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Bacterial genome sequencing

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https://www.readbyqxmd.com/read/28535266/mechanism-of-bacterial-gene-rearrangement-spra-catalyzed-precise-dna-recombination-and-its-directionality-control-by-sprb-ensure-the-gene-rearrangement-and-stable-expression-of-spsm-during-sporulation-in-bacillus-subtilis
#1
Kimihiro Abe, Takuo Takamatsu, Tsutomu Sato
A sporulation-specific gene, spsM, is disrupted by an active prophage, SPβ, in the genome of Bacillus subtilis. SPβ excision is required for two critical steps: the onset of the phage lytic cycle and the reconstitution of the spsM-coding frame during sporulation. Our in vitro study demonstrated that SprA, a serine-type integrase, catalyzed integration and excision reactions between attP of SPβ and attB within spsM, while SprB, a recombination directionality factor, was necessary only for the excision between attL and attR in the SPβ lysogenic chromosome...
May 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28534105/bacterial-diversity-of-cosmopolitan-culex-pipiens-and-invasive-aedes-japonicus-from-germany
#2
Sina Zotzmann, Antje Steinbrink, Kathrin Schleich, Felix Frantzmann, Chinhda Xoumpholphakdy, Manuela Spaeth, Claire Valiente Moro, Patrick Mavingui, Sven Klimpel
Symbiotic bacteria have gained significant attention in recent years. For example, microbiota of some mosquito species seems to influence the development and transmission of pathogens. Furthermore, several attempts using bacteria as a paratransgenetic tool have been made in order to assist the control of mosquito-borne diseases. In this study, we examined the bacterial diversity of wild-caught adult Culex (Cx.) pipiens and laboratory-reared adult Aedes japonicus (Ae. japonicus) in Germany using a culture-independent method...
May 22, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28534088/the-ppar-gamma-binding-sequence-pal3-is-necessary-for-basal-but-dispensable-for-high-fat-diet-regulated-human-renin-expression-in-the-kidney
#3
Peter Lachmann, Jenny Selbmann, Linda Hickmann, Bernd Hohenstein, Christian Hugo, Vladimir T Todorov
We reported earlier that PPAR-gamma regulates renin transcription through a human-specific atypical binding sequence termed hRen-Pal3. Here we developed a mouse model to investigate the functional relevance of the hRen-Pal3 sequence in vivo since it might be responsible for the increased renin production in obesity and thus for the development of accompanying arterial hypertension. We used bacterial artificial chromosome construct and co-placement strategy to generate two transgenic mouse lines expressing the human renin gene from identical genomic locus without affecting the intrinsic mouse renin expression...
May 22, 2017: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/28533988/strainseeker-fast-identification-of-bacterial-strains-from-raw-sequencing-reads-using-user-provided-guide-trees
#4
Märt Roosaare, Mihkel Vaher, Lauris Kaplinski, Märt Möls, Reidar Andreson, Maarja Lepamets, Triinu Kõressaar, Paul Naaber, Siiri Kõljalg, Maido Remm
BACKGROUND: Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees. RESULTS: A tool named StrainSeeker was developed that constructs a list of specific k-mers for each node of any given Newick-format tree and enables the identification of bacterial isolates in 1-2 min...
