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https://www.readbyqxmd.com/read/28098813/reverse-vaccinology-an-approach-for-identifying-leptospiral-vaccine-candidates
#1
REVIEW
Odir A Dellagostin, André A Grassmann, Caroline Rizzi, Rodrigo A Schuch, Sérgio Jorge, Thais L Oliveira, Alan J A McBride, Daiane D Hartwig
Leptospirosis is a major public health problem with an incidence of over one million human cases each year. It is a globally distributed, zoonotic disease and is associated with significant economic losses in farm animals. Leptospirosis is caused by pathogenic Leptospira spp. that can infect a wide range of domestic and wild animals. Given the inability to control the cycle of transmission among animals and humans, there is an urgent demand for a new vaccine. Inactivated whole-cell vaccines (bacterins) are routinely used in livestock and domestic animals, however, protection is serovar-restricted and short-term only...
January 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28098550/determination-of-elizabethkingia-diversity-by-maldi-tof-mass-spectrometry-and-whole-genome-sequencing
#2
Helle Brander Eriksen, Heidi Gumpert, Cecilie Haase Faurholt, Henrik Westh
In a hospital-acquired infection with multidrug-resistant Elizabethkingia, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene analysis identified the pathogen as Elizabethkingia miricola. Whole-genome sequencing, genus-level core genome analysis, and in silico DNA-DNA hybridization of 35 Elizabethkingia strains indicated that the species taxonomy should be further explored.
February 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28098486/identification-and-characterization-of-genes-on-a-single-subgenome-in-the-hexaploid-wheat-triticum-aestivum-l-genotype-chinese-spring
#3
Jian Ma, Zhi Zheng, Jiri Stiller, Xiu-Jin Lan, Yaxi Liu, Mei Deng, Penghao Wang, Zhien Pu, Guangdeng Chen, Qian-Tao Jiang, Yuming Wei, You-Liang Zheng
Gene loss during the formation of hexaploid bread wheat has been repeatedly reported. However, our knowledge on genome-wide analysis of the genes present on a single subgenome (SSG) in bread wheat is still limited. In this study, by analysing the 'Chinese Spring' chromosome arm shotgun sequences together with high-confidence gene models, we detected 433 genes on a SSG. Greater gene loss was observed in A and D subgenomes compared with B subgenome. More than 79% of the orthologs for these SSG genes were detected in diploid and tetraploid relatives of hexaploid wheat...
November 1, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28098174/novel-g9-rotavirus-strains-co-circulate-in-children-and-pigs-taiwan
#4
Fang-Tzy Wu, Krisztián Bányai, Baoming Jiang, Luke Tzu-Chi Liu, Szilvia Marton, Yhu-Chering Huang, Li-Min Huang, Ming-Hui Liao, Chao A Hsiung
Molecular epidemiologic studies collecting information of the spatiotemporal distribution of rotavirus VP7 (G) and VP4 (P) genotypes have shown evidence for the increasing global importance of genotype G9 rotaviruses in humans and pigs. Sequence comparison of the VP7 gene of G9 strains identified different lineages to prevail in the respective host species although some of these lineages appear to be shared among heterologous hosts providing evidence of interspecies transmission events. The majority of these events indicates the pig-to-human spillover, although a reverse route of transmission cannot be excluded either...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28098143/efficient-dna-free-genome-editing-of-bread-wheat-using-crispr-cas9-ribonucleoprotein-complexes
#5
Zhen Liang, Kunling Chen, Tingdong Li, Yi Zhang, Yanpeng Wang, Qian Zhao, Jinxing Liu, Huawei Zhang, Cuimin Liu, Yidong Ran, Caixia Gao
Substantial efforts are being made to optimize the CRISPR/Cas9 system for precision crop breeding. The avoidance of transgene integration and reduction of off-target mutations are the most important targets for optimization. Here, we describe an efficient genome editing method for bread wheat using CRISPR/Cas9 ribonucleoproteins (RNPs). Starting from RNP preparation, the whole protocol takes only seven to nine weeks, with four to five independent mutants produced from 100 immature wheat embryos. Deep sequencing reveals that the chance of off-target mutations in wheat cells is much lower in RNP mediated genome editing than in editing with CRISPR/Cas9 DNA...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098136/exome-and-genome-sequencing-of-nasopharynx-cancer-identifies-nf-%C3%AE%C2%BAb-pathway-activating-mutations
