keyword
MENU ▼
Read by QxMD icon Read
search

Bacterial genome sequencing

keyword
https://www.readbyqxmd.com/read/29351633/evolutionary-genetics-of-cytoplasmic-incompatibility-genes-cifa-and-cifb-in-prophage-wo-of-wolbachia
#1
Amelia R I Lindsey, Danny W Rice, Sarah R Bordenstein, Andrew W Brooks, Seth R Bordenstein, Irene L G Newton
The bacterial endosymbiont Wolbachia manipulates arthropod reproduction to facilitate its maternal spread through host populations. The most common manipulation is cytoplasmic incompatibility (CI): Wolbachia-infected males produce modified sperm that cause embryonic mortality, unless rescued by embryos harboring the same Wolbachia. The genes underlying CI, cifA and cifB, were recently identified in the eukaryotic association module of Wolbachia's prophage WO. Here, we use transcriptomic and genomic approaches to address three important evolutionary facets of the cif genes...
January 17, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29351563/a-consensus-linkage-map-of-lentil-based-on-dart-markers-from-three-ril-mapping-populations
#2
Duygu Ates, Secil Aldemir, Ahmad Alsaleh, Semih Erdogmus, Seda Nemli, Abdullah Kahriman, Hakan Ozkan, Albert Vandenberg, Bahattin Tanyolac
BACKGROUND: Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. MATERIALS AND METHODS: A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39)...
2018: PloS One
https://www.readbyqxmd.com/read/29351318/invasive-bacterial-disease-trends-and-characterization-of-group-b-streptococcal-isolates-among-young-infants-in-southern-mozambique-2001-2015
#3
Betuel Sigaúque, Miwako Kobayashi, Delfino Vubil, Ariel Nhacolo, Alberto Chaúque, Benild Moaine, Sérgio Massora, Inácio Mandomando, Tacilta Nhampossa, Quique Bassat, Fabiana Pimenta, Clara Menéndez, Maria da Gloria Carvalho, Eusebio Macete, Stephanie J Schrag
BACKGROUND: Maternal group B streptococcal (GBS) vaccines under development hold promise to prevent GBS disease in young infants. Sub-Saharan Africa has the highest estimated disease burden, although data on incidence and circulating strains are limited. We described invasive bacterial disease (IBD) trends among infants <90 days in rural Mozambique during 2001-2015, with a focus on GBS epidemiology and strain characteristics. METHODS: Community-level birth and mortality data were obtained from Manhiça's demographic surveillance system...
2018: PloS One
https://www.readbyqxmd.com/read/29349599/evolution-of-eukaryal-and-archaeal-pseudouridine-synthase-pus10
#4
Elisabeth Fitzek, Archi Joardar, Ramesh Gupta, Matt Geisler
In archaea, pseudouridine (Ψ) synthase Pus10 modifies uridine (U) to Ψ at positions 54 and 55 of tRNA. In contrast, Pus10 is not found in bacteria, where modifications at those two positions are carried out by TrmA (U54 to m5U54) and TruB (U55 to Ψ55). Many eukaryotes have an apparent redundancy; their genomes contain orthologs of archaeal Pus10 and bacterial TrmA and TruB. Although eukaryal Pus10 genes share a conserved catalytic domain with archaeal Pus10 genes, their biological roles are not clear for the two reasons...
January 18, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29348333/draft-genome-sequence-and-annotation-of-the-obligate-bacterial-endosymbiont-caedibacter-taeniospiralis-causative-agent-of-the-killer-phenotype-in-paramecium-tetraurelia
#5
Nestor Zaburannyi, Katrin Grosser, Gilles Gasparoni, Rolf Müller, Martina Schrallhammer, Martin Simon
Caedibacter taeniospiralis is an obligate endosymbiont living in the cytoplasm of Paramecium tetraureliaC. taeniospiralis causes the so-called killer trait, eliminating intraspecific competitors of its host when released into the medium by the concerted action of the unusual protein structure R-body (refractile body) in addition to an as-yet-unknown toxin.
January 18, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29346586/plasflow-predicting-plasmid-sequences-in-metagenomic-data-using-genome-signatures
#6
Pawel S Krawczyk, Leszek Lipinski, Andrzej Dziembowski
Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346073/extensive-conservation-of-prokaryotic-ribosomal-binding-sites-in-known-and-novel-picobirnaviruses
#7
Siddharth R Krishnamurthy, David Wang
Currently, the Leviviridae and Cystoviridae are the only two recognized families of prokaryotic RNA viruses. Picobirnaviruses, which are bisegmented double-stranded RNA viruses commonly found in animal stool samples, are currently thought to be animal viruses, but have not been propagated in cell culture or in an animal model. We hypothesize that picobirnaviruses are prokaryotic RNA viruses. We identified and analyzed the genomes of 38 novel picobirnaviruses and determined that a classical bacterial sequence motif, the ribosomal binding site (RBS), is present in the 5' untranslated regions (5' UTRs) of all of the novel as well as all previously published picobirnavirus sequences...
