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Bacterial genome sequencing

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https://www.readbyqxmd.com/read/29774437/lexa-binds-to-transcription-regulatory-site-of-cell-division-gene-ftsz-in-toxic-cyanobacterium-microcystis-aeruginosa
#1
Takashi Honda, Daichi Morimoto, Yoshihiko Sako, Takashi Yoshida
Previously, we showed that DNA replication and cell division in toxic cyanobacterium Microcystis aeruginosa are coordinated by transcriptional regulation of cell division gene ftsZ and that an unknown protein specifically bound upstream of ftsZ (BpFz; DNA-binding protein to an upstream site of ftsZ) during successful DNA replication and cell division. Here, we purified BpFz from M. aeruginosa strain NIES-298 using DNA-affinity chromatography and gel-slicing combined with gel electrophoresis mobility shift assay (EMSA)...
May 17, 2018: Marine Biotechnology
https://www.readbyqxmd.com/read/29774245/evaluation-of-phylogenetic-reconstruction-methods-using-bacterial-whole-genomes-a-simulation-based-study
#2
John A Lees, Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen D Bentley, Simon R Harris
Background : Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods : We simulated data from a defined "true tree" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29774086/complete-genome-sequence-of-thiodictyon-syntrophicum-sp-nov-strain-cad16-t-a-photolithoautotrophic-purple-sulfur-bacterium-isolated-from-the-alpine-meromictic-lake-cadagno
#3
Samuel M Luedin, Joël F Pothier, Francesco Danza, Nicola Storelli, Niels-Ulrik Frigaard, Matthias Wittwer, Mauro Tonolla
" Thiodictyon syntrophicum" sp. nov. strain Cad16T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria . The type strain Cad16T was isolated from the chemocline of the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16T represents a key species within this sulfur-driven bacterial ecosystem with respect to carbon fixation. The 7.74-Mbp genome of strain Cad16T has been sequenced and annotated. It encodes 6237 predicted protein sequences and 59 RNA sequences...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29773790/crispr-cas9-mediated-gene-targeting-in-arabidopsis-using-sequential-transformation
#4
Daisuke Miki, Wenxin Zhang, Wenjie Zeng, Zhengyan Feng, Jian-Kang Zhu
Homologous recombination-based gene targeting is a powerful tool for precise genome modification and has been widely used in organisms ranging from yeast to higher organisms such as Drosophila and mouse. However, gene targeting in higher plants, including the most widely used model plant Arabidopsis thaliana, remains challenging. Here we report a sequential transformation method for gene targeting in Arabidopsis. We find that parental lines expressing the bacterial endonuclease Cas9 from the egg cell- and early embryo-specific DD45 gene promoter can improve the frequency of single-guide RNA-targeted gene knock-ins and sequence replacements via homologous recombination at several endogenous sites in the Arabidopsis genome...
May 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29773743/genomic-insights-into-the-emergence-and-spread-of-antimicrobial-resistant-bacterial-pathogens
#5
REVIEW
Stephen Baker, Nicholas Thomson, François-Xavier Weill, Kathryn E Holt
Whole-genome sequencing (WGS) has been vital for revealing the rapid temporal and spatial evolution of antimicrobial resistance (AMR) in bacterial pathogens. Some antimicrobial-resistant pathogens have outpaced us, with untreatable infections appearing in hospitals and the community. However, WGS has additionally provided us with enough knowledge to initiate countermeasures. Although we cannot stop bacterial adaptation, the predictability of many evolutionary processes in AMR bacteria offers us an opportunity to channel them using new control strategies...
May 18, 2018: Science
https://www.readbyqxmd.com/read/29773633/complete-genome-sequences-of-two-bioluminescent-vibrio-campbellii-strains-isolated-from-biofouling-communities-in-the-bay-of-bengal
#6
Sophie M Colston, Gregory A Ellis, Seongwon Kim, Hemantha W Wijesekera, Dagmar H Leary, Baochuan Lin, Benjamin C Kirkup, W Judson Hervey, Gary J Vora
Vibrio campbellii is a pathogen of aquatic animals and has been proposed as a bacterial partner in the formation of bioluminescent milky seas. We present here the complete genome sequences assembled from Illumina and Oxford Nanopore data for two bioluminescent Vibrio campbellii strains (BoB-53 and BoB-90) isolated from biofouled moorings in the Bay of Bengal.
