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https://www.readbyqxmd.com/read/28346895/wheat-genomics-comes-of-age
#1
REVIEW
Cristobal Uauy
Advances in wheat genomics have lagged behind other major cereals (e.g., rice and maize) due to its highly repetitive and large polyploid genome. Recent technological developments in sequencing and assembly methods, however, have largely overcome these barriers. The community now moves to an era centred on functional characterisation of the genome. This includes understanding sequence and structural variation as well as how information is integrated across multiple homoeologous genomes. This understanding promises to uncover variation previously hidden from natural and human selection due to the often observed functional redundancy between homoeologs...
March 24, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28346704/the-chloroplast-rna-helicase-ise2-is-required-for-multiple-chloroplast-rna-processing-steps-in-arabidopsis-thaliana
#2
Krzysztof Bobik, Tyra N McCray, Ben Ernest, Jessica C Fernandez, Katharine A Howell, Thomas Lane, Margaret Staton, Tessa M Burch-Smith
INCREASED SIZE EXCLUSION LIMIT2 (ISE2) is a chloroplast-localized RNA helicase that is indispensable for proper plant development. Chloroplasts in leaves with reduced ISE2 expression have previously been shown to exhibit reduced thylakoid contents and increased stromal volume, indicative of defective development. It has recently been reported that ISE2 is required for the splicing of group II introns from chloroplast transcripts. The current study extends these findings, and presents evidence for ISE2's role in multiple aspects of chloroplast RNA processing beyond group II intron splicing...
March 27, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28346470/relationship-of-microbial-communities-and-suppressiveness-of-trichoderma-fortified-composts-for-pepper-seedlings-infected-by-phytophthora-nicotianae
#3
Margarita Ros, Iulia Raut, Ana Belén Santisima-Trinidad, Jose Antonio Pascual
The understanding of the dynamic of soil-borne diseases is related to the microbial composition of the rhizosphere which is the key to progress in the field of biological control. Trichoderma spp. is commonly used as a biological control agent. The use of next generation sequencing approaches and quantitative PCR are two successful approaches to assess the effect of using compost as substrate fortified with two Trichoderma strains (Trichoderma harzianum or Trichoderma asperellum) on bacterial and fungal communities in pepper rhizosphere infected with Phytophthora nicotianae...
2017: PloS One
https://www.readbyqxmd.com/read/28346340/a-place-to-call-home-an-analysis-of-the-bacterial-communities-in-two-tethya-rubra-samaai-and-gibbons-2005-populations-in-algoa-bay-south-africa
#4
Samantha C Waterworth, Meesbah Jiwaji, Jarmo-Charles J Kalinski, Shirley Parker-Nance, Rosemary A Dorrington
Sponges are important sources of bioactive secondary metabolites. These compounds are frequently synthesized by bacterial symbionts, which may be recruited from the surrounding seawater or transferred to the sponge progeny by the parent. In this study, we investigated the bacterial communities associated with the sponge Tethya rubra Samaai and Gibbons 2005. Sponge specimens were collected from Evans Peak and RIY Banks reefs in Algoa Bay, South Africa and taxonomically identified by spicule analysis and molecular barcoding...
March 25, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28346228/somatic-mutations-and-progressive-monosomy-modify-samd9-related-phenotypes-in-humans
#5
Federica Buonocore, Peter Kühnen, Jenifer P Suntharalingham, Ignacio Del Valle, Martin Digweed, Harald Stachelscheid, Noushafarin Khajavi, Mohammed Didi, Angela F Brady, Oliver Blankenstein, Annie M Procter, Paul Dimitri, Jerry K H Wales, Paolo Ghirri, Dieter Knöbl, Brigitte Strahm, Miriam Erlacher, Marcin W Wlodarski, Wei Chen, George K Kokai, Glenn Anderson, Deborah Morrogh, Dale A Moulding, Shane A McKee, Charlotte M Niemeyer, Annette Grüters, John C Achermann
It is well established that somatic genomic changes can influence phenotypes in cancer, but the role of adaptive changes in developmental disorders is less well understood. Here we have used next-generation sequencing approaches to identify de novo heterozygous mutations in sterile α motif domain-containing protein 9 (SAMD9, located on chromosome 7q21.2) in 8 children with a multisystem disorder termed MIRAGE syndrome that is characterized by intrauterine growth restriction (IUGR) with gonadal, adrenal, and bone marrow failure, predisposition to infections, and high mortality...
