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genome assembly brucella

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https://www.readbyqxmd.com/read/27811090/draft-genome-sequences-of-five-clinical-strains-of-brucella-melitensis-isolated-from-patients-residing-in-kuwait
#1
Mohd Wasif Khan, Nazima Habibi, Faraz Shaheed, Abu Salim Mustafa
Human brucellosis is a neglected and underrecognized infection of widespread geographic distribution. Brucellosis is present on all inhabited continents and endemic in many areas of the world, including Kuwait and the Middle East. Here, we present draft genome assemblies of five Brucella melitensis strains isolated from brucellosis patients in Kuwait.
November 3, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27595444/identification-of-brucella-melitensis-rev-1-vaccine-strain-genetic-markers-towards-understanding-the-molecular-mechanism-behind-virulence-attenuation
#2
Mohammad Nouh Issa, Yaqoub Ashhab
Brucella melitensis Rev.1 is an avirulent strain that is widely used as a live vaccine to control brucellosis in small ruminants. Although an assembled draft version of Rev.1 genome has been available since 2009, this genome has not been investigated to characterize this important vaccine. In the present work, we used the draft genome of Rev.1 to perform a thorough genomic comparison and sequence analysis to identify and characterize the panel of its unique genetic markers. The draft genome of Rev.1 was compared with genome sequences of 36 different Brucella melitensis strains from the Brucella project of the Broad Institute of MIT and Harvard...
September 22, 2016: Vaccine
https://www.readbyqxmd.com/read/26702310/on-genome-annotation-of-brucellaphage-gadvasu-bpg-discovery-of-orfans-for-integrated-systems-biology-approaches
#3
Deepti Chachra, Pushpinder Kaur, Prasad Siddavatam, Prashanth Suravajhala, Hari Mohan Saxena
Brucellaphage Gadvasu (BpG) is a lytic phage infecting Brucella spp. Brucellaphages contain dsDNA as genetic material and are short-tailed particles with host-specificity. Here, we report the challenges on annotation in the complete genome sequence of BpG when compared with that of a recent broad host-range brucellaphage Pr, an original reference genome. The extracted DNA was subjected to genome sequencing with Illumina technology and assembled using SSAKE/Velvet. A significant number of genes were found to be similar between the phages with sequence analysis revealing conserved open reading frames that correspond to 33 gene ontology classifiers, transcriptional terminators and a few putative transcriptional promoters...
December 2015: Systems and Synthetic Biology
https://www.readbyqxmd.com/read/25820207/comparison-of-brucella-canis-genomes-isolated-from-different-countries-shows-multiple-variable-regions
#4
COMPARATIVE STUDY
Miryan Margot Sánchez-Jiménez, Juan Pablo Isaza, Juan F Alzate, Martha Olivera-Angel
Brucella canis is a pathogenic bacterium for dogs and its zoonotic potential has been increasing in recent years. In this study, we report the sequencing, annotation and analysis of the genome of Brucella canis strain Oliveri isolated from a dog in a breeding kennel in Medellín, Colombia, South America. Whole genome shotgun sequencing was carried out using the ROCHE 454 GS FLX Titanium technology at the National Center for Genomic Sequencing-CNSG in Medellin, Colombia. The assembly procedure was performed using Newbler v2...
July 2015: Genomics
https://www.readbyqxmd.com/read/25291772/complete-genome-assembly-of-reference-strain-ochrobactrum-anthropi-atcc-49687
#5
T D Minogue, H A Daligault, K W Davenport, K A Bishop-Lilly, D C Bruce, P S Chain, O Chertkov, S R Coyne, T Freitas, K G Frey, J Jaissle, G I Koroleva, J T Ladner, G F Palacios, C L Redden, Y Xu, S L Johnson
Ochrobactrum anthropi is an occasional cause of nosocomial infections; however, interest in the organism lies in its phylogenetic proximity to the genus Brucella. Here, we present the 4.9-Mb finished genome of Ochrobactrum anthropi ATCC 49687, most commonly used as an exclusionary reference organism.
2014: Genome Announcements
https://www.readbyqxmd.com/read/25237024/whole-genome-sequences-of-24-brucella-strains
#6
T D Minogue, H A Daligault, K W Davenport, K A Bishop-Lilly, S M Broomall, D C Bruce, P S Chain, O Chertkov, S R Coyne, K G Frey, H S Gibbons, J Jaissle, G I Koroleva, J T Ladner, C-C Lo, G F Palacios, C L Redden, C N Rosenzweig, M B Scholz, Y Xu, S L Johnson
Brucella species are intracellular zoonotic pathogens which cause, among other pathologies, increased rates of abortion in ruminants. Human infections are generally associated with exposure to contaminated and unpasteurized dairy products; however Brucellae have been developed as bioweapons. Here we present 17 complete and 7 scaffolded genome assemblies of Brucella strains.
2014: Genome Announcements
https://www.readbyqxmd.com/read/25035330/whole-genome-sequence-of-brucella-canis-strain-sva13-isolated-from-an-infected-dog
#7
Rene Kaden, Joakim Agren, Sevinc Ferrari, Martina Lindberg, Stina Bäckman, Tara Wahab
An outbreak of canine brucellosis in Sweden was confirmed by the National Veterinary Institute (SVA) in August 2013. The whole genome of the causative agent was sequenced, assembled, and analyzed.