January 12, 2018: Virology
https://www.readbyqxmd.com/read/29345635/genetic-risk-dysbiosis-and-treatment-stratification-using-host-genome-and-gut-microbiome-in-inflammatory-bowel-disease
#8
Ahmed Moustafa, Weizhong Li, Ericka L Anderson, Emily H M Wong, Parambir S Dulai, William J Sandborn, William Biggs, Shibu Yooseph, Marcus B Jones, J Craig Venter, Karen E Nelson, John T Chang, Amalio Telenti, Brigid S Boland
OBJECTIVES: Inflammatory bowel diseases (IBD), comprised of Crohn's disease (CD) and ulcerative colitis (UC), are characterized by a complex pathophysiology that is thought to result from an aberrant immune response to a dysbiotic luminal microbiota in genetically susceptible individuals. New technologies support the joint assessment of host-microbiome interaction. METHODS: Using whole genome sequencing and shotgun metagenomics, we studied the clinical features, host genome, and stool microbial metagenome of 85 IBD patients, and compared the results to 146 control individuals...
January 18, 2018: Clinical and Translational Gastroenterology
https://www.readbyqxmd.com/read/29340898/epidemiological-aspects-of-healthcare-associated-infections-and-microbial-genomics
#9
C Mirande, I Bizine, A Giannetti, N Picot, A van Belkum
Hospital-acquired infections (HAIs) are a cause of continuously increasing morbidity and mortality. Most of these infections are caused by a limited set of bacterial species, which share the capability to efficiently spread from patient to patient and to easily acquire antibiotic resistance determinants. This renders correct and rapid species identification and antibiotic susceptibility testing (AST) important and underscores the relevance of bacterial epidemiological typing. The latter is needed for the sensitive detection and exact tracing of nosocomial spread of these potentially multidrug-resistant microorganisms (MDRO)...
January 17, 2018: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/29339416/exploring-the-almost-unknown-archaeal-two-component-systems
#10
Tino Krell
Two-component systems (TCS) exist in bacteria and archaea. In contrast to bacterial TCSs little information is available on their archaeal counterparts. In this issue Galperin and coworkers present a bioinformatics analysis of TCS genes from archaeal genome sequences. This study identified different aspects in which bacterial and archaeal TCS mediated signaling differ and forms a sound basis for the experimental design of studies to increase our knowledge on this poorly investigated protein family.
January 16, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29339415/genome-wide-identification-by-transposon-insertion-sequencing-of-escherichia-coli-k1-genes-essential-for-in-vitro-growth-gastrointestinal-colonizing-capacity-and-survival-in-serum
#11
Alex J McCarthy, Richard A Stabler, Peter W Taylor
Escherichia coli K1 strains are major causative agents of invasive disease of the new born. The age dependency of infection can be reproduced in the neonatal rat. Colonization of the small intestine following oral administration of K1 bacteria leads rapidly to invasion of the blood circulation; bacteria that avoid capture by the mesenteric lymphatic system and evade antibacterial mechanisms in the blood may disseminate to cause organ-specific infections such as meningitis. Some E. coli K1 surface constituents, in particular the polysialic acid capsule, are known to contribute to invasive potential but a comprehensive picture of the factors that determine the fully virulent phenotype has not so far emerged...
January 16, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29338683/genomic-repeats-misassembly-and-reannotation-a-case-study-with-long-read-resequencing-of-porphyromonas-gingivalis-reference-strains
#12
Luis Acuña-Amador, Aline Primot, Edouard Cadieu, Alain Roulet, Frédérique Barloy-Hubler
BACKGROUND: Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a major obstacle to genotypic and phenotypic interpretation. In this work, we began with an example from the class Bacteroidia in the phylum Bacteroidetes, which is preponderant among human orodigestive microbiota...
January 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29337163/utility-of-ultra-deep-sequencing-for-detection-of-varicella-zoster-virus-antiviral-resistance-mutations
#13
Mélanie Mercier-Darty, David Boutolleau, Raphaël Lepeule, Christophe Rodriguez, Sonia Burrel
We report the first application of ultra-deep sequencing (UDS) to varicella-zoster virus (VZV) genotypic antiviral testing in a case of acyclovir-resistant VZV infection initially detected by Sanger sequencing within a deeply immunocompromised heart transplant recipient. As added-value compared to Sanger analysis, UDS revealed complex dynamics of viral population under antiviral pressure. Varicella-zoster virus (VZV) is a ubiquitous human herpesvirus affecting populations worldwide. VZV is commonly acquired in youth whose primary infection usually manifests as benign varicella (chickenpox)...
