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Bacterial genome sequencing

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https://www.readbyqxmd.com/read/28213279/tethering-rna-to-chromatin-for-fluorescence-microscopy-based-analysis-of-nuclear-organization
#1
Teresa Pankert, Thibaud Jegou, Maïwen Caudron-Herger, Karsten Rippe
Nuclear RNAs emerge as important factors to orchestrate the dynamic organization of the nucleus into functional subcompartments. By tethering RNAs to distinct genomic loci, the RNA-dependent chromatin changes can be dissected by fluorescence microscopic analysis. Here we describe how this approach is implemented in mammalian cells. It involves two high-affinity protein-nucleic acid interactions that can established with number of different protein domains and DNA and RNA sequences. A prototypic system is described here in detail: It consists of the binding of MS2 bacteriophage coat protein to its RNA recognition sequence and the interaction between the bacterial LacI repressor protein to its target lacO operator DNA sequences...
February 14, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28213104/isolation-and-characterization-of-a-virulent-bacteriophage-infecting-acinetobacter-johnsonii-from-activated-sludge
#2
Niansi Fan, Rong Qi, Min Yang
A double-stranded DNA phage named AJO1, infecting Acinetobacter johnsonii, which plays an important role in wastewater treatment, was isolated from activated sludge in a full-scale municipal wastewater treatment plant. Based on morphological taxonomy, AJO1, with an icosahedral head 55 ± 2 nm in diameter and a non-contractile tail 8 ± 2 nm in length, was classified as a member of the Podoviridae family. Bacterial infection characteristics were as follows: no polyvalent infectivity, optimal multiplicity of infection of 10(-2); eclipse and burst size of 30 min and 51...
February 14, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28209828/draft-genome-sequence-of-edwardsiellapiscicida-strain-acc35-1-isolated-from-diseased-turbot-scophthalmus-maximus-in-europe
#3
Noemí Buján, Alicia E Toranzo, Beatriz Magariños
Edwardsiella piscicida is a bacterial fish pathogen with a high degree of virulence. The strain ACC35.1 was isolated from diseased turbot in Europe. The draft genome sequence comprises 3.84 Mb with a G+C content of 59.8% and >3,450 protein-coding genes.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28209394/ensifer-shofinae-sp-nov-a-novel-rhizobial-species-isolated-from-root-nodules-of-soybean-glycine-max
#4
Wen Hao Chen, Sheng Hui Yang, Zhao Hu Li, Xiao Xia Zhang, Xin Hua Sui, En Tao Wang, Wen Xin Chen, Wen Feng Chen
Two bacterial strains isolated from root nodules of soybean were characterized phylogenetically as members of a distinct group in the genus Ensifer based on 16S rRNA gene comparisons. They were also verified as a separated group by the concatenated sequence analyses of recA, atpD and glnII (with similarities ≤93.9% to the type strains for defined species), and by the average nucleotide identities (ANI) between the whole genome sequence of the representative strain CCBAU 251167(T) and those of the closely related strains in Ensifer glycinis and Ensifer fredii (90...
February 2, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28209133/house-spider-genome-uncovers-evolutionary-shifts-in-the-diversity-and-expression-of-black-widow-venom-proteins-associated-with-extreme-toxicity
#5
Kerry L Gendreau, Robert A Haney, Evelyn E Schwager, Torsten Wierschin, Mario Stanke, Stephen Richards, Jessica E Garb
BACKGROUND: Black widow spiders are infamous for their neurotoxic venom, which can cause extreme and long-lasting pain. This unusual venom is dominated by latrotoxins and latrodectins, two protein families virtually unknown outside of the black widow genus Latrodectus, that are difficult to study given the paucity of spider genomes. Using tissue-, sex- and stage-specific expression data, we analyzed the recently sequenced genome of the house spider (Parasteatoda tepidariorum), a close relative of black widows, to investigate latrotoxin and latrodectin diversity, expression and evolution...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28207977/adaptation-of-the-pathogen-pseudomonas-syringae-during-experimental-evolution-on-a-native-versus-alternative-host-plant
#6
Sean Meaden, Britt Koskella
The specialization and distribution of pathogens among species has substantial impact on disease spread, especially when reservoir hosts can maintain high pathogen densities or select for increased pathogen virulence. Theory predicts that optimal within-host growth rate will vary among host genotypes/species, and therefore that pathogens infecting multiple hosts should experience different selection pressures depending on the host environment in which they are found. This should be true for pathogens with broad host ranges, but also those experiencing opportunistic infections on novel hosts or that spill over among host populations...