2017: PeerJ
https://www.readbyqxmd.com/read/28533514/isolation-and-genomic-characterization-of-a-dehalococcoides-strain-suggests-genomic-rearrangement-during-culture
#5
Masafumi Yohda, Kentaro Ikegami, Yuto Aita, Mizuki Kitajima, Ayane Takechi, Megumi Iwamoto, Tomomi Fukuda, Noriyoshi Tamura, Junji Shibasaki, Seiji Koike, Daisuke Komatsu, Sakari Miyagi, Minoru Nishimura, Yoshihito Uchino, Akino Shiroma, Makiko Shimoji, Hinako Tamotsu, Noriko Ashimine, Misuzu Shinzato, Shun Ohki, Kazuma Nakano, Kuniko Teruya, Kazuhito Satou, Takashi Hirano, Osami Yagi
We have developed and characterized a bacterial consortium that reductively dechlorinates trichloroethene to ethene. Quantitative PCR analysis for the 16S rRNA and reductive dehalogenase genes showed that the consortium is highly enriched with Dehalococcoides spp. that have two vinyl chloride reductive dehalogenase genes, bvcA and vcrA, and a trichloroethene reductive dehalogenase gene, tceA. The metagenome analysis of the consortium by the next generation sequencer SOLiD 3 Plus suggests that a Dehalococcoides sp...
May 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28531216/impact-of-mutations-in-toll-like-receptor-pathway-genes-on-esophageal-carcinogenesis
#6
Daffolyn Rachael Fels Elliott, Juliane Perner, Xiaodun Li, Martyn F Symmons, Brett Verstak, Matthew Eldridge, Lawrence Bower, Maria O'Donovan, Nick J Gay, Rebecca C Fitzgerald
Esophageal adenocarcinoma (EAC) develops in an inflammatory microenvironment with reduced microbial diversity, but mechanisms for these influences remain poorly characterized. We hypothesized that mutations targeting the Toll-like receptor (TLR) pathway could disrupt innate immune signaling and promote a microenvironment that favors tumorigenesis. Through interrogating whole genome sequencing data from 171 EAC patients, we showed that non-synonymous mutations collectively affect the TLR pathway in 25/171 (14...
May 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28525986/the-lspc3-41i-restriction-modification-system-is-the-major-determinant-for-genetic-manipulations-of-lysinibacillus-sphaericus-c3-41
#7
Pan Fu, Yong Ge, Yiming Wu, Ni Zhao, Zhiming Yuan, Xiaomin Hu
BACKGROUND: Lysinibacillus sphaericus has been widely used in integrated mosquito control program and it is one of the minority bacterial species unable to metabolize carbohydrates. In consideration of the high genetic conservation at genomic level and difficulty of genetic horizontal transfer, it is hypothesized that effective restriction-modification (R-M) systems existed in mosquitocidal L. sphaericus. RESULTS: In this study, six type II R-M systems including LspC3-41I were predicted in L...
May 19, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28525966/gene-expression-of-vibrio-parahaemolyticus-growing-in-laboratory-isolation-conditions-compared-to-those-common-in-its-natural-ocean-environment
#8
Katherine García, Cristian Yáñez, Nicolás Plaza, Francisca Peña, Pedro Sepúlveda, Diliana Pérez-Reytor, Romilio T Espejo
BACKGROUND: Vibrio parahaemolyticus is an autochthonous marine bacterial species comprising strains able to grow in broth containing bile salts at 37 °C, a condition seldom found in the ocean. However, this condition is used for isolation in the laboratory because it is considered a necessary property for pathogenesis. In this context, revealing how gene expression enables V. parahaemolyticus to adapt to this particular condition -common to almost all V. parahaemolyticus isolates- will improve our understanding of the biology of this important pathogen...
May 19, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28525649/genome-sequence-compression-based-on-optimized-context-weighting
#9
M Chen, J J Shao, X M Jia
Context weighting is an important technology for genome compression. In this study, we discuss the relationship between the weighting of context models and the weighting of the description lengths corresponding to their respective context models. It indicates that weighting of context models is equivalent to the weighting of their description lengths. With these discussions, we present the weights optimization algorithm based on the minimum description length, and suggest implementing the least-square algorithm for the optimization of the weights...