May 17, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29771278/a-pelota-like-gene-regulates-root-development-and-defence-responses-in-rice
#7
Wona Ding, Jing Wu, Jin Ye, Wenjuan Zheng, Shanshan Wang, Xinni Zhu, Jiaqin Zhou, Zhichong Pan, Botao Zhang, Shihua Zhu
Background and Aims: Pelota (Pelo) are evolutionarily conserved genes reported to be involved in ribosome rescue, cell cycle control and meiotic cell division. However, there is little known about their function in plants. The aim of this study was to elucidate the function of an ethylmethane sulphonate (EMS)-derived mutation of a Pelo-like gene in rice (named Ospelo). Methods: A dysfunctional mutant was used to characterize the function of OsPelo. Analyses of its expression and sub-cellular localization were performed...
May 16, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29769695/genomic-and-functional-characterisation-of-incx3-plasmids-encoding-bla-shv-12-in-escherichia-coli-from-human-and-animal-origin
#8
Apostolos Liakopoulos, Jeanet van der Goot, Alex Bossers, Jonathan Betts, Michael S M Brouwer, Arie Kant, Hilde Smith, Daniela Ceccarelli, Dik Mevius
The blaSHV-12 β-lactamase gene is one of the most prevalent genes conferring resistance to extended-spectrum β-lactams in Enterobacteriaceae disseminating within and between reservoirs, mostly via plasmid-mediated horizontal gene transfer. Yet, studies regarding the biology of plasmids encoding blaSHV-12 are very limited. In this study, we revealed the emergence of IncX3 plasmids alongside IncI1α/γ in blaSHV-12 in animal-related Escherichia coli isolates. Four representative blaSHV-12 -encoding IncX3 plasmids were selected for genome sequencing and further genetic and functional characterization...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769381/tosr-mediated-regulation-of-adhesins-and-biofilm-formation-in-uropathogenic-escherichia-coli
#9
Courtney L Luterbach, Valerie S Forsyth, Michael D Engstrom, Harry L T Mobley
Uropathogenic Escherichia coli strains utilize a variety of adherence factors that assist in colonization of the host urinary tract. TosA (<u>t</u>ype <u>o</u>ne <u>s</u>ecretion <u>A</u>) is a nonfimbrial adhesin that is predominately expressed during murine urinary tract infection (UTI), binds to kidney epithelial cells, and promotes survival during invasive infections. The tosRCBDAEF operon encodes the secretory machinery necessary for TosA localization to the E...
June 27, 2018: MSphere
https://www.readbyqxmd.com/read/29769016/whole-genome-sequencing-data-of-1110-mycobacterium-tuberculosis-isolates-identifies-insertions-and-deletions-associated-with-drug-resistance
#10
Xi Zeng, Jamie Sui-Lam Kwok, Kevin Yi Yang, Kenneth Siu-Sing Leung, Mai Shi, Zhiyuan Yang, Wing-Cheong Yam, Stephen Kwok-Wing Tsui
BACKGROUND: Drug resistance in Mycobacterium tuberculosis (MTB) is one of the major challenges in tuberculosis (TB) treatment. However, known mutations cannot explain all of the cases of resistance and little research has focused on the relationship between insertions / deletions (indels) and drug resistance. RESULTS: Here, we retrieved whole genome sequencing data of 743 drug-resistant MTB strains and 367 pan-susceptible strains from TB patients from the public domain to identify novel genomic markers of drug resistance...
