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https://www.readbyqxmd.com/read/28922761/rapid-mapping-and-cloning-of-the-virescent-1-gene-in-cotton-by-bulked-segregant-analysis-next-generation-sequencing-and-virus-induced-gene-silencing-strategies
#1
Jiankun Zhu, Jiedan Chen, Fengkai Gao, Chenyu Xu, Huaitong Wu, Kun Chen, Zhanfeng Si, Hu Yan, Tianzhen Zhang
Map-based gene cloning is a vital strategy for the identification of the quantitative trait loci or genes underlying important agronomic traits. The conventional map-based cloning method is powerful but generally time-consuming and labor-intensive. In this context, we introduce an improved bulked segregant analysis method in combination with a virus-induced gene silencing (VIGS) strategy for rapid and reliable gene mapping, identification and functional verification. This method was applied to a multiple recessive marker line of upland cotton, Texas 582 (T582), and identified unique genomic positions harboring mutant loci, showing the reliability and efficacy of this method...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28921927/fast-and-cost-effective-single-nucleotide-polymorphism-snp-detection-in-the-absence-of-a-reference-genome-using-semi-deep-next-generation-random-amplicon-sequencing-ramseq
#2
Helmut Bayerl, Robert H S Kraus, Carsten Nowak, Daniel W Foerster, Joerns Fickel, Ralph Kuehn
Biodiversity has suffered a dramatic global decline during the past decades and monitoring tools are urgently needed providing data for the development and evaluation of conservation efforts both on a species and a genetic level. However, in wild species the assessment of genetic diversity is often hampered by the lack of suitable genetic markers. In this article we present Random Amplicon Sequencing (RAMseq), a novel approach for fast and cost-effective detection of single nucleotide polymorphisms (SNPs) in non-model species by semi-deep sequencing of random amplicons...
September 15, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28921648/rna-therapeutics-in-oncology-advances-challenges-and-future-directions
#3
A Robert MacLeod, Stanley T Crooke
RNA-based therapeutic technologies represent a rapidly expanding class of therapeutic opportunities with the power to modulate cellular biology in ways never before possible. With RNA-targeted therapeutics, inhibitors of previously undruggable proteins, gene expression modulators, and even therapeutic proteins can be rationally designed based on sequence information alone, something that is not possible with other therapeutic modalities. The most advanced RNA therapeutic modalities are antisense oligonucleotides (ASOs) and small interfering RNAs...
October 2017: Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/28921530/sympatric-parallel-diversification-of-major-oak-clades-in-the-americas-and-the-origins-of-mexican-species-diversity
#4
Andrew L Hipp, Paul S Manos, Antonio González-Rodríguez, Marlene Hahn, Matthew Kaproth, John D McVay, Susana Valencia Avalos, Jeannine Cavender-Bares
Oaks (Quercus, Fagaceae) are the dominant tree genus of North America in species number and biomass, and Mexico is a global center of oak diversity. Understanding the origins of oak diversity is key to understanding biodiversity of northern temperate forests. A phylogenetic study of biogeography, niche evolution and diversification patterns in Quercus was performed using 300 samples, 146 species. Next-generation sequencing data were generated using the restriction-site associated DNA (RAD-seq) method. A time-calibrated maximum likelihood phylogeny was inferred and analyzed with bioclimatic, soils, and leaf habit data to reconstruct the biogeographic and evolutionary history of the American oaks...
September 18, 2017: New Phytologist
https://www.readbyqxmd.com/read/28921387/analysis-of-24-genes-reveals-a-monogenic-cause-in-11-1-of-cases-with-steroid-resistant-nephrotic-syndrome-at-a-single-center
#5
Weizhen Tan, Svjetlana Lovric, Shazia Ashraf, Jia Rao, David Schapiro, Merlin Airik, Shirlee Shril, Heon Yung Gee, Michelle Baum, Ghaleb Daouk, Michael A Ferguson, Nancy Rodig, Michael J G Somers, Deborah R Stein, Asaf Vivante, Jillian K Warejko, Eugen Widmeier, Friedhelm Hildebrandt
BACKGROUND: Steroid-resistant nephrotic syndrome (SRNS) is the second most frequent cause of end-stage renal disease (ESRD) among patients manifesting at under 25 years of age. We performed mutation analysis using a high-throughput PCR-based microfluidic technology in 24 single-gene causes of SRNS in a cohort of 72 families, who presented with SRNS before the age of 25 years. METHODS: Within an 18-month interval, we obtained DNA samples, pedigree information, and clinical information from 77 consecutive children with SRNS from 72 different families seen at Boston Children's Hospital (BCH)...