March 27, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28345786/a-de-novo-nonsense-mutation-in-zbtb18-plus-a-de-novo-15q13-3-microdeletion-in-a-6-year-old-female
#6
Nadja Ehmke, Sylvio Karge, Johannes Buchmann, Dirk Korinth, Denise Horn, Olaf Reis, Frank Häßler
ZBTB18 has been proposed as candidate gene for microcephaly and abnormalities of the corpus callosum based on overlapping microdeletions of 1q43q44. More recently, de novo mutations of ZBTB18 have been identified in patients with syndromic and non-syndromic intellectual disability. Heterozygous microdeletions of 15q13.3 encompassing the candidate gene CHRNA7 are associated with developmental delay or intellectual disability with speech problems, hypotonia, and seizures. They are characterized by significant variability and reduced penetrance...
March 27, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28345240/prenatal-dna-sequencing-clinical-counseling-and-diagnostic-laboratory-considerations
#7
Ahmad N Abou Tayoun, Nancy B Spinner, Heidi L Rehm, Robert C Green, Diana W Bianchi
Clinical diagnostic laboratories are producing next generation sequencing (NGS)-based test results that are becoming increasingly incorporated into patient care. Whole genome and exome sequencing on fetal material derived from amniocytes, chorionic villi, or products of conception is starting to be offered clinically in specialized centers, but it has not yet become routine practice. The technical, interpretation and ethical challenges are greatest in the area of prenatal medicine because the fetus has a limited health history and the physical examination is only indirectly available via prenatal sonography...
March 27, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28344976/a-metataxonomic-approach-could-be-considered-for-cattle-clinical-mastitis-diagnostics
#8
Joanne W H Oultram, Erika K Ganda, Sarah C Boulding, Rodrigo C Bicalho, Georgios Oikonomou
Mastitis is one of the most costly diseases affecting the dairy industry, and identification of the causative microorganism(s) is essential. Here, we report the use of next-generation sequencing of bacterial 16S rRNA genes for clinical mastitis diagnosis. We used 65 paired milk samples, collected from the mastitic and a contralateral healthy quarter of mastitic dairy cattle to evaluate the technique as a potential alternative to bacterial culture or targeted PCR. One large commercial dairy farm was used, with one trained veterinarian collecting the milk samples...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/28344162/identification-of-genetic-markers-of-resistance-to-echinocandins-azoles-and-5-fluorocytosine-in-candida-glabrata-by-next-generation-sequencing-a-feasibility-study
#9
Chayanika Biswas, Sharon C-A Chen, Catriona Halliday, Karina Kennedy, E Geoffrey Playford, Deborah J Marriott, Monica A Slavin, Tania C Sorrell, Vitali Sintchenko
OBJECTIVES: Multi-antifungal drug resistance in Candida glabrata is increasing. We examined the feasibility of next generation sequencing (NGS) to investigate the presence of antifungal drug resistance markers in C. glabrata. METHODS: The antifungal susceptibility of 12 clinical isolates and one ATCC strain of C. glabrata was determined using the Sensititre YeastOne® YO10 assay. These included three isolate pairs where the second isolate of each pair had developed a rise in drug MICs...