May 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29768466/core-non-coding-rnas-of-piscirickettsia-salmonis
#11
Cristopher Segovia, Raul Arias-Carrasco, Alejandro J Yañez, Vinicius Maracaja-Coutinho, Javier Santander
Piscirickettsia salmonis, a fastidious Gram-negative intracellular facultative bacterium, is the causative agent o Piscirickettsiosis. P. salmonis has broad host range with a nearly worldwide distribution, causing significant mortality. The molecular regulatory mechanisms of P. salmonis pathogenesis are relatively unknown, mainly due to its difficult in vitro culture and genomic differences between genogroups. Bacterial non-coding RNAs (ncRNAs) are important post-transcriptional regulators of bacterial physiology and virulence that are predominantly transcribed from intergenic regions (trans-acting) or antisense strand of open reading frames (cis-acting)...
2018: PloS One
https://www.readbyqxmd.com/read/29768437/oral-health-status-in-historic-population-macroscopic-and-metagenomic-evidence
#12
Claire Willmann, Xavier Mata, Kristian Hanghoej, Laure Tonasso, Lenka Tisseyre, Céline Jeziorski, Elodie Cabot, Pierre Chevet, Eric Crubézy, Ludovic Orlando, Rémi Esclassan, Catherine Thèves
Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked...
2018: PloS One
https://www.readbyqxmd.com/read/29766351/comparative-whole-genome-re-sequencing-analysis-in-upland-new-rice-for-africa-insights-into-the-breeding-history-and-respective-genome-compositions
#13
Naoki Yamamoto, Richard Garcia, Tomohiro Suzuki, Celymar Angela Solis, Yuichi Tada, Ramaiah Venuprasad, Ajay Kohli
BACKGROUND: Increasing rice demand is one of the consequences of the steadily improving socio-economic status of the African countries. New Rice for Africa (NERICA), which are interspecific hybrids between Asian and African rice varieties, are one of successful breeding products utilizing biodiversity across the two different rice crop species. Upland NERICA varieties (NU) exhibit agronomic traits of value for the harsh eco-geography, including shorter duration, higher yield and stress tolerance, compared to local African varieties...
May 15, 2018: Rice
https://www.readbyqxmd.com/read/29765365/human-activity-determines-the-presence-of-integron-associated-and-antibiotic-resistance-genes-in-southwestern-british-columbia
#14
Miguel I Uyaguari-Díaz, Matthew A Croxen, Zhiyao Luo, Kirby I Cronin, Michael Chan, Waren N Baticados, Matthew J Nesbitt, Shaorong Li, Kristina M Miller, Damion Dooley, William Hsiao, Judith L Isaac-Renton, Patrick Tang, Natalie Prystajecky
The dissemination of antibiotic resistant bacteria from anthropogenic sources into the environment poses an emerging public health threat. Antibiotic resistance genes (ARGs) and gene-capturing systems such as integron-associated integrase genes ( intI ) play a key role in alterations of microbial communities and the spread of antibiotic resistant bacteria into the environment. In order to assess the effect of anthropogenic activities on watersheds in southwestern British Columbia, the presence of putative antibiotic resistance and integrase genes was analyzed in the microbiome of agricultural, urban influenced, and protected watersheds...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29763729/in-silico-identification-of-molecular-mimics-involved-in-the-pathogenesis-of-clostridium-botulinum-atcc-3502-strain
#15
Tulika Bhardwaj, Shafiul Haque, Pallavi Somvanshi
Bacterial pathogens invade and disrupt the host defense system by means of protein sequences structurally similar at global and local level both. The sharing of homologous sequences between the host and the pathogenic bacteria mediates the infection and defines the concept of molecular mimicry. In this study, various computational approaches were employed to elucidate the pathogenicity of Clostridium at genome-wide level. Genome-wide study revealed that the pathogen mimics the host (Homo sapiens) and unraveled the complex pathogenic pathway of causing infections...
