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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/28922394/sequence-features-of-viral-and-human-internal-ribosome-entry-sites-predictive-of-their-activity
#2
Alexey A Gritsenko, Shira Weingarten-Gabbay, Shani Elias-Kirma, Ronit Nir, Dick de Ridder, Eran Segal
Translation of mRNAs through Internal Ribosome Entry Sites (IRESs) has emerged as a prominent mechanism of cellular and viral initiation. It supports cap-independent translation of select cellular genes under normal conditions, and in conditions when cap-dependent translation is inhibited. IRES structure and sequence are believed to be involved in this process. However due to the small number of IRESs known, there have been no systematic investigations of the determinants of IRES activity. With the recent discovery of thousands of novel IRESs in human and viruses, the next challenge is to decipher the sequence determinants of IRES activity...
September 18, 2017: PLoS Computational Biology
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/28921387/analysis-of-24-genes-reveals-a-monogenic-cause-in-11-1-of-cases-with-steroid-resistant-nephrotic-syndrome-at-a-single-center
#4
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/28920846/detection-of-the-incx3-plasmid-carrying-blakpc-3-in-a-serratia-marcescens-strain-isolated-from-a-kidney-liver-transplanted-patient
#5
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
#6
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/28919547/deep-sequencing-to-resolve-complex-diversity-of-apicomplexan-parasites-in-platypuses-and-echidnas-proof-of-principle-for-wildlife-disease-investigation
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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/28915855/massive-parallel-sequencing-as-a-new-diagnostic-approach-for-phenylketonuria-and-tetrahydrobiopterin-deficiency-in-thailand
#15
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
https://www.readbyqxmd.com/read/28915716/implementation-and-utilization-of-the-molecular-tumor-board-to-guide-precision-medicine
#16
REVIEW
Shuko Harada, Rebecca Arend, Qian Dai, Jessica A Levesque, Thomas S Winokur, Rongjun Guo, Martin J Heslin, Lisle Nabell, L Burt Nabors, Nita A Limdi, Kevin A Roth, Edward E Partridge, Gene P Siegal, Eddy S Yang
BACKGROUND: With rapid advances in genomic medicine, the complexity of delivering precision medicine to oncology patients across a university health system demanded the creation of a Molecular Tumor Board (MTB) for patient selection and assessment of treatment options. The objective of this report is to analyze our progress to date and discuss the importance of the MTB in the implementation of personalized medicine. MATERIALS AND METHODS: Patients were reviewed in the MTB for appropriateness for comprehensive next generation sequencing (NGS) cancer gene set testing based on set criteria that were in place...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915579/microrna-profiling-associated-with-non-small-cell-lung-cancer-next-generation-sequencing-detection-experimental-validation-and-prognostic-value
#17
Sandra Gallach, Eloisa Jantus-Lewintre, Silvia Calabuig-Fariñas, David Montaner, Sergio Alonso, Rafael Sirera, Ana Blasco, Marta Usó, Ricardo Guijarro, Miguel Martorell, Carlos Camps
BACKGROUND: The average five-year survival for non-small cell lung cancer (NSCLC) patients is approximately 15%. Emerging evidence indicates that microRNAs (miRNAs) constitute a new class of gene regulators in humans that may play an important role in tumorigenesis. Hence, there is growing interest in studying their role as possible new biomarkers whose expression is aberrant in cancer. Therefore, in this study we identified dysregulated miRNAs by next generation sequencing (NGS) and analyzed their prognostic value...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915445/exploring-the-association-of-rs10490924-polymorphism-with-age-related-macular-degeneration-an-in-silico-approach
#18
Farhad Jahanfar, Hamed Hamishehkar
The polymorphism rs10490924 (A69S) in the age-related maculopathy susceptibility 2 (ARMS2) gene is highly associated with age-related macular degeneration, which is the leading cause of blindness among the elderly population. The ARMS2 gene encodes a putative small (11kDa) protein, which the function and localization of the ARMS2 protein remain under debate. For a better understanding of functional impacts of the A69S mutation, we performed a detailed analysis of the ARMS2 sequence with a broad set of bioinformatics tools...
September 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28915117/molecular-genetic-and-clinical-delineation-of-22-patients-with-congenital-hypogonadotropic-hypogonadism
#19
Kohei Aoyama, Haruo Mizuno, Tatsushi Tanaka, Takao Togawa, Yutaka Negishi, Kei Ohashi, Ikumi Hori, Masako Izawa, Takashi Hamajima, Shinji Saitoh
BACKGROUND: Congenital hypogonadotropic hypogonadism (CHH) is classified as Kallmann syndrome (KS) with anosmia/hyposmia or normosmic (n)CHH. Here, we investigated the genetic causes and phenotype-genotype correlations in Japanese patients with CHH. METHODS: We enrolled 22 Japanese patients with CHH from 21 families (18 patients with KS and 4 with nCHH) and analyzed 27 genes implicated in CHH by next-generation and Sanger sequencing. RESULTS: We detected 12 potentially pathogenic mutations in 11 families, with three having a mutation in ANOS1 (X-linked recessive); three and four having a mutation in FGFR1 and CHD7, respectively (autosomal dominant); and one having two TACR3 mutations (autosomal recessive)...
September 15, 2017: Journal of Pediatric Endocrinology & Metabolism: JPEM
https://www.readbyqxmd.com/read/28914635/clinical-genetics-of-craniosynostosis
#20
Andrew O M Wilkie, David Johnson, Steven A Wall
PURPOSE OF REVIEW: When providing accurate clinical diagnosis and genetic counseling in craniosynostosis, the challenge is heightened by knowledge that etiology in any individual case may be entirely genetic, entirely environmental, or anything in between. This review will scope out how recent genetic discoveries from next-generation sequencing have impacted on the clinical genetic evaluation of craniosynostosis. RECENT FINDINGS: Survey of a 13-year birth cohort of patients treated at a single craniofacial unit demonstrates that a genetic cause of craniosynostosis can be identified in one quarter of cases...
September 14, 2017: Current Opinion in Pediatrics
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