#6
Yvonne Y Li, Grace T Y Chung, Vivian W Y Lui, Ka-Fai To, Brigette B Y Ma, Chit Chow, John K S Woo, Kevin Y Yip, Jeongsun Seo, Edwin P Hui, Michael K F Mak, Maria Rusan, Nicole G Chau, Yvonne Y Y Or, Marcus H N Law, Peggy P Y Law, Zoey W Y Liu, Hoi-Lam Ngan, Pok-Man Hau, Krista R Verhoeft, Peony H Y Poon, Seong-Keun Yoo, Jong-Yeon Shin, Sau-Dan Lee, Samantha W M Lun, Lin Jia, Anthony W H Chan, Jason Y K Chan, Paul B S Lai, Choi-Yi Fung, Suet-Ting Hung, Lin Wang, Ann Margaret V Chang, Simion I Chiosea, Matthew L Hedberg, Sai-Wah Tsao, Andrew C van Hasselt, Anthony T C Chan, Jennifer R Grandis, Peter S Hammerman, Kwok-Wai Lo
Nasopharyngeal carcinoma (NPC) is an aggressive head and neck cancer characterized by Epstein-Barr virus (EBV) infection and dense lymphocyte infiltration. The scarcity of NPC genomic data hinders the understanding of NPC biology, disease progression and rational therapy design. Here we performed whole-exome sequencing (WES) on 111 micro-dissected EBV-positive NPCs, with 15 cases subjected to further whole-genome sequencing (WGS), to determine its mutational landscape. We identified enrichment for genomic aberrations of multiple negative regulators of the NF-κB pathway, including CYLD, TRAF3, NFKBIA and NLRC5, in a total of 41% of cases...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28096531/the-first-imported-case-of-rift-valley-fever-in-china-reveals-a-genetic-reassortment-of-different-viral-lineages
#7
Jingyuan Liu, Yulan Sun, Weifeng Shi, Shuguang Tan, Yang Pan, Shujuan Cui, Qingchao Zhang, Xiangfeng Dou, Yanning Lv, Xinyu Li, Xitai Li, Lijuan Chen, Chuansong Quan, Qianli Wang, Yingze Zhao, Qiang Lv, Wenhao Hua, Hui Zeng, Zhihai Chen, Haofeng Xiong, Chengyu Jiang, Xinghuo Pang, Fujie Zhang, Mifang Liang, Guizhen Wu, George F Gao, William J Liu, Ang Li, Quanyi Wang
We report the first imported case of Rift Valley fever (RVF) in China. The patient returned from Angola, a non-epidemic country, with an infection of a new reassortant from different lineages of Rift Valley fever viruses (RVFVs). The patient developed multiorgan dysfunction and gradually recovered with continuous renal replacement therapy and a short regimen of methylprednisolone treatment. The disordered cytokines and chemokines in the plasma of the patient revealed hypercytokinemia, but the levels of protective cytokines were low upon admission and fluctuated as the disease improved...
January 18, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/28096484/evolutionary-dynamics-of-pandemic-methicillin-sensitive-staphylococcus-aureus-st398-and-its-international-spread-via-routes-of-human-migration
#8
Anne-Catrin Uhlemann, Paul R McAdam, Sean B Sullivan, Justin R Knox, Hossein Khiabanian, Raul Rabadan, Peter R Davies, J Ross Fitzgerald, Franklin D Lowy
: Methicillin-susceptible Staphylococcus aureus (MSSA) accounts for the majority of S. aureus infections globally, and yet surprisingly little is known about its clonal evolution. We applied comparative whole-genome sequencing (WGS) analyses to epidemiologically and geographically diverse ST398-MSSA, a pandemic lineage affecting both humans and livestock. Bayesian phylogenetic analysis predicted divergence of human-associated ST398-MSSA ~40 years ago. Isolates from Midwestern pigs and veterinarians differed substantially from those in New York City (NYC)...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28096395/genomic-analysis-reveals-major-determinants-of-cis-regulatory-variation-in-capsella-grandiflora
#9
Kim A Steige, Benjamin Laenen, Johan Reimegård, Douglas G Scofield, Tanja Slotte
Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE)...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28095770/the-unique-genomic-landscape-surrounding-the-epsps-gene-in-glyphosate-resistant-amaranthus-palmeri-a-repetitive-path-to-resistance
#10
William T Molin, Alice A Wright, Amy Lawton-Rauh, Christopher A Saski
BACKGROUND: The expanding number and global distributions of herbicide resistant weedy species threaten food, fuel, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amaranthus palmeri S. Wats has rapidly evolved resistance to glyphosate primarily through massive amplification and insertion of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene across the genome. Increased EPSPS gene copy numbers results in higher titers of the EPSPS enzyme, the target of glyphosate, and confers resistance to glyphosate treatment...