September 18, 2017: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
https://www.readbyqxmd.com/read/28920925/expression-of-piwi-protein-miwi2-defines-a-distinct-population-of-multiciliated-cells
#6
Gregory A Wasserman, Aleksander D Szymaniak, Anne C Hinds, Kazuko Yamamoto, Hirofumi Kamata, Nicole Ms Smith, Kristie L Hilliard, Claudia Carrieri, Adam T Labadorf, Lee J Quinton, Xingbin Ai, Xaralabos Varelas, Felicia Chen, Joseph P Mizgerd, Alan Fine, Dónal O'Carroll, Matthew R Jones
P-element-induced wimpy testes (Piwi) proteins are known for suppressing retrotransposon activation in the mammalian germline. However, whether Piwi protein or Piwi-dependent functions occur in the mammalian soma is unclear. Contrary to germline-restricted expression, we observed that Piwi-like Miwi2 mRNA is indeed expressed in epithelial cells of the lung in adult mice and that it is induced during pneumonia. Further investigation revealed that MIWI2 protein localized to the cytoplasm of a discrete population of multiciliated airway epithelial cells...
September 18, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28920846/detection-of-the-incx3-plasmid-carrying-blakpc-3-in-a-serratia-marcescens-strain-isolated-from-a-kidney-liver-transplanted-patient
#7
Floriana Gona, Carla Caio, Gioacchino Iannolo, Francesco Monaco, Giuseppina Di Mento, Nicola Cuscino, Ignazio Fontana, Giovanna Panarello, Gaetano Maugeri, Maria Lina Mezzatesta, Stefania Stefani, Pier Giulio Conaldi
Dissemination of resistance to carbapenems among Enterobacteriaceae through plasmids is an increasingly important concern in health care worldwide. Here we report the first description of an IncX3 plasmid carrying the blaKPC-3 gene in a strain of Serratia marcescens isolated from a kidney-liver transplanted patient at the transplantation centre ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione, Palermo, Italy). To localize the transposable element containing the resistance-associated gene Next-Generation Sequencing of the bacterial DNA was performed...
September 18, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28920165/distinctive-patterns-in-the-taxonomical-resolution-of-bacterioplankton-in-the-sediment-and-pore-waters-of-contrasted-freshwater-lakes
#8
J Keshri, A S Pradeep Ram, T Sime-Ngando
Bacteria assemblages in lake sediments play a key role in various biogeochemical processes, yet their association with interstitial pore waters has been scarcely investigated. In this study, we utilized Illumina next-generation amplicon sequencing of the 16S rRNA gene to characterize the seasonal bacterial communities in the sediments and pore waters of three contrasted temperate freshwater lakes, namely Pavin, Aydat, and Grangent (French Massif Central). Despite occupying seemingly similar habitats, bacterial communities differed substantially between sediments and pore waters at all seasons with low sharing of operational taxonomic units (OTUs, 6...
September 17, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28919931/improving-hierarchical-models-using-historical-data-with-applications-in-high-throughput-genomics-data-analysis
#9
Ben Li, Yunxiao Li, Zhaohui S Qin
Modern high-throughput biotechnologies such as microarray and next generation sequencing produce a massive amount of information for each sample assayed. However, in a typical high-throughput experiment, only limited amount of data are observed for each individual feature, thus the classical 'large p, small n' problem. Bayesian hierarchical model, capable of borrowing strength across features within the same dataset, has been recognized as an effective tool in analyzing such data. However, the shrinkage effect, the most prominent feature of hierarchical features, can lead to undesirable over-correction for some features...