May 18, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28525571/one-year-genome-evolution-of-lausannevirus-in-allopatric-versus-sympatric-conditions
#10
Linda Mueller, Claire Bertelli, Trestan Pillonel, Nicolas Salamin, Gilbert Greub
Amoeba-resisting microorganisms (ARMs) raised a great interest during the last decade. Among them, some large DNA viruses present huge genomes up to 2.5 Mb long, exceeding the size of small bacterial genomes. The rate of genome evolution in terms of mutation, deletion and gene acquisition in these genomes is yet unknown. Given the suspected high plasticity of viral genomes, the microevolution of the 346 kb genome of Lausannevirus, a member of Megavirales, was studied. Hence, Lausannevirus was co-cultured within the amoeba Acanthamoeba castellanii over one year...
May 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28522725/draft-genome-sequences-of-five-enterococcus-species-isolated-from-the-gut-of-patients-with-suspected-clostridium-difficile-infection
#11
Eduardo Castro-Nallar, Sandro L Valenzuela, Sebastián Baquedano, Carolina Sánchez, Fabiola Fernández, Annette N Trombert
We present draft genome sequences of five Enterococcus species from patients suspected of Clostridium difficile infection. Genome completeness was confirmed by presence of bacterial orthologs (97%). Gene searches using Hidden-Markov models revealed that the isolates harbor between seven and 11 genes involved in antibiotic resistance to tetracyclines, beta-lactams, and vancomycin.
May 18, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28521002/changes-in-microbiome-during-and-after-travellers-diarrhea-what-we-know-and-what-we-do-not
#12
David A Rasko
The study of bacterial pathogens has advanced from culture on plates to basic biochemical studies; to sequencing reference genomes and attempting to ascribe those qualities to the whole species; to evaluating complete communities based on the universal marker of the 16S rRNA gene; to now sequencing all available nucleic acids in any sample to characterize the community as a whole. These types of scientific advances highlight that there are multiple layers of information within any sample, and to some extent we are only now beginning to be able to identify, categorize and understand the complex interactions of the host, pathogen and microbiome...
April 1, 2017: Journal of Travel Medicine
https://www.readbyqxmd.com/read/28516866/invasive-serotype-35b-pneumococci-including-an-expanding-serotype-switch-lineage-united-states-2015-2016
#13
Sopio Chochua, Benjamin J Metcalf, Zhongya Li, Hollis Walker, Theresa Tran, Lesley McGee, Bernard Beall
We used whole-genome sequencing to characterize 199 nonvaccine serotype 35B pneumococcal strains that caused invasive pneumococcal disease (IPD) in the United States during 2015-2016 and related these findings to previous serotype 35B IPD data obtained by Active Bacterial Core surveillance. Penicillin-nonsusceptible 35B IPD increased during post-pneumococcal 7-valent conjugate vaccine years (2001-2009) and increased further after implementation of pneumococcal 13-valent conjugate vaccine in 2010. This increase was caused primarily by the 35B/sequence type (ST) 558 lineage...
June 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28516483/capabilities-and-limitations-of-dgge-for-the-analysis-of-hydrocarbonoclastic-prokaryotic-communities-directly-in-environmental-samples
#14
Dina M Al-Mailem, Mayada K Kansour, Samir S Radwan
Prokaryotic communities in pristine and oil-contaminated desert soil, seawater, and hypersaline coastal soil were analyzed using culture-dependent and culture-independent approaches. The former technique was the dilution-plating method. For the latter, total genomic DNA was extracted and the 16S rRNA genes were amplified using a universal bacterial primer pair and primer pairs specific for Actinobacteria, Gammaproteobacteria, and Archaea. The amplicons were resolved using denaturing gradient gel electrophoresis (DGGE) and sequenced, and the sequences were compared to those in GenBank...
May 18, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28510224/dna-supercoiling-is-a-fundamental-regulatory-principle-in-the-control-of-bacterial-gene-expression
#15
REVIEW
Charles J Dorman, Matthew J Dorman
Although it has become routine to consider DNA in terms of its role as a carrier of genetic information, it is also an important contributor to the control of gene expression. This regulatory principle arises from its structural properties. DNA is maintained in an underwound state in most bacterial cells and this has important implications both for DNA storage in the nucleoid and for the expression of genetic information. Underwinding of the DNA through reduction in its linking number potentially imparts energy to the duplex that is available to drive DNA transactions, such as transcription, replication and recombination...