January 11, 2018: Antiviral Research
https://www.readbyqxmd.com/read/29336192/how-mass-spectrometric-approaches-applied-to-bacterial-identification-have-revolutionized-the-study-of-human-gut-microbiota
#14
Grégory Dubourg, Hervé Chaudet, Jean-Christophe Lagier, Didier Raoult
Describing the human hut gut microbiota is one the most exciting challenges of the 21st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions...
January 16, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29331569/salinivibrio-kushneri-sp-nov-a-moderately-halophilic-bacterium-isolated-from-salterns
#15
Clara López-Hermoso, Rafael R de la Haba, Cristina Sánchez-Porro, Antonio Ventosa
Ten Gram-strain-negative, facultatively anaerobic, moderately halophilic bacterial strains, designated AL184T, IB560, IB563, IC202, IC317, MA421, ML277, ML318, ML328A and ML331, were isolated from water ponds of five salterns located in Spain. The cells were motile, curved rods and oxidase and catalase positive. All of them grew optimally at 37°C, at pH 7.2-7.4 and in the presence of 7.5% (w/v) NaCl. Based on phylogenetic analyses of the 16S rRNA, the isolates were most closely related to Salinivibrio sharmensis BAGT (99...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29330592/genomic-characterization-of-key-bacteriophages-to-formulate-the-potential-biocontrol-agent-to-combat-enteric-pathogenic-bacteria
#16
Krupa M Parmar, Nishant A Dafale, Hitesh Tikariha, Hemant J Purohit
Combating bacterial pathogens has become a global concern especially when the antibiotics and chemical agents are failing to control the spread due to its resistance. Bacteriophages act as a safe biocontrol agent by selectively lysing the bacterial pathogens without affecting the natural beneficial microflora. The present study describes the screening of prominent enteric pathogens NDK1, NDK2, NDK3, and NDK4 (Escherichia, Klebsiella, Enterobacter, and Serratia) mostly observed in domestic wastewater; against which KNP1, KNP2, KNP3, and KNP4 phages were isolated...
January 12, 2018: Archives of Microbiology
https://www.readbyqxmd.com/read/29330416/virtual-genome-walking-across-the-32%C3%A2-gb-ambystoma-mexicanum-genome-assembling-gene-models-and-intronic-sequence
#17
Teri Evans, Andrew D Johnson, Matthew Loose
Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model species has been sequenced to 20× coverage but the reads could not be conventionally assembled. Using an alternative strategy, we have assembled subsets of these reads into scaffolds describing over 19,000 gene models. We call this method Virtual Genome Walking as it locally assembles whole genome reads based on a reference transcriptome, identifying exons and iteratively extending them into surrounding genomic sequence...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29329601/nicotiana-glauca-whole-genome-investigation-for-ct-dna-study
#18
Galina Khafizova, Pavel Dobrynin, Dmitrii Polev, Tatiana Matveeva
OBJECTIVE: Nicotiana glauca (tree tobacco) is a naturally transgenic plant, containing sequences acquired from Agrobacterium rhizogenes by horizontal gene transfer. Besides, N. glauca contains a wide profile of alkaloids of medical interest. DATA DESCRIPTION: We report a high-depth sequencing and de novo assembly of N. glauca full genome and analysis of genome elements with bacterial origin. The draft genome assembly is 3.2 Gb, with N50 size of 31.1 kbp. Comparative analysis confirmed the presence of single, previously described gT insertion...
January 12, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29329409/recent-development-of-ori-finder-system-and-doric-database-for-microbial-replication-origins
#19
Hao Luo, Chun-Lan Quan, Chong Peng, Feng Gao
DNA replication begins at replication origins in all three domains of life. Identification and characterization of replication origins are important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. The Z-curve method has been used in the identification of replication origins in archaeal genomes successfully since 2002. Furthermore, the Web servers of Ori-Finder and Ori-Finder 2 have been developed to predict replication origins in both bacterial and archaeal genomes based on the Z-curve method, and the replication origins with manual curation have been collected into an online database, DoriC...
January 9, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29327481/the-genome-and-microbiome-of-a-dikaryotic-fungus-inocybe-terrigena-inocybaceae-revealed-by-metagenomics
#20
Mohammad Bahram, Dan Vanderpool, Mari Pent, Markus Hiltunen, Martin Ryberg
Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr...
January 12, 2018: Environmental Microbiology Reports
keyword
keyword
104573
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"