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https://www.readbyqxmd.com/read/29786090/crispr-off-target-analysis-in-genetically-engineered-rats-and-mice
#1
Keith R Anderson, Maximilian Haeussler, Colin Watanabe, Vasantharajan Janakiraman, Jessica Lund, Zora Modrusan, Jeremy Stinson, Qixin Bei, Andrew Buechler, Charles Yu, Sobha R Thamminana, Lucinda Tam, Michael-Anne Sowick, Tuija Alcantar, Natasha O'Neil, Jinjie Li, Linda Ta, Lisa Lima, Merone Roose-Girma, Xin Rairdan, Steffen Durinck, Søren Warming
Despite widespread use of CRISPR, comprehensive data on the frequency and impact of Cas9-mediated off-targets in modified rodents are limited. Here we present deep-sequencing data from 81 genome-editing projects on mouse and rat genomes at 1,423 predicted off-target sites, 32 of which were confirmed, and show that high-fidelity Cas9 versions reduced off-target mutation rates in vivo. Using whole-genome sequencing data from ten mouse embryos, treated with a single guide RNA (sgRNA), and from their genetic parents, we found 43 off-targets, 30 of which were predicted by an adapted version of GUIDE-seq...
May 21, 2018: Nature Methods
https://www.readbyqxmd.com/read/29785674/assembly-of-a-complete-genome-sequence-for-gemmata-obscuriglobus-reveals-a-novel-prokaryotic-rrna-operon-gene-architecture
#2
Josef D Franke, Wilson R Blomberg, Robert T Todd, Robert W Thomas, Anna M Selmecki
Gemmata obscuriglobus is a Gram-negative bacterium with several intriguing biological features. Here, we present a complete, de novo whole genome assembly for G. obscuriglobus which consists of a single, circular 9 Mb chromosome, with no plasmids detected. The genome was annotated using the NCBI Prokaryotic Genome Annotation pipeline to generate common gene annotations. Analysis of the rRNA genes revealed three interesting features for a bacterium. First, linked G. obscuriglobus rrn operons have a unique gene order, 23S-5S-16S, compared to typical prokaryotic rrn operons (16S-23S-5S)...
May 21, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29785619/comparative-analyses-of-the-mitochondrial-genome-of-the-sheep-ked-melophagus-ovinus-diptera-hippoboscidae-from-different-geographical-origins-in-china
#3
Jia-Min Tang, Fen Li, Tian-Yin Cheng, De-Yong Duan, Guo-Hua Liu
The sheep ked Melophagus ovinus is mainly found in Europe, Northwestern Africa, and Asia. Although M. ovinus is an important ectoparasite of sheep in many countries, the population genetics, molecular biology, and systematics of this ectoparasite remain poorly understood. Herein, we determined the mitochondrial (mt) genome of M. ovinus from Gansu Province, China (MOG) and compared with that of M. ovinus Xinjiang Uygur Autonomous Region, China (MOX). The mt genome sequence (15,044 bp) of M. ovinus MOG was significantly shorter (529 bp) than M...
May 22, 2018: Parasitology Research
https://www.readbyqxmd.com/read/29785479/ngspanpipe-a-pipeline-for-pan-genome-identification-in-microbial-strains-from-experimental-reads
#4
Umay Kulsum, Arti Kapil, Harpreet Singh, Punit Kaur
Recent advancements in sequencing technologies have decreased both time span and cost for sequencing the whole bacterial genome. High-throughput Next-Generation Sequencing (NGS) technology has led to the generation of enormous data concerning microbial populations publically available across various repositories. As a consequence, it has become possible to study and compare the genomes of different bacterial strains within a species or genus in terms of evolution, ecology and diversity. Studying the pan-genome provides insights into deciphering microevolution, global composition and diversity in virulence and pathogenesis of a species...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29785397/whole-genome-sequencing-of-greater-amberjack-seriola-dumerili-for-snp-identification-on-aligned-scaffolds-and-genome-structural-variation-analysis-using-parallel-resequencing
#5
Kazuo Araki, Jun-Ya Aokic, Junya Kawase, Kazuhisa Hamada, Akiyuki Ozaki, Hiroshi Fujimoto, Ikki Yamamoto, Hironori Usuki
Greater amberjack ( Seriola dumerili ) is distributed in tropical and temperate waters worldwide and is an important aquaculture fish. We carried out de novo sequencing of the greater amberjack genome to construct a reference genome sequence to identify single nucleotide polymorphisms (SNPs) for breeding amberjack by marker-assisted or gene-assisted selection as well as to identify functional genes for biological traits. We obtained 200 times coverage and constructed a high-quality genome assembly using next generation sequencing technology...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29785087/transcriptomic-impacts-of-rumen-epithelium-induced-by-butyrate-infusion-in-dairy-cattle-in-dry-period
#6
Ransom L Baldwin, Robert W Li, Yankai Jia, Cong-Jun Li
The purpose of this study was to evaluate the effects of butyrate infusion on rumen epithelial transcriptome. Next-generation sequencing (NGS) and bioinformatics are used to accelerate our understanding of regulation in rumen epithelial transcriptome of cattle in the dry period induced by butyrate infusion at the level of the whole transcriptome. Butyrate, as an essential element of nutrients, is a histone deacetylase (HDAC) inhibitor that can alter histone acetylation and methylation, and plays a prominent role in regulating genomic activities influencing rumen nutrition utilization and function...