February 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28207002/detecting-natural-adaptation-of-the-streptococcus-thermophilus-crispr-cas-systems-in-research-and-classroom-settings
#7
Alexander P Hynes, Marie-Laurence Lemay, Luc Trudel, Hélène Deveau, Michel Frenette, Denise M Tremblay, Sylvain Moineau
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas systems have been adapted into a powerful genome-editing tool. The basis for the flexibility of the tool lies in the adaptive nature of CRISPR-Cas as a bacterial immune system. Here, we describe a protocol to experimentally demonstrate the adaptive nature of this bacterial immune system by challenging the model organism for the study of CRISPR adaptation, Streptococcus thermophilus, with phages in order to detect natural CRISPR immunization...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28206708/physiological-metabolic-and-biotechnological-features-of-extremely-thermophilic-microorganisms
#8
REVIEW
James A Counts, Benjamin M Zeldes, Laura L Lee, Christopher T Straub, Michael W W Adams, Robert M Kelly
The current upper thermal limit for life as we know it is approximately 120°C. Microorganisms that grow optimally at temperatures of 75°C and above are usually referred to as 'extreme thermophiles' and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, heterotrophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs-basically, anywhere there is hot water...
February 16, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28205635/deciphering-the-distance-to-antibiotic-resistance-for-the-pneumococcus-using-genome-sequencing-data
#9
Fredrick M Mobegi, Amelieke J H Cremers, Marien I de Jonge, Stephen D Bentley, Sacha A F T van Hijum, Aldert Zomer
Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing in clinical phenotyping of bacteria is challenging due to the lack of reliable and accurate approaches. Here, we report a method for predicting microbial resistance patterns using genome sequencing data. We analyzed whole genome sequences of 1,680 Streptococcus pneumoniae isolates from four independent populations using GWAS and identified probable hotspots of genetic variation which correlate with phenotypes of resistance to essential classes of antibiotics...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28205536/genomic-structure-and-insertion-sites-of-helicobacter-pylori-prophages-from-various-geographical-origins
#10
Filipa F Vale, Alexandra Nunes, Mónica Oleastro, João P Gomes, Daniel A Sampaio, Raquel Rocha, Jorge M B Vítor, Lars Engstrand, Ben Pascoe, Elvire Berthenet, Samuel K Sheppard, Matthew D Hitchings, Francis Mégraud, Jamuna Vadivelu, Philippe Lehours
Helicobacter pylori genetic diversity is known to be influenced by mobile genomic elements. Here we focused on prophages, the least characterized mobile elements of H. pylori. We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of distinct disease types, ranging from gastritis to gastric cancer, and geographic origins, covering most continents. The genome sizes of these prophages range from 22.6-33.0 Kbp, consisting of 27-39 open reading frames...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28205377/culture-independent-genomics-of-a-novel-chlamydial-pathogen-of-fish-provides-new-insight-into-host-specific-adaptations-utilised-by-these-intracellular-bacteria
#11
Alyce Taylor-Brown, Trestan Pillonel, Andrew Bridle, Weihong Qi, Nathan Bachmann, Terrence L Miller, Gilbert Greub, Barbara Nowak, Helena M B Seth-Smith, Lloyd Vaughan, Adam Polkinghorne
Several Chlamydiales families are associated with epitheliocystis, a common condition of the fish gill epithelium. These families share common ancestors with the Chlamydiaceae and environmental Chlamydiae. Due to the lack of culture systems, little is known about the biology of these chlamydial fish pathogens. We investigated epitheliocystis in cultured Orange-spotted grouper (Epinephelus coioides) from North Queensland, Australia. Basophilic inclusions were present in the gills of 22/31 fish and the presence of the chlamydial pathogen in the cysts was confirmed by in situ hybridisation...
