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Bacterial genome sequencing

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https://www.readbyqxmd.com/read/28926997/effects-of-cellular-methylation-on-transgene-expression-and-site-specific-integration-of-adeno-associated-virus
#1
Diptiman Chanda, Jonathan A Hensel, Jerome T Higgs, Rajat Grover, Niroop Kaza, Selvarangan Ponnazhagan
DNA methylation is a major epigenetic event that affects not only cellular gene expression but that also has the potential to influence bacterial and viral DNA in their host-dependent functions. Adeno-associated virus (AAV) genome contains a high degree of CpG sequences capable of methylation in its terminal repeat sequences, which are the sole elements retained in AAV-based vectors used in gene therapy. The present study determined the influence of methylation status of the host cell on wild type (wt) AAV integration and recombinant (r) AAV transgene expression in HeLa cells...
September 18, 2017: Genes
https://www.readbyqxmd.com/read/28926571/whole-genome-sequencing-illuminates-the-evolution-and-spread-of-multidrug-resistant-tuberculosis-in-southwest-nigeria
#2
Madikay Senghore, Jacob Otu, Adam Witney, Florian Gehre, Emma L Doughty, Gemma L Kay, Phillip Butcher, Kayode Salako, Aderemi Kehinde, Nneka Onyejepu, Emmanuel Idigbe, Tumani Corrah, Bouke de Jong, Mark J Pallen, Martin Antonio
Nigeria has an emerging problem with multidrug-resistant tuberculosis (MDR-TB). Whole-genome sequencing was used to understand the epidemiology of tuberculosis and genetics of multi-drug resistance among patients from two tertiary referral centers in Southwest Nigeria. In line with previous molecular epidemiology studies, most isolates of Mycobacterium tuberculosis from this dataset belonged to the Cameroon clade within the Euro-American lineage. Phylogenetic analysis showed this clade was undergoing clonal expansion in this region, and suggests that it was involved in community transmission of sensitive and multidrug-resistant tuberculosis...
2017: PloS One
https://www.readbyqxmd.com/read/28926145/a-crispr-reimagining-new-twists-and-turns-of-crispr-beyond-the-genome-engineering-revolution
#3
Robert J Plummer, Yi Guo, Ying Peng
Despite its explosive applications in genome engineering, CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) has been developed into a versatile tool beyond its well-known nuclease function. In this prospect article, we summarize a few exciting "off-label" applications of CRISPR including manipulating DNA sequences, visualizing chromosomal loci in living cells, and modulating transcription and chromatin structures. These novel applications will likely elevate CRISPR tools into yet another level of sophistication and diversity, leading to many more exciting cell biological discoveries...
September 19, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28925024/complete-characterization-of-new-isolates-of-neptunomonas-phycophila-leads-to-emend-its-description-and-opens-possibilities-of-biotechnological-applications
#4
Ana L Diéguez, Phillip Pichon, Sabela Balboa, Thorolf Magnesen, Jesús L Romalde
Five strains were isolated from gonad of Great scallop (Pecten maximus) broodstock in a Norwegian hatchery. The study of 16S rRNA gene sequences showed that these isolates belong to Neptunomonas phycophila, a bacterium originally isolated from a symbiont of the anemone Aiptasia tagetes from Puerto Rico. The gyrB and rpoB genes sequences confirmed the affiliation of the scallop isolates to this species. Phenotypic characterization was performed and some differences between the Norwegian isolates and the type strain of N...
September 18, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28924022/pan-genomic-analyses-identify-key-helicobacter-pylori-pathogenic-loci-modified-by-carcinogenic-host-microenvironments
#5
Jennifer M Noto, Abha Chopra, John T Loh, Judith Romero-Gallo, M Blanca Piazuelo, Mark Watson, Shay Leary, Amber C Beckett, Keith T Wilson, Timothy L Cover, Simon Mallal, Dawn A Israel, Richard M Peek
OBJECTIVE: Helicobacter pylori is the strongest risk factor for gastric cancer; however, the majority of infected individuals do not develop disease. Pathological outcomes are mediated by complex interactions among bacterial, host and environmental constituents, and two dietary factors linked with gastric cancer risk are iron deficiency and high salt. We hypothesised that prolonged adaptation of H. pylori to in vivo carcinogenic microenvironments results in genetic modification important for disease...
September 18, 2017: Gut
https://www.readbyqxmd.com/read/28923972/small-genome-symbiont-underlies-cuticle-hardness-in-beetles
#6
Hisashi Anbutsu, Minoru Moriyama, Naruo Nikoh, Takahiro Hosokawa, Ryo Futahashi, Masahiko Tanahashi, Xian-Ying Meng, Takashi Kuriwada, Naoki Mori, Kenshiro Oshima, Masahira Hattori, Manabu Fujie, Noriyuki Satoh, Taro Maeda, Shuji Shigenobu, Ryuichi Koga, Takema Fukatsu
Beetles, representing the majority of the insect species diversity, are characterized by thick and hard cuticle, which plays important roles for their environmental adaptation and underpins their inordinate diversity and prosperity. Here, we report a bacterial endosymbiont extremely specialized for sustaining beetle's cuticle formation. Many weevils are associated with a γ-proteobacterial endosymbiont lineage Nardonella, whose evolutionary origin is estimated as older than 100 million years, but its functional aspect has been elusive...