March 23, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28344011/the-epidemiology-pathogenesis-transmission-diagnosis-and-management-of-multidrug-resistant-extensively-drug-resistant-and-incurable-tuberculosis
#10
REVIEW
Keertan Dheda, Tawanda Gumbo, Gary Maartens, Kelly E Dooley, Ruth McNerney, Megan Murray, Jennifer Furin, Edward A Nardell, Leslie London, Erica Lessem, Grant Theron, Paul van Helden, Stefan Niemann, Matthias Merker, David Dowdy, Annelies Van Rie, Gilman K H Siu, Jotam G Pasipanodya, Camilla Rodrigues, Taane G Clark, Frik A Sirgel, Aliasgar Esmail, Hsien-Ho Lin, Sachin R Atre, H Simon Schaaf, Kwok Chiu Chang, Christoph Lange, Payam Nahid, Zarir F Udwadia, C Robert Horsburgh, Gavin J Churchyard, Dick Menzies, Anneke C Hesseling, Eric Nuermberger, Helen McIlleron, Kevin P Fennelly, Eric Goemaere, Ernesto Jaramillo, Marcus Low, Carolina Morán Jara, Nesri Padayatchi, Robin M Warren
Global tuberculosis incidence has declined marginally over the past decade, and tuberculosis remains out of control in several parts of the world including Africa and Asia. Although tuberculosis control has been effective in some regions of the world, these gains are threatened by the increasing burden of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis. XDR tuberculosis has evolved in several tuberculosis-endemic countries to drug-incurable or programmatically incurable tuberculosis (totally drug-resistant tuberculosis)...
March 15, 2017: Lancet Respiratory Medicine
https://www.readbyqxmd.com/read/28342698/targeted-exome-sequencing-and-chromosomal-microarray-for-the-molecular-diagnosis-of-nevoid-basal-cell-carcinoma-syndrome
#11
Yoshihiro Matsudate, Takuya Naruto, Yumiko Hayashi, Mitsuyoshi Minami, Mikiko Tohyama, Kenji Yokota, Daisuke Yamada, Issei Imoto, Yoshiaki Kubo
BACKGROUND: Nevoid basal cell carcinoma syndrome (NBCCS) is an autosomal dominant disorder mainly caused by heterozygous mutations of PTCH1. In addition to characteristic clinical features, detection of a mutation in causative genes is reliable for the diagnosis of NBCCS; however, no mutations have been identified in some patients using conventional methods. OBJECTIVE: To improve the method for the molecular diagnosis of NBCCS. METHODS: We performed targeted exome sequencing (TES) analysis using a multi-gene panel, including PTCH1, PTCH2, SUFU, and other sonic hedgehog signaling pathway-related genes, based on next-generation sequencing (NGS) technology in 8 cases in whom possible causative mutations were not detected by previously performed conventional analysis and 2 recent cases of NBCCS...
March 11, 2017: Journal of Dermatological Science
https://www.readbyqxmd.com/read/28342387/isolation-and-characterization-of-a-novel-putative-human-polyomavirus
#12
Tarik Gheit, Sankhadeep Dutta, Javier Oliver, Alexis Robitaille, Shalaka Hampras, Jean-Damien Combes, Sandrine McKay-Chopin, Florence Le Calvez-Kelm, Neil Fenske, Basil Cherpelis, Anna R Giuliano, Silvia Franceschi, James McKay, Dana E Rollison, Massimo Tommasino
The small double-stranded DNA polyomaviruses (PyVs) form a family of 73 species, whose natural hosts are primarily mammals and birds. So far, 13 PyVs have been isolated in humans, and some of them have clearly been associated with several diseases, including cancer. In this study, we describe the isolation of a novel PyV in human skin using a sensitive degenerate PCR protocol combined with next-generation sequencing. The new virus, named Lyon IARC PyV (LIPyV), has a circular genome of 5269 nucleotides. Phylogenetic analyses showed that LIPyV is related to the raccoon PyV identified in neuroglial tumours in free-ranging raccoons...