February 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28205241/septic-transfusion-case-caused-by-a-platelet-pool-with-visible-clotting-due-to-contamination-with-staphylococcus-aureus
#12
Maria Loza-Correa, Yuntong Kou, Mariam Taha, Miloslav Kalab, Jennifer Ronholm, Patrick M Schlievert, Michael P Cahill, Robert Skeate, Christine Cserti-Gazdewich, Sandra Ramirez-Arcos
BACKGROUND: Contamination of platelet concentrates (PCs) with Staphylococcus aureus is one of the most significant ongoing transfusion safety risks in developed countries. CASE REPORT: This report describes a transfusion reaction in an elderly patient diagnosed with acute myeloid leukemia, transfused with a 4-day-old buffy coat PC through a central venous catheter. The transfusion was interrupted when a large fibrous clot in the PC obstructed infusion pump flow...
February 16, 2017: Transfusion
https://www.readbyqxmd.com/read/28203245/small-rnas-derived-from-the-t-dna-of-agrobacterium-rhizogenes-in-hairy-roots-of-phaseolus-vulgaris
#13
Pablo Peláez, Alejandrina Hernández-López, Georgina Estrada-Navarrete, Federico Sanchez
Agrobacterium rhizogenes is a pathogenic bacteria that causes hairy root disease by transferring bacterial DNA into the plant genome. It is an essential tool for industry and research due to its capacity to produce genetically modified roots and whole organisms. Here, we identified and characterized small RNAs generated from the transfer DNA (T-DNA) of A. rhizogenes in hairy roots of common bean (Phaseolus vulgaris). Distinct abundant A. rhizogenes T-DNA-derived small RNAs (ArT-sRNAs) belonging to several oncogenes were detected in hairy roots using high-throughput sequencing...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28203231/error-prone-dnae2-balances-the-genome-mutation-rates-in-myxococcus-xanthus-dk1622
#14
Ran Peng, Jiang-He Chen, Wan-Wan Feng, Zheng Zhang, Jun Yin, Ze-Shuo Li, Yue-Zhong Li
dnaE is an alpha subunit of the tripartite protein complex of DNA polymerase III that is responsible for the replication of bacterial genome. The dnaE gene is often duplicated in many bacteria, and the duplicated dnaE gene was reported dispensable for cell survivals and error-prone in DNA replication in a mystery. In this study, we found that all sequenced myxobacterial genomes possessed two dnaE genes. The duplicate dnaE genes were both highly conserved but evolved divergently, suggesting their importance in myxobacteria...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28202080/mentholation-affects-the-cigarette-microbiota-by-selecting-for-bacteria-resistant-to-harsh-environmental-conditions-and-selecting-against-potential-bacterial-pathogens
#15
Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Emma Claye, Kelsey R Babik, Molly C Reid, Eoghan M Smyth, Lauren E Hittle, Joseph N Paulson, Raul Cruz-Cano, Mihai Pop, Stephanie S Buehler, Pamela I Clark, Amy R Sapkota, Emmanuel F Mongodin
BACKGROUND: There is a paucity of data regarding the microbial constituents of tobacco products and their impacts on public health. Moreover, there has been no comparative characterization performed on the bacterial microbiota associated with the addition of menthol, an additive that has been used by tobacco manufacturers for nearly a century. To address this knowledge gap, we conducted bacterial community profiling on tobacco from user- and custom-mentholated/non-mentholated cigarette pairs, as well as a commercially-mentholated product...