June 2017: Statistics in Biosciences
https://www.readbyqxmd.com/read/28919550/improving-the-genotyping-resolution-of-cryptosporidium-hominis-subtype-iba10g2-using-one-step-pcr-based-amplicon-sequencing
#10
Jessica Beser, Björn M Hallström, Abdolreza Advani, Sofia Andersson, Gabriel Östlund, Jadwiga Winiecka-Krusnell, Marianne Lebbad, Erik Alm, Karin Troell, Romanico B G Arrighi
Cryptosporidium hominis gp60 subtype IbA10G2 is a common cause of cryptosporidiosis. This subtype is responsible for many waterborne outbreaks as well as sporadic cases and is considered virulent and highly important in the epidemiology of cryptosporidiosis. Due to low heterogeneity within the genome of C. hominis it has been difficult to identify epidemiological markers with higher resolution than gp60. However, new markers are required in order to improve outbreak investigations and studies of the transmission dynamics of this clinically important subtype...
September 14, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28919547/deep-sequencing-to-resolve-complex-diversity-of-apicomplexan-parasites-in-platypuses-and-echidnas-proof-of-principle-for-wildlife-disease-investigation
#11
Jan Šlapeta, Stefan Saverimuttu, Larry Vogelnest, Cheryl Sangster, Frances Hulst, Karrie Rose, Paul Thompson, Richard Whittington
The short-beaked echidna (Tachyglossus aculeatus) and the platypus (Ornithorhynchus anatinus) are iconic egg-laying monotremes (Mammalia: Monotremata) from Australasia. The aim of this study was to demonstrate the utility of diversity profiles in disease investigations of monotremes. Using small subunit (18S) rDNA amplicon deep-sequencing we demonstrated the presence of apicomplexan parasites and confirmed by direct and cloned amplicon gene sequencing Theileria ornithorhynchi, Theileria tachyglossi, Eimeria echidnae and Cryptosporidium fayeri...
September 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28919163/multiplex-pcr-and-ngs-based-identification-of-mrna-splicing-variants-analysis-of-brca1-splicing-pattern-as-a-model
#12
Jan Hojny, Petra Zemankova, Filip Lhota, Jan Sevcik, Viktor Stranecky, Hana Hartmannova, Katerina Hodanova, Ondrej Mestak, David Pavlista, Marketa Janatova, Jana Soukupova, Michal Vocka, Zdenek Kleibl, Petra Kleiblova
Alternative pre-mRNA splicing increases transcriptome plasticity by forming naturally-occurring alternative splicing variants (ASVs). Alterations of splicing processes, caused by DNA mutations, result in aberrant splicing and the formation of aberrant mRNA isoforms. Analyses of hereditary cancer predisposition genes reveal many DNA variants with unknown clinical significance (VUS) that potentially affect pre-mRNA splicing. Therefore, a comprehensive description of ASVs is an essential prerequisite for the interpretation of germline VUS in high-risk individuals...
September 14, 2017: Gene
https://www.readbyqxmd.com/read/28918274/distribution-comparison-and-risk-assessment-of-free-floating-and-particle-attached-bacterial-pathogens-in-urban-recreational-water-implications-for-water-quality-management
#13
Tingting Fang, Qijia Cui, Yong Huang, Peiyan Dong, Hui Wang, Wen-Tso Liu, Quanhui Ye
The risk of pathogen exposure in recreational water is a concern worldwide. Moreover, suspended particles, as ideal shelters for pathogens, in these waters also need attention. However, the risk caused by the pathogen-particle attachment is largely unknown. Accordingly, water samples in three recreational lakes in Beijing were collected and separated into free-floating (FL, 0.22-5μm) and particle-attached (PA, >5μm) fractions. Next-generation sequencing (NGS) was employed to determine the diversity of genera containing pathogens, and quantitative PCR (qPCR) was used to assess the presence of genes from Escherichia coli (uidA), Salmonella enterica (invA), Aeromonas spp...