2018: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/29785015/frequent-transmission-of-the-mycobacterium-tuberculosis-beijing-lineage-and-positive-selection-for-the-esxw-beijing-variant-in-vietnam
#7
Kathryn E Holt, Paul McAdam, Phan Vuong Khac Thai, Nguyen Thuy Thuong Thuong, Dang Thi Minh Ha, Nguyen Ngoc Lan, Nguyen Huu Lan, Nguyen Thi Quynh Nhu, Hoang Thanh Hai, Vu Thi Ngoc Ha, Guy Thwaites, David J Edwards, Artika P Nath, Kym Pham, David B Ascher, Jeremy Farrar, Chiea Chuen Khor, Yik Ying Teo, Michael Inouye, Maxine Caws, Sarah J Dunstan
To examine the transmission dynamics of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients in Ho Chi Minh City, Vietnam, we sequenced the whole genomes of 1,635 isolates and compared these with 3,144 isolates from elsewhere. The data identify an underlying burden of disease caused by the endemic Mtb lineage 1 associated with the activation of long-term latent infection, and a threefold higher burden associated with the more recently introduced Beijing lineage and lineage 4 Mtb strains. We find that Beijing lineage Mtb is frequently transferred between Vietnam and other countries, and detect higher levels of transmission of Beijing lineage strains within this host population than the endemic lineage 1 Mtb...
May 21, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29785002/using-single-molecule-mrna-fluorescent-in-situ-hybridization-rna-fish-to-quantify-mrnas-in-individual-murine-oocytes-and-embryos
#8
Fang Xie, Kelsey A Timme, Jennifer R Wood
Changes in abundance of mRNAs during oocyte growth and maturation and during pre-implantation embryo development have been documented using quantitative real-time RT-PCR (qPCR), microarray analyses, and whole genome sequencing. However, these techniques require amplification of mRNAs, normalization using housekeeping genes, can be biased for abundant transcripts, and/or require large numbers of oocytes and embryos which can be difficult to acquire from mammalian species. We optimized a single molecule RNA fluorescence in situ hybridization (RNA-FISH) protocol, which amplifies fluorescence signal to detect candidate transcripts, for use with individual oocytes and embryos...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784861/genome-variation-and-molecular-epidemiology-of-salmonella-typhimurium-pathovariants
#9
Priscilla Branchu, Matt Bawn, Robert A Kingsley
Salmonella enterica serovar Typhimurium ( S Typhimurium) is one of approximately 2500 distinct serovars of the genus Salmonella , but is exceptional in its wide distribution in the environment, livestock, and wild animals. S Typhimurium causes a large proportion of non-typhoid Salmonella (NTS) infections, accounting for a quarter of infections, second only to S Enteritidis in incidence. S Typhimurium was once considered the archetypal broad host range Salmonella serovar due to its wide distribution in livestock and wild animals and much of what we know of the interaction of Salmonella with the host comes from research using a small number of laboratory strains of the serovar (LT2, SL1344, ATCC14028)...
May 21, 2018: Infection and Immunity
https://www.readbyqxmd.com/read/29784605/code-seq-an-augmented-whole-exome-sequencing-enables-the-accurate-detection-of-cnvs-and-mutations-in-mendelian-obesity-and-intellectual-disability
#10
Louise Montagne, Mehdi Derhourhi, Amélie Piton, Bénédicte Toussaint, Emmanuelle Durand, Emmanuel Vaillant, Dorothée Thuillier, Stefan Gaget, Franck De Graeve, Iandry Rabearivelo, Amélie Lansiaux, Bruno Lenne, Sylvie Sukno, Rachel Desailloud, Miriam Cnop, Ramona Nicolescu, Lior Cohen, Jean-François Zagury, Mélanie Amouyal, Jacques Weill, Jean Muller, Olivier Sand, Bruno Delobel, Philippe Froguel, Amélie Bonnefond
OBJECTIVE: The molecular diagnosis of extreme forms of obesity, in which accurate detection of both copy number variations (CNVs) and point mutations, is crucial for an optimal care of the patients and genetic counseling for their families. Whole-exome sequencing (WES) has benefited considerably this molecular diagnosis, but its poor ability to detect CNVs remains a major limitation. We aimed to develop a method (CoDE-seq) enabling the accurate detection of both CNVs and point mutations in one step...