January 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28095098/reduced-penetrance-in-a-large-caucasian-pedigree-with-stickler-syndrome
#11
Stuart W Tompson, Charles Johnson, Diana Abbott, Benjamin Bakall, Vincent Soler, Tammy L Yanovitch, Kristina N Whisenhunt, Thomas Klemm, Steve Rozen, Edwin M Stone, Max Johnson, Terri L Young
BACKGROUND: In a four-generation Caucasian family variably diagnosed with autosomal dominant (AD) Stickler or Wagner disease, commercial gene screening failed to identify a mutation in COL2A1 or VCAN. We utilized linkage mapping and exome sequencing to identify the causal variant. MATERIALS AND METHODS: Genomic DNA samples collected from 40 family members were analyzed. A whole-genome linkage scan was performed using Illumina HumanLinkage-24 BeadChip followed by two-point and multipoint linkage analyses using FASTLINK and MERLIN...
January 17, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28094797/whole-genome-sequencing-data-and-de-novo-draft-assemblies-for-66-teleost-species
#12
Martin Malmstrøm, Michael Matschiner, Ole K Tørresen, Kjetill S Jakobsen, Sissel Jentoft
Teleost fishes comprise more than half of all vertebrate species, yet genomic data are only available for 0.2% of their diversity. Here, we present whole genome sequencing data for 66 new species of teleosts, vastly expanding the availability of genomic data for this important vertebrate group. We report on de novo assemblies based on low-coverage (9-39×) sequencing and present detailed methodology for all analyses. To facilitate further utilization of this data set, we present statistical analyses of the gene space completeness and verify the expected phylogenetic position of the sequenced genomes in a large mitogenomic context...
January 17, 2017: Scientific Data
https://www.readbyqxmd.com/read/28094312/unraveling-the-microbial-processes-of-black-band-disease-in-corals-through-integrated-genomics
#13
Yui Sato, Edmund Y S Ling, Dmitrij Turaev, Patrick Laffy, Karen D Weynberg, Thomas Rattei, Bette L Willis, David G Bourne
Coral disease outbreaks contribute to the ongoing degradation of reef ecosystems, however, microbial mechanisms underlying the onset and progression of most coral diseases are poorly understood. Black band disease (BBD) manifests as a cyanobacterial-dominated microbial mat that destroys coral tissues as it rapidly spreads over coral colonies. To elucidate BBD pathogenesis, we apply a comparative metagenomic and metatranscriptomic approach to identify taxonomic and functional changes within microbial lesions during in-situ development of BBD from a comparatively benign stage termed cyanobacterial patches...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28093659/clinical-and-molecular-relevance-of-mutant-allele-tumor-heterogeneity-in-breast-cancer
#14
Ding Ma, Yi-Zhou Jiang, Xi-Yu Liu, Yi-Rong Liu, Zhi-Ming Shao
PURPOSE: Intra-tumor heterogeneity (ITH) plays a pivotal role in driving breast cancer progression and therapeutic resistance. We used a mutant-allele tumor heterogeneity (MATH) algorithm to measure ITH and explored its correlation with clinical parameters and multi-omics data. METHODS: We assessed 916 female breast cancer patients from The Cancer Genome Atlas. We calculated the MATH values from whole-exome sequencing data and further investigated their correlation with clinical characteristics, somatic mutations, somatic copy number alterations (SCNAs), and gene enrichment...
January 16, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28093063/whole-genome-sequence-based-genomic-prediction-in-laying-chickens-with-different-genomic-relationship-matrices-to-account-for-genetic-architecture
#15
Guiyan Ni, David Cavero, Anna Fangmann, Malena Erbe, Henner Simianer
BACKGROUND: With the availability of next-generation sequencing technologies, genomic prediction based on whole-genome sequencing (WGS) data is now feasible in animal breeding schemes and was expected to lead to higher predictive ability, since such data may contain all genomic variants including causal mutations. Our objective was to compare prediction ability with high-density (HD) array data and WGS data in a commercial brown layer line with genomic best linear unbiased prediction (GBLUP) models using various approaches to weight single nucleotide polymorphisms (SNPs)...