March 22, 2017: Virology
https://www.readbyqxmd.com/read/28341673/a-next-generation-sequencing-approach-to-characterize-the-impacts-of-land-based-sources-of-pollution-on-the-microbiota-of-southeast-florida-coral-reefs
#13
Christopher Staley, Thomas Kaiser, Maribeth L Gidley, Ian C Enochs, Paul R Jones, Kelly D Goodwin, Christopher D Sinigalliano, Michael J Sadowsky, Chan Lan Chun
Coral reefs are dynamic ecosystems known for decades to be endangered due, in large part, to anthropogenic impacts from land-based sources of pollution (LBSP). In this study, we utilized an Illumina-based next-generation sequencing approach to characterize prokaryotic and fungal communities from samples collected off the southeast coast of Florida. Water samples from coastal inlet discharges, oceanic outfalls of municipal wastewater treatment plants, treated wastewater effluent before discharge, open ocean samples, and coral tissue samples (mucus and polyps) were characterized to determine relationships between microbial communities in these matrices and those in reef water and coral tissues...
March 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28341602/cytosolic-yb-1-and-nsun2-are-the-only-proteins-recognizing-specific-motifs-present-in-mrnas-enriched-in-exosomes
#14
Olga A Kossinova, Alexander V Gopanenko, Svetlana N Tamkovich, Olga A Krasheninina, Alexey E Tupikin, Elena Kiseleva, Darya D Yanshina, Alexey A Malygin, Alia G Ven'yaminova, Marsel R Kabilov, Galina G Karpova
Exosomes, membranous vesicles secreted by various cells, are involved in intercellular communication and carry vast repertoires of RNAs and proteins. Processes mediating RNA sorting into exosomes are currently poorly understood. Using bioinformatics approaches, three structural motifs ACCAGCCU, CAGUGAGC and UAAUCCCA have been discovered as enriched in exosomal mRNAs and long noncoding RNAs. Here, utilizing short RNA hairpins, each containing one of the motifs, in a pull-down assay of cytosolic extract of human embryonic kidney 293 (HEK293) cells, we prove that multifunctional RNA-binding protein YB-1 specifically interacts with all three motifs, whereas methyltransferase NSUN2 recognizes only the motif CAGUGAGC...
March 21, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28341590/guidelines-for-validation-of-next-generation-sequencing-based-oncology-panels-a-joint-consensus-recommendation-of-the-association-for-molecular-pathology-and-college-of-american-pathologists
#15
REVIEW
Lawrence J Jennings, Maria E Arcila, Christopher Corless, Suzanne Kamel-Reid, Ira M Lubin, John Pfeifer, Robyn L Temple-Smolkin, Karl V Voelkerding, Marina N Nikiforova
Next-generation sequencing (NGS) methods for cancer testing have been rapidly adopted by clinical laboratories. To establish analytical validation best practice guidelines for NGS gene panel testing of somatic variants, a working group was convened by the Association of Molecular Pathology with liaison representation from the College of American Pathologists. These joint consensus recommendations address NGS test development, optimization, and validation, including recommendations on panel content selection and rationale for optimization and familiarization phase conducted before test validation; utilization of reference cell lines and reference materials for evaluation of assay performance; determining of positive percentage agreement and positive predictive value for each variant type; and requirements for minimal depth of coverage and minimum number of samples that should be used to establish test performance characteristics...
March 21, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28341588/targeted-next-generation-sequencing-of-51-genes-involved-in-primary-electrical-disease
#16
Dorien Proost, Johan Saenen, Geert Vandeweyer, Annelies Rotthier, Maaike Alaerts, Emeline M Van Craenenbroeck, Joachim Van Crombruggen, Geert Mortier, Wim Wuyts, Christiaan Vrints, Jurgen Del Favero, Bart Loeys, Lut Van Laer
Primary electrical disease (PED) is characterized by cardiac arrhythmias, which can lead to sudden cardiac death in the absence of detectable structural heart disease. PED encompasses a diversity of inherited syndromes, predominantly Brugada syndrome, early repolarization syndrome, long QT syndrome, short QT syndrome, arrhythmogenic right ventricular cardiomyopathy, and catecholaminergic polymorphic ventricular tachycardia. To overcome the diagnostic challenges imposed by the clinical and genetic heterogeneity of PED, we developed a targeted gene panel for next-generation sequencing of 51 PED genes...