May 16, 2018: Molecular Metabolism
https://www.readbyqxmd.com/read/29783821/-clinical-and-genetic-analysis-of-eleven-pediatric-patients-with-alagille-syndrome
#11
L Guo, S T Zhao, Y Cheng, M Deng, H Li, Y Z Song, X R Cai, Q Zhou
Objective: To explore the clinical and molecular genetic features of patients with Alagille syndrome (AS). Methods: The clinical data of eleven pediatric patients, who were suspected to have AS at the Department of Pediatrics in the First Affiliated Hospital of Jinan University from August 2010 to March 2017, were collected and analyzed. Genomic DNA was extracted from peripheral blood leukocytes of the patients and their parents. For 5 patients collected before March 2006, all JAG1 exons and their flanking sequences were directly sequenced...
May 2, 2018: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/29783622/risk-mitigation-for-immunocompromised-consumers-of-mucormycete-spoiled-and-fermented-foods-germain-guidance-and-remaining-needs
#12
REVIEW
Abigail B Snyder, Randy W Worobo
Mucoralean invasive fungal infections, while unusual among the general population, have a high mortality rate among immunocompromised individuals who become infected. They are also common spoilage organisms in cultured dairy products, some fresh produce, and baked goods. Additionally, Mucor and Rhizopus spp. are utilized in the production of traditional fermented foods including mold ripened cheeses and fermented soy products. The risk that consumption of these foods poses to immunocompromised consumers has been previously identified...
May 18, 2018: Microorganisms
https://www.readbyqxmd.com/read/29783026/a-prolonged-and-large-outbreak-of-invasive-group-a-streptococcal-disease-within-a-nursing-home-repeated-intra-facility-transmission-of-a-single-strain
#13
S A Nanduri, B J Metcalf, M A Arwady, C Edens, M A Lavin, J Morgan, W Clegg, A Beron, J P Albertson, R Link-Gelles, A Ogundimu, J Gold, D Jackson, S Chochua, N Stone, C Van Beneden, K Fleming-Dutra, B Beall
OBJECTIVES: Multiple invasive group A streptococcal (GAS) infections were reported to public health by a skilled nursing facility (Facility A) in Illinois between May 2014 and August 2016. Cases continued despite interventions including antibiotic prophylaxis for all residents and staff. Two other geographically close facilities reported contemporaneous outbreaks of GAS. We investigated potential reasons for ongoing transmission. METHODS: We obtained epidemiologic data from chart review of cases and review of facility and public health records from previous investigations into the outbreak...
May 18, 2018: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/29782933/whole-genome-sequencing-and-analyses-identify-high-genetic-heterogeneity-and-diversity-of-rotavirus-genotype-p-6-strains-circulating-in-africa
#14
Martin M Nyaga, Yi Tan, Mapaseka L Seheri, Rebecca A Halpin, Asmik Akopov, Karla M Stucker, Nadia B Fedorova, Susmita Shrivastava, A Duncan Steele, Jason M Mwenda, Brett E Pickett, Suman R Das, M Jeffery Mphahlele
Rotavirus A (RVA) exhibits a wide genotype diversity globally. Little is known about the genetic composition of genotype P[6] from Africa. This study investigated possible evolutionary mechanisms leading to genetic diversity of genotype P[6] VP4 sequences. Phylogenetic analyses on 167 P[6] VP4 full-length sequences were conducted, which included six porcine-origin sequences. Of the 167 sequences, 57 were newly acquired through whole genome sequencing as part of this study. The other 110 sequences were all publicly-available global P[6] VP4 full-length sequences downloaded from GenBank...
May 18, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29780850/canada-wide-epidemic-of-emm74-group-a-streptococcus-invasive-disease
#15
Sarah Teatero, Allison McGeer, Gregory J Tyrrell, Linda Hoang, Hanan Smadi, Marc-Christian Domingo, Paul N Levett, Michael Finkelstein, Ken Dewar, Agron Plevneshi, Taryn B T Athey, Jonathan B Gubbay, Michael R Mulvey, Irene Martin, Walter Demczuk, Nahuel Fittipaldi
Background: The number of invasive group A Streptococcus (iGAS) infections due to hitherto extremely rare type emm74 strains has increased in several Canadian provinces since late 2015. We hypothesized that the cases recorded in the different provinces are linked and caused by strains of an emm74 clone that recently emerged and expanded explosively. Methods: We analyzed both active and passive surveillance data for iGAS infections and used whole-genome sequencing to investigate the phylogenetic relationships of the emm74 strains responsible for these invasive infections country-wide...