2014: Genome Announcements
https://www.readbyqxmd.com/read/22967795/improved-variation-calling-via-an-iterative-backbone-remapping-and-local-assembly-method-for-bacterial-genomes
#8
COMPARATIVE STUDY
Hongseok Tae, Robert E Settlage, Shamira Shallom, Jasmin H Bavarva, Dale Preston, Gregory N Hawkins, L Garry Adams, Harold R Garner
Sequencing data analysis remains limiting and problematic, especially for low complexity repeat sequences and transposon elements due to inherent sequencing errors and short sequence read lengths. We have developed a program, ReviSeq, which uses a hybrid method composed of iterative remapping and local assembly upon a bacterial sequence backbone. Application of this method to six Brucella suis field isolates compared to the newly revised B. suis 1330 reference genome identified on average 13, 15, 19 and 9 more variants per sample than STAMPY/SAMtools, BWA/SAMtools, iCORN and BWA/PINDEL pipelines, and excluded on average 4, 2, 3 and 19 variants per sample, respectively...
November 2012: Genomics
https://www.readbyqxmd.com/read/22919638/the-small-protein-cydx-is-required-for-function-of-cytochrome-bd-oxidase-in-brucella-abortus
#9
Yao-Hui Sun, Maarten F de Jong, Andreas B den Hartigh, Christelle M Roux, Hortensia G Rolán, Renée M Tsolis
A large number of hypothetical genes potentially encoding small proteins of unknown function are annotated in the Brucella abortus genome. Individual deletion of 30 of these genes identified four mutants, in BAB1_0355, BAB2_0726, BAB2_0470, and BAB2_0450 that were highly attenuated for infection. BAB2_0726, an YbgT-family protein located at the 3' end of the cydAB genes encoding cytochrome bd ubiquinal oxidase, was designated cydX. A B. abortus cydX mutant lacked cytochrome bd oxidase activity, as shown by increased sensitivity to H(2)O(2), decreased acid tolerance and increased resistance to killing by respiratory inhibitors...
2012: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/22038969/revised-genome-sequence-of-brucella-suis-1330
#10
Hongseok Tae, Shamira Shallom, Robert Settlage, Dale Preston, L Garry Adams, Harold R Garner
Brucella suis is a causative agent of porcine brucellosis. We report the resequencing of the original sample upon which the published sequence of Brucella suis 1330 is based and describe the differences between the published assembly and our assembly at 12 loci.
November 2011: Journal of Bacteriology
https://www.readbyqxmd.com/read/21559467/comparing-de-novo-genome-assembly-the-long-and-short-of-it
#11
Giuseppe Narzisi, Bud Mishra
Recent advances in DNA sequencing technology and their focal role in Genome Wide Association Studies (GWAS) have rekindled a growing interest in the whole-genome sequence assembly (WGSA) problem, thereby, inundating the field with a plethora of new formalizations, algorithms, heuristics and implementations. And yet, scant attention has been paid to comparative assessments of these assemblers' quality and accuracy. No commonly accepted and standardized method for comparison exists yet. Even worse, widely used metrics to compare the assembled sequences emphasize only size, poorly capturing the contig quality and accuracy...
2011: PloS One
https://www.readbyqxmd.com/read/18809265/the-putative-penicillin-binding-proteins-1-and-2-are-important-for-viability-growth-and-cell-morphology-of-brucella-melitensis
#12
Aloka B Bandara, Gerhardt G Schurig, Nammalwar Sriranganathan, Rajeev Prasad, Stephen M Boyle
The penicillin-binding proteins (PBPs) are enzymes that regulate the assembly of the peptidoglycan layer of the bacterial cell wall. The genome of Brucella melitensis strain 16M possesses seven pbp genes: three in pbp-1 family (designated as 1A, 1B, and 1C); one in pbp-2 family; and three in pbp-6 family (designated as 6A, 6B, and 6C). We investigated the importance of pbp-1 and pbp-2 genes to viability, cell morphology and infectivity of B. melitensis. A recombinant B. melitensis strain (designated 16MDeltapbp1C) was generated by disrupting the pbp-1C of strain 16M by allelic exchange...
February 2, 2009: Veterinary Microbiology
https://www.readbyqxmd.com/read/14707177/hierarchical-scaffolding-with-bambus
#13
COMPARATIVE STUDY
Mihai Pop, Daniel S Kosack, Steven L Salzberg
The output of a genome assembler generally comprises a collection of contiguous DNA sequences (contigs) whose relative placement along the genome is not defined. A procedure called scaffolding is commonly used to order and orient these contigs using paired read information. This ordering of contigs is an essential step when finishing and analyzing the data from a whole-genome shotgun project. Most recent assemblers include a scaffolding module; however, users have little control over the scaffolding algorithm or the information produced...
January 2004: Genome Research
https://www.readbyqxmd.com/read/11918819/bacterial-secrets-of-secretion-euroconference-on-the-biology-of-type-iv-secretion-processes
#14
Christian Baron, David OCallaghan, Erich Lanka
Type IV secretion systems (TFSS) mediate secretion or direct cell-to-cell transfer of virulence factors (proteins or protein-DNA complexes) from many Gram-negative animal, human and plant pathogens, such as Agrobacterium tumefaciens, Bartonella tribocorum, Bordetella pertussis, Brucella suis, Helicobacter pylori, Legionella pneumophila and Rickettsia prowazekii, into eukaryotic cells. Bacterial conjugation is also classified as a TFSS-like process mediating the spread of broad-host-range plasmids between Gram-negative bacteria such as RP4 and R388, which carry antibiotic resistance genes...
March 2002: Molecular Microbiology
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