y Cheng, Maria I New, Rezan A Kadir, K C Allen Chan, Tak Y Leung, Y M Dennis Lo, Rossa W K Chiu
BACKGROUND: Researchers have developed approaches for the noninvasive prenatal testing of single gene diseases. One approach that allows for the noninvasive assessment of both maternally and paternally inherited mutations involves the analysis of single nucleotide polymorphisms (SNPs) in maternal plasma DNA with reference to parental haplotype information. In the past, parental haplotypes were resolved by complex experimental methods or inferential approaches, such as through the analysis of DNA from other affected family members...
December 8, 2016: Clinical Chemistry
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