March 21, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28341485/modulation-of-gut-microbiota-contributes-to-curcumin-mediated-attenuation-of-hepatic-steatosis-in-rats
#17
Wenhuan Feng, Hongdong Wang, Pengzi Zhang, Caixia Gao, Junxian Tao, Zhijuan Ge, Dalong Zhu, Yan Bi
BACKGROUND: Structural disruption of gut microbiota contributes to the development of non-alcoholic fatty liver disease (NAFLD) and modulating the gut microbiota represents a novel strategy for NAFLD prevention. Although previous studies have demonstrated that curcumin alleviates hepatic steatosis, its effect on the gut microbiota modulation has not been investigated. METHODS: Next generation sequencing and multivariate analysis were utilized to evaluate the structural changes of gut microbiota in a NAFLD rat model induced by high fat-diet (HFD) feeding...
March 21, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28341207/transcriptome-analysis-of-airborne-pm2-5-induced-detrimental-effects-on-human-keratinocytes
#18
Hyoung-June Kim, Il-Hong Bae, Eui Dong Son, Juyearl Park, Nari Cha, Hyewon Na, Changjo Jung, You-Seak Go, Dae-Yong Kim, Tae Ryong Lee, Dong Wook Shin
Ambient air pollution is becoming more severe worldwide, posing a serious threat to human health. Fine airborne particles of particulate matter (PM2.5) show higher cytotoxicity than other coarse fractions. Indeed, PM2.5 induces cardiovascular or respiratory damage; however, few studies have evaluated the detrimental effect of PM2.5 to normal human skin. We used a next-generation sequencing-based (RNA-Seq) method with transcriptome and Gene Ontology (GO) enrichment analysis to determine the harmful influences of PM2...
March 21, 2017: Toxicology Letters
https://www.readbyqxmd.com/read/28340976/population-genetic-data-for-12-x-str-loci-in-the-northern-han-chinese-and-statsx-package-as-tools-for-population-statistics-on-x-str
#19
Fei Guo
The X-chromosomal short tandem repeat (X-STR) has the advantage in female traces identification against male contamination and in complex kinship cases. In this study, a total of 516 Northern Han Chinese were genotyped using the Investigator(®) Argus X-12 QS Kit and pairwise genetic distances (FST) were measured between Northern Han Chinese and 35 published populations using the same 12 X-STR loci in four presumed linkage groups (LG). Meanwhile, the StatsX package was compiled to aid the analysis of population statistics on X-STR...
January 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28340953/clinical-features-of-chinese-patients-with-gerstmann-str%C3%A3-ussler-scheinker-identified-by-targeted-next-generation-sequencing
#20
Hong-Fu Li, Zhi-Jun Liu, Hai-Lin Dong, Juan-Juan Xie, Shao-Yun Zhao, Wang Ni, Yi Dong, Zhi-Ying Wu
Gerstmann-Sträussler-Scheinker (GSS) is an autosomal dominant neurodegenerative disease due to mutations within prion protein (PRNP) gene. Clinically, it is not easy to distinguish GSS from spinocerebellar ataxia (SCA), especially in the early stage of disease. We aimed to identify genetic mutations in 8 Chinese pedigrees with dominant ataxia but excluded dynamic mutations of SCA genes. Targeted next-generation sequencing was performed in the 8 probands. A customized panel was designed to capture 24 known causative genes, including 15 autosomal dominant SCA genes and 9 dementia-related genes...
January 2017: Neurobiology of Aging
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