May 12, 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29762724/aai-profiler-fast-proteome-wide-exploratory-analysis-reveals-taxonomic-identity-misclassification-and-contamination
#16
Alan J Medlar, Petri Törönen, Liisa Holm
We present AAI-profiler, a web server for exploratory analysis and quality control in comparative genomics. AAI-profiler summarizes proteome-wide sequence search results to identify novel species, assess the need for taxonomic reclassification and detect multi-isolate and contaminated samples. AAI-profiler visualises results using a scatterplot that shows the Average Amino-acid Identity (AAI) from the query proteome to all similar species in the sequence database. Taxonomic groups are indicated by colour and marker styles, making outliers easy to spot...
May 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29760866/short-genome-report-of-cellulose-producing-commensal-escherichia-coli-1094
#17
Joaquin Bernal-Bayard, Laura Gomez-Valero, Aimee Wessel, Varun Khanna, Christiane Bouchier, Jean-Marc Ghigo
Bacterial surface colonization and biofilm formation often rely on the production of an extracellular polymeric matrix that mediates cell-cell and cell-surface contacts. In Escherichia coli and many Betaproteobacteria and Gammaproteobacteria cellulose is often the main component of the extracellular matrix. Here we report the complete genome sequence of the cellulose producing strain E. coli 1094 and compare it with five other closely related genomes within E. coli phylogenetic group A. We present a comparative analysis of the regions encoding genes responsible for cellulose biosynthesis and discuss the changes that could have led to the loss of this important adaptive advantage in several E...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29756170/further-characteristics-of-arcanobacterium-pinnipediorum-dsm-28752-t-and-arcanobacterium-wilhelmae-dsm-102162-t-two-novel-species-of-genus-arcanobacterium
#18
Osama Sammra, Jörg Rau, Jörn Wickhorst, Mazen Alssahen, Abdulwahed Ahmed Hassan, Christoph Lämmler, Ellen Prenger-Berninghoff, Amir Abdulmawjood
The newly described type strains Arcanobacterium pinnipediorum DSM 28752T and Arcanobacterium wilhelmae DSM 102162T , initially isolated from an anal swab of a harbor seal (Sammra et al. Int J Syst Evol Microbiol 65:4539-4543, 2015) and the genital tract of a rhinoceros (Sammra et al. Int J Syst Evol Microbiol 67:2093-2097, 2017), could be further characterized by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and Fourier transform infrared (FT-IR) spectroscopy and by sequencing the genomic targets 16S-23S rDNA intergenic spacer region (ISR) and the genes rpoB, gap, and tuf...
May 13, 2018: Folia Microbiologica
https://www.readbyqxmd.com/read/29755805/analysis-of-bacterial-diversity-in-different-heavy-oil-wells-of-a-reservoir-in-south-oman-with-alkaline-ph
#19
Biji Shibulal, Saif N Al-Bahry, Yahya M Al-Wahaibi, Abdulkadir E Elshafie, Ali S Al-Bemani, Sanket J Joshi
The identification of potential hydrocarbon utilizing bacteria is an essential requirement in microbial enhanced oil recovery (MEOR). Molecular approaches like proteomic and genomic characterization of the isolates are replacing the traditional method of identification with systemic classification. Genotypic profiling of the isolates includes fingerprint or pattern-based technique and sequence-based technique. Understanding community structure and dynamics is essential for studying diversity profiles and is challenging in the case of microbial analysis...
2018: Scientifica
https://www.readbyqxmd.com/read/29755603/bacterial-crispr-regions-general-features-and-their-potential-for-epidemiological-molecular-typing-studies
#20
REVIEW
Zahra Karimi, Ali Ahmadi, Ali Najafi, Reza Ranjbar
Introduction: CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci as novel and applicable regions in prokaryotic genomes have gained great attraction in the post genomics era. Methods: These unique regions are diverse in number and sequence composition in different pathogenic bacteria and thereby can be a suitable candidate for molecular epidemiology and genotyping studies. Results:Furthermore, the arrayed structure of CRISPR loci (several unique repeats spaced with the variable sequence) and associated cas genes act as an active prokaryotic immune system against viral replication and conjugative elements...
2018: Open Microbiology Journal
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