January 16, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28092682/limited-heterogeneity-of-known-driver-gene-mutations-among-the-metastases-of-individual-patients-with-pancreatic-cancer
#16
Alvin P Makohon-Moore, Ming Zhang, Johannes G Reiter, Ivana Bozic, Benjamin Allen, Deepanjan Kundu, Krishnendu Chatterjee, Fay Wong, Yuchen Jiao, Zachary A Kohutek, Jungeui Hong, Marc Attiyeh, Breanna Javier, Laura D Wood, Ralph H Hruban, Martin A Nowak, Nickolas Papadopoulos, Kenneth W Kinzler, Bert Vogelstein, Christine A Iacobuzio-Donahue
The extent of heterogeneity among driver gene mutations present in naturally occurring metastases-that is, treatment-naive metastatic disease-is largely unknown. To address this issue, we carried out 60× whole-genome sequencing of 26 metastases from four patients with pancreatic cancer. We found that identical mutations in known driver genes were present in every metastatic lesion for each patient studied. Passenger gene mutations, which do not have known or predicted functional consequences, accounted for all intratumoral heterogeneity...
January 16, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28092681/genomic-analysis-of-globally-diverse-mycobacterium-tuberculosis-strains-provides-insights-into-the-emergence-and-spread-of-multidrug-resistance
#17
Abigail L Manson, Keira A Cohen, Thomas Abeel, Christopher A Desjardins, Derek T Armstrong, Clifton E Barry, Jeannette Brand, Sinéad B Chapman, Sang-Nae Cho, Andrei Gabrielian, James Gomez, Andreea M Jodals, Moses Joloba, Pontus Jureen, Jong Seok Lee, Lesibana Malinga, Mamoudou Maiga, Dale Nordenberg, Ecaterina Noroc, Elena Romancenco, Alex Salazar, Willy Ssengooba, A A Velayati, Kathryn Winglee, Aksana Zalutskaya, Laura E Via, Gail H Cassell, Susan E Dorman, Jerrold Ellner, Parissa Farnia, James E Galagan, Alex Rosenthal, Valeriu Crudu, Daniela Homorodean, Po-Ren Hsueh, Sujatha Narayanan, Alexander S Pym, Alena Skrahina, Soumya Swaminathan, Martie Van der Walt, David Alland, William R Bishai, Ted Cohen, Sven Hoffner, Bruce W Birren, Ashlee M Earl
Multidrug-resistant tuberculosis (MDR-TB), caused by drug-resistant strains of Mycobacterium tuberculosis, is an increasingly serious problem worldwide. Here we examined a data set of whole-genome sequences from 5,310 M. tuberculosis isolates from five continents. Despite the great diversity of these isolates with respect to geographical point of isolation, genetic background and drug resistance, the patterns for the emergence of drug resistance were conserved globally. We have identified harbinger mutations that often precede multidrug resistance...
January 16, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28091882/identification-of-some-main-streptococcus-iniae-associated-proteins-relationship
#18
Fatima El Aamri, José Ángel Guillén, Daniel Padilla, Félix Acosta, Fernando Real
The surface-associated proteins play a key role in bacterial physiology and pathogenesis, and are the major targets in the development of new vaccines. These proteins contribute to the adaptation of bacteria to different hosts and environments. To study differences at the genomic level, we first sequenced the whole genome of Streptococcus iniae from fish (IUSA-1 strain) and compared it to Streptococcus iniae from human (9117 strain), revealing a high similitude between both strains. To gain further insights into host- and environment-specific differences, we then studied proteins in silico and by High Performance Liquid Chromatography...
January 14, 2017: Veterinary Research Communications
https://www.readbyqxmd.com/read/28090080/you-are-where-you-live
#19
Samuel E Kidman, Josephine M Bryant
This month's Genome Watch discusses how whole-genome sequencing of bacteria from several body sites has provided insights into the spatial diversity of bacteria within patients.
January 16, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28090077/clinical-and-biological-insights-from-viral-genome-sequencing
#20
Charlotte J Houldcroft, Mathew A Beale, Judith Breuer
Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages...
January 16, 2017: Nature Reviews. Microbiology
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