May 2018: Open Forum Infectious Diseases
https://www.readbyqxmd.com/read/29780504/gene-specific-loci-quantitative-and-single-base-resolution-analysis-of-5-formylcytosine-by-compound-mediated-polymerase-chain-reaction
#16
Yafen Wang, Chaoxing Liu, Xiong Zhang, Wei Yang, Fan Wu, Guangrong Zou, Xiaocheng Weng, Xiang Zhou
5-Formylcytosine (5fC) is known as one of the key players in the process of active DNA demethylation and displays essential epigenetic functions in mammals. In spite of the blooming development of whole genome sequencing methods for this modified cytosine base, the easily operated gene specific-loci detection of 5fC has rarely been reported. Herein, we present a compound-mediated analysis of the content and site of 5fC by the polymerase chain reaction (PCR) assay. The molecule, namely azi-BP, which can selectively label 5fC and form a huge group through a click chemistry reaction, hindering the amplification activity of Taq DNA polymerase, acts as a "roadblock" and enables the quantitative analysis of 5fC by quantitative polymerase chain reaction (qPCR)...
April 21, 2018: Chemical Science
https://www.readbyqxmd.com/read/29780368/-salmonella-enterica-prophage-sequence-profiles-reflect-genome-diversity-and-can-be-used-for-high-discrimination-subtyping
#17
Walid Mottawea, Marc-Olivier Duceppe, Andrée A Dupras, Valentine Usongo, Julie Jeukens, Luca Freschi, Jean-Guillaume Emond-Rheault, Jeremie Hamel, Irena Kukavica-Ibrulj, Brian Boyle, Alexander Gill, Elton Burnett, Eelco Franz, Gitanjali Arya, Joel T Weadge, Samantha Gruenheid, Martin Wiedmann, Hongsheng Huang, France Daigle, Sylvain Moineau, Sadjia Bekal, Roger C Levesque, Lawrence D Goodridge, Dele Ogunremi
Non-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP) typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella ...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29780002/whole-genome-sequencing-algorithm-for-blood-group-typing
#18
Robert Flower, Eileen Roulis, Catherine Hyland
No abstract text is available yet for this article.
May 17, 2018: Lancet Haematology
https://www.readbyqxmd.com/read/29780001/automated-typing-of-red-blood-cell-and-platelet-antigens-a-whole-genome-sequencing-study
#19
William J Lane, Connie M Westhoff, Nicholas S Gleadall, Maria Aguad, Robin Smeland-Wagman, Sunitha Vege, Daimon P Simmons, Helen H Mah, Matthew S Lebo, Klaudia Walter, Nicole Soranzo, Emanuele Di Angelantonio, John Danesh, David J Roberts, Nick A Watkins, Willem H Ouwehand, Adam S Butterworth, Richard M Kaufman, Heidi L Rehm, Leslie E Silberstein, Robert C Green
BACKGROUND: There are more than 300 known red blood cell (RBC) antigens and 33 platelet antigens that differ between individuals. Sensitisation to antigens is a serious complication that can occur in prenatal medicine and after blood transfusion, particularly for patients who require multiple transfusions. Although pre-transfusion compatibility testing largely relies on serological methods, reagents are not available for many antigens. Methods based on single-nucleotide polymorphism (SNP) arrays have been used, but typing for ABO and Rh-the most important blood groups-cannot be done with SNP typing alone...
May 17, 2018: Lancet Haematology
https://www.readbyqxmd.com/read/29779775/accuracy-of-whole-genome-sequencing-versus-phenotypic-mgit-and-commercial-molecular-tests-for-detection-of-drug-resistant-mycobacterium-tuberculosis-isolated-from-patients-in-brazil-and-mozambique
#20
Cinara Silva Feliciano, Evangelina Inacio Namburete, Jéssica Rodrigues Plaça, Kamila Peronni, Anzaan Dippenaar, Robin Mark Warren, Wilson Araújo Silva, Valdes Roberto Bollela
BACKGROUND: The fast and accurate diagnosis of drug-resistant tuberculosis (DR-TB) is critical to reducing the spread of disease. Although commercial genotypic drug-susceptibility tests (DST) are close to the goal, they are still not able to detect all relevant DR-TB related mutations. Whole genome sequencing (WGS) allows better comprehension of DR-TB with a great discriminatory power. We aimed to evaluate WGS in M. tuberculosis isolates compared with phenotypic and genotypic DST. METHODS: This cross-sectional study evaluated 30 isolates from patients with detected DR-TB in Brazil and Mozambique...
May 2018: Tuberculosis
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