September 14, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28917829/a-chinese-boy-with-geleophysic-dysplasia-caused-by-compound-heterozygous-mutations-in-adamtsl2
#14
Li Dongxiao, Dong Hui, Zheng Hong, Song Jinqing, Li Xiyuan, Jin Ying, Liu Yupeng, Yang Yanling
Geleophysic dysplasia, belonging to the group of acromelic dysplasia, is a rare genetic disease. Two genes, FBN1 and ADAMTSL2, were known to be linked to this disorder. The disorder presents as extreme short stature, short limbs, small hands and feet, stubby fingers and toes, joint stiffness, toe walking, skin thickening, progressive cardiac valvular thickening and characteristic facial features, including a round face with full cheeks. Here, we report the first Chinese case with geleophysic dysplasia type 1 based on clinical and genetic features...
September 13, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28916791/genomic-structure-and-evolution-of-the-mating-type-locus-in-the-green-seaweed-ulva-partita
#15
Tomokazu Yamazaki, Kensuke Ichihara, Ryogo Suzuki, Kenshiro Oshima, Shinichi Miyamura, Kazuyoshi Kuwano, Atsushi Toyoda, Yutaka Suzuki, Sumio Sugano, Masahira Hattori, Shigeyuki Kawano
The evolution of sex chromosomes and mating loci in organisms with UV systems of sex/mating type determination in haploid phases via genes on UV chromosomes is not well understood. We report the structure of the mating type (MT) locus and its evolutionary history in the green seaweed Ulva partita, which is a multicellular organism with an isomorphic haploid-diploid life cycle and mating type determination in the haploid phase. Comprehensive comparison of a total of 12.0 and 16.6 Gb of genomic next-generation sequencing data for mt(-) and mt(+) strains identified highly rearranged MT loci of 1...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916718/potential-sperm-contributions-to-the-murine-zygote-predicted-by-in-silico-analysis
#16
Panagiotis Ntostis, Deborah Carter, David Iles, J D Huntriss, Maria Tzetis, David Miller
Paternal contributions to the zygote are thought to extend beyond delivery of the genome and paternal RNAs have been linked to epigenetic transgenerational inheritance in different species. In addition, sperm-egg fusion activates several downstream processes that contribute to zygote formation, including PLC zeta-mediated egg activation and maternal RNA clearance. Since a third of the preimplantation developmental period in the mouse occurs prior to the first cleavage stage, there is ample time for paternal RNAs or their encoded proteins potentially to interact and participate in early zygotic activities...
September 15, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28916543/cryopyrin-associated-periodic-syndromes-in-italian-patients-evaluation-of-the-rate-of-somatic-nlrp3-mosaicism-and-phenotypic-characterization
#17
Denise Lasigliè, Anna Mensa-Vilaro, Denise Ferrera, Roberta Caorsi, Federica Penco, Giuseppe Santamaria, Marco Di Duca, Giulia Amico, Kenji Nakagawa, Francesca Antonini, Alberto Tommasini, Rita Consolini, Antonella Insalaco, Marco Cattalini, Laura Obici, Romina Gallizzi, Francesca Santarelli, Genny Del Zotto, Mariasavina Severino, Anna Rubartelli, Roberto Ravazzolo, Alberto Martini, Isabella Ceccherini, Ryuta Nishikomori, Marco Gattorno, Juan I Arostegui, Silvia Borghini
OBJECTIVE: To evaluate the rate of somatic NLRP3 mosaicism in an Italian cohort of mutation-negative patients with cryopyrin-associated periodic syndrome (CAPS). METHODS: The study enrolled 14 patients with a clinical phenotype consistent with CAPS in whom Sanger sequencing of the NLRP3 gene yielded negative results. Patients' DNA were subjected to amplicon-based NLRP3 deep sequencing. RESULTS: Low-level somatic NLRP3 mosaicism has been detected in 4 patients, 3 affected with chronic infantile neurological cutaneous and articular syndrome and 1 with Muckle-Wells syndrome...