September 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28510216/dna-supercoiling-is-a-fundamental-regulatory-principle-in-the-control-of-bacterial-gene-expression
#16
REVIEW
Charles J Dorman, Matthew J Dorman
Although it has become routine to consider DNA in terms of its role as a carrier of genetic information, it is also an important contributor to the control of gene expression. This regulatory principle arises from its structural properties. DNA is maintained in an underwound state in most bacterial cells and this has important implications both for DNA storage in the nucleoid and for the expression of genetic information. Underwinding of the DNA through reduction in its linking number potentially imparts energy to the duplex that is available to drive DNA transactions, such as transcription, replication and recombination...
November 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28509971/description-of-chryseobacterium-timonianum-sp-nov-isolated-from-a-patient-with-pneumonia
#17
Rita Abou Abdallah, Teresa Cimmino, Sophie Baron, Frédéric Cadoret, Caroline Michelle, Didier Raoult, Pierre-Edouard Fournier, Fadi Bittar
Using a polyphasic taxonomic strategy, an aerobic, Gram-negative, non-motile, yellow pigmented rod isolated from a sputum sample of a patient with pneumonia was characterised. This bacterial strain, designated G972(T), could not be identified by our systematic MALDI-TOF screening on a MicroFlex. This led to the sequencing of the 16S rRNA gene, which shows 98.57% sequence identity with that of Chryseobacterium indologenes 16777(T), the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species...
May 16, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28509419/live-cell-crispr-imaging-in-plants-reveals-dynamic-telomere-movements
#18
Steven Dreissig, Simon Schiml, Patrick Schindele, Oda Weiss, Twan Rutten, Veit Schubert, Evgeny Gladilin, Michael Florian Mette, Holger Puchta, Andreas Houben
Elucidating the spatio-temporal organization of the genome inside the nucleus is imperative to understand the regulation of genes and non-coding sequences during development and environmental changes. Emerging techniques of chromatin imaging promise to bridge the long-standing gap between sequencing studies which reveal genomic information and imaging studies that provide spatial and temporal information of defined genomic regions. Here, we demonstrate such an imaging technique based on two orthologues of the bacterial CRISPR-Cas9 system...
May 16, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28508147/identification-of-beta-lactamases-and-beta-lactam-related-proteins-in-human-pathogenic-bacteria-using-a-computational-search-approach
#19
Aniel Jessica Leticia Brambila-Tapia, Ernesto Perez-Rueda, Humberto Barrios, Nory Omayra Dávalos-Rodríguez, Ingrid Patricia Dávalos-Rodríguez, Ernesto Germán Cardona-Muñoz, Mario Salazar-Páramo
A systematic analysis of beta-lactamases based on comparative proteomics has not been performed thus far. In this report, we searched for the presence of beta-lactam-related proteins in 591 bacterial proteomes belonging to 52 species that are pathogenic to humans. The amino acid sequences for 19 different types of beta-lactamases (ACT, CARB, CifA, CMY, CTX, FOX, GES, GOB, IMP, IND, KPC, LEN, OKP, OXA, OXY, SHV, TEM, NDM, and VIM) were obtained from the ARG-ANNOT database and were used to construct 19 HMM profiles, which were used to identify potential beta-lactamases in the completely sequenced bacterial proteomes...
May 16, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28506246/vipie-web-pipeline-for-parallel-characterization-of-viral-populations-from-multiple-ngs-samples
#20
Jake Lin, Lenka Kramna, Reija Autio, Heikki Hyöty, Matti Nykter, Ondrej Cinek
BACKGROUND: Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. RESULTS: We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters...
May 15, 2017: BMC Genomics
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