February 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28197157/loop-mediated-isothermal-amplification-method-for-the-rapid-detection-of-ralstonia-solanacearum-phylotype-i-mulberry-strains-in-china
#16
Wen Huang, Hao Zhang, Jingsheng Xu, Shuai Wang, Xiangjiu Kong, Wei Ding, Jin Xu, Jie Feng
Ralstonia solanacearum phylotype I mulberry strains are causative agent of bacterial wilt of mulberry. Current diagnostic methods are not adopted to the mulberry wilt disease. In this study, we developed a rapid method, loop-mediated isothermal amplification (LAMP), to detect R. solanacearum phylotype I mulberry strains. A set of six primers was designed to target the clone MG67 sequence in this LAMP detection which can be completed in 20 min at 64°C. The results of the LAMP reaction could be observed with the naked eye due to magnesium pyrophosphate precipitate produced during the reaction or the color change after adding SYBR Green I...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28193905/assessment-of-insertion-sequence-mobilization-as-an-adaptive-response-to-oxidative-stress-in-acinetobacter-baumannii-using-is-seq
#17
Meredith S Wright, Stephanie Mountain, Karen Beeri, Mark D Adams
Insertion sequence (IS) elements are found throughout bacterial genomes and contribute to genome variation by interrupting genes or altering gene expression. Few of the more than thirty IS elements described in Acinetobacter baumannii have been characterized for transposition activity or expression effects. A targeted sequencing method, IS-seq, was developed to efficiently map the locations of new insertion events in A. baumannii genomes and was used to identify novel IS sites following growth in the presence of hydrogen peroxide, which causes oxidative stress...
February 13, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28193166/vacsol-a-high-throughput-in-silico-pipeline-to-predict-potential-therapeutic-targets-in-prokaryotic-pathogens-using-subtractive-reverse-vaccinology
#18
Muhammad Rizwan, Anam Naz, Jamil Ahmad, Kanwal Naz, Ayesha Obaid, Tamsila Parveen, Muhammad Ahsan, Amjad Ali
BACKGROUND: With advances in reverse vaccinology approaches, a progressive improvement has been observed in the prediction of putative vaccine candidates. Reverse vaccinology has changed the way of discovery and provides a mean to propose target identification in reduced time and labour. In this regard, high throughput genomic sequencing technologies and supporting bioinformatics tools have greatly facilitated the prompt analysis of pathogens, where various predicted candidates have been found effective against certain infections and diseases...
February 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28192430/computational-identification-of-the-selenocysteine-trna-trnasec-in-genomes
#19
Didac Santesmasses, Marco Mariotti, Roderic Guigó
Selenocysteine (Sec) is known as the 21st amino acid, a cysteine analogue with selenium replacing sulphur. Sec is inserted co-translationally in a small fraction of proteins called selenoproteins. In selenoprotein genes, the Sec specific tRNA (tRNASec) drives the recoding of highly specific UGA codons from stop signals to Sec. Although found in organisms from the three domains of life, Sec is not universal. Many species are completely devoid of selenoprotein genes and lack the ability to synthesize Sec. Since tRNASec is a key component in selenoprotein biosynthesis, its efficient identification in genomes is instrumental to characterize the utilization of Sec across lineages...
February 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28192255/molecular-characterization-of-a-fish-specific-toll-like-receptor-22-tlr22-gene-from-common-carp-cyprinus-carpio-l-evolutionary-relationship-and-induced-expression-upon-immune-stimulants
#20
Hua Li, Guiwen Yang, Fei Ma, Ting Li, Huiting Yang, Jan H W M Rombout, Liguo An
In the host innate immune system, various pattern recognition receptors (PRRs) recognize conserved pathogens-associated molecular patterns (PAMPs), and represent an efficient first line of defense against invading pathogens. TLR22 is one of the fish-specific Toll-like receptors (TLRs), identified in a variety of fish species. In this study, we report the cloning and identification of a TLR22 cDNA from the gills of common carp (Cyprinus carpio L.). The full-length CcTLR22 cDNA was 3301 bp long, including a 32 bp 5'-untranslated region (UTR), an open reading frame (ORF) of 2838 bp and a 432 bp 3'-UTR...
February 11, 2017: Fish & Shellfish Immunology
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