September 15, 2017: Journal of Rheumatology
https://www.readbyqxmd.com/read/28916377/clinical-and-molecular-characterization-of-two-chinese-patients-with-type-2-congenital-generalized-lipodystrophy
#18
Ruimin Chen, Xin Yuan, Jian Wang, Ying Zhang
BACKGROUND: Type 2 congenital generalized lipodystrophy (CGL2, OMIM 269700) is a rare autosomal recessive disease, characterized by the generalized absence of adipose tissue at birth or in early infancy. Pathogenic variants in BSCL2 gene have been reported to be responsible for CGL2. The aim of this study is to analyze the clinical and genetic characteristics of two Chinese patients with CGL2, and with particular focus on the BSCL2 gene sequence variants. METHODS: Medical history, clinical manifestations, physical examination, laboratory data, and ultrasonography findings were analyzed for the two patients with CGL2...
September 12, 2017: Gene
https://www.readbyqxmd.com/read/28916186/clinical-immunological-and-genetic-spectrum-of-696-patients-with-combined-immunode%C3%AF-ciency
#19
Hassan Abolhassani, Janet Chou, Wayne Bainter, Craig Platt, Mahmood Tavassoli, Toba Momen, Marzieh Tavakol, Mohammad Hossein Eslamian, Mohammad Gharagozlou, Masoud Movahedi, Mohsen Ghadami, Amir Ali Hamidieh, Gholamreza Azizi, Reza Yazdani, Mohsen Afarideh, Alireza Ghajar, Arash Havaei, Zahra Chavoushzadeh, Seyed Alireza Mahdaviani, Taher Cheraghi, Nasrin Behniafard, Reza Amin, Soheila Aleyasin, Reza Faridhosseini, Farahzad Jabbari-Azad, Mohammamd Nabavi, Mohammad Hassan Bemanian, Saba Arshi, Rasol Molatefi, Roya Sherkat, Mahboubeh Mansouri, Mehrnaz Mesdaghi, Delara Babaie, Iraj Mohammadzadeh, Javad Ghaffari, Alireza Shafiei, Najmeddin Kalantari, Hamid Ahanchian, Maryam Khoshkhui, Habib Soheili, Abbas Dabbaghzadeh, Afshin Shirkani, Rasoul Nasiri Kalmarzi, Seyed Hamidreza Mortazavi, Javad Tafaroji, Abbas Khalili, Javad Mohammadi, Babak Negahdari, Mohammad-Taghi Joghataei, Basel K Al-Ramadi, Capucine Picard, Nima Parvaneh, Nima Rezaei, Talal Chatila, Michel J Massaad, Sevgi Keles, Lennart Hammarström, Raif S Geha, Asghar Aghamohammadi
BACKGROUND: Combined immunodeficiencies (CIDs) are diseases of defective adaptive immunity with diverse clinical phenotypes. Although CIDs are more prevalent in the Middle East than Western countries, the resources for genetic diagnosis are limited. OBJECTIVES: This study aims to characterize the categories of CID patients in Iran clinically and genetically. METHODS: Clinical and laboratory data were obtained from 696 patients with CIDs. Patients were subdivided into those with syndromic (344 patients) and non-syndromic CIDs (352 patients)...
September 12, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28915855/massive-parallel-sequencing-as-a-new-diagnostic-approach-for-phenylketonuria-and-tetrahydrobiopterin-deficiency-in-thailand
#20
Pongsathorn Chaiyasap, Chupong Ittiwut, Chalurmpon Srichomthong, Apiruk Sangsin, Kanya Suphapeetiporn, Vorasuk Shotelersuk
BACKGROUND: Hyperphenylalaninemia (HPA) can be classified into phenylketonuria (PKU) which is caused by mutations in the phenylalanine hydroxylase (PAH) gene, and BH4 deficiency caused by alterations in genes involved in tetrahydrobiopterin (BH4) biosynthesis pathway. Dietary restriction of phenylalanine is considered to be the main treatment of PKU to prevent irreversible intellectual disability. However, the same dietary intervention in BH4 deficiency patients is not as effective, as BH4 is also a cofactor in many neurotransmitter syntheses...
September 16, 2017: BMC Medical Genetics
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