September 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28922869/genome-organization-of-sphingobium-indicum-b90a-an-archetypal-hexachlorocyclohexane-hch-degrading-genotype
#7
Helianthous Verma, Abhay Bajaj, Roshan Kumar, Jasvinder Kaur, Shailly Anand, Namita Nayyar, Akshita Puri, Yogendra Singh, Jitendra P Khurana, Rup Lal
Among sphingomonads, Sphingobium indicum B90A is widely investigated for its ability to degrade a manmade pesticide, γ-hexachlorocyclohexane (γ-HCH) and its isomers (α-, β-, δ-, and ε-HCH). In this study, complete genome of strain B90A was constructed using Single Molecule Real Time Sequencing (SMRT) and Illumina platform. The complete genome revealed that strain B90A harbors four replicons: one chromosome (3,654,322 bp) and three plasmids designated as pSRL1 (139,218 bp), pSRL2 (108,430 bp) and pSRL3 (43,761 bp)...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28920850/ramlibacter-alkalitolerans-sp-nov-alkali-tolerant-bacterium-isolated-from-soil-of-ginseng
#8
Do-Hoon Lee, Chang-Jun Cha
A novel bacterial strain, designated CJ661T, was isolated from soil of ginseng in Anseong, South Korea. Cells of strain CJ661T were white-coloured, Gram-staining-negative, non-motile, aerobic and rod-shaped. Strain CJ661T grew optimally at 30 °C and pH 7.0. The analysis of 16S rRNA gene sequence of strain CJ661T showed that it belongs to the genus Ramlibacter within the family Comamonadaceae and was most closely related to Ramlibacter ginsenosidimutans KCTC 22276T (98.1 %), followed by Ramlibacter henchirensis DSM 14656T (97...
September 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28920843/rejection-of-reclassification-of-lactobacillus-kimchii-and-lactobacillus-bobalius-as-later-subjective-synonyms-of-lactobacillus-paralimentarius-using-comparative-genomics
#9
Seung-Jo Yang, Byung-Yong Kim, Jongsik Chun
Lactobacillus bobalius, Lactobacillus kimchii and Lactobacillus paralimentarius belong to the genus Lactobacillus and show close phylogenetic relationships. In a previous study, L. bobalius and L. kimchii were proposed to be reclassified as later heterotypic synonyms of L. paralimentarius using high 16S rRNA gene sequence similarities (≥99.5 %) and DNA-DNA hybridization values (≥82 %). We determined high quality whole genome assemblies of the type strains of L. bobalius and L. kimchii, which were then compared with that of L...
September 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28920840/flavobacterium-dispersum-sp-nov-isolated-from-a-freshwater-spring
#10
Wen-Ming Chen, Ching-Ling Su, Shih-Yi Sheu
A novel bacterial strain MVW-23T was isolated from a freshwater spring in Taiwan. The strain was Gram-staining-negative, strictly aerobic, motile by gliding, rod-shaped and formed translucent yellow colonies. Optimal growth occurred at 20-30 °C, pH 7.0, and in the presence of 0.5-1 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain MVW-23T belonged to the genus Flavobacterium and showed the highest levels of sequence similarity with respect to Flavobacterium denitrificans ED5T (97...
September 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28920837/bacillus-solisilvae-sp-nov-isolated-from-forest-soil
#11
Tong Pan, Hairong He, Xiaochong Wang, Yibo Shen, Junwei Zhao, Kai Yan, Xiangjing Wang, Chongxi Liu, Ji Zhang, Wensheng Xiang
A novel Gram-stain-positive, motile, endospore-forming, rod-shaped bacterial strain, NEAU-cbsb5T, was isolated from forest soil from Changbai Mountain, Heilongjiang Province, China. The isolate grew at 15-40 °C (optimum 30 °C), at pH 6.0-8.0 (optimum pH 7.0) and in the presence of up to 4 % (w/v) NaCl, although NaCl was not required for growth. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NEAU-cbsb5T formed a distinct lineage within the genus Bacillus and was most closely related to Bacillus acidiceler DSM 18954T (99...
September 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28919972/cytogenetic-maps-of-homoeologous-chromosomes-a-h01-and-d-h01-and-their-integration-with-the-genome-assembly-in-gossypium-hirsutum
#12
Yuling Liu, Zhen Liu, Renhai Peng, Yuhong Wang, Zhongli Zhou, Xiaoyan Cai, Xingxing Wang, Zhenmei Zhang, Kunbo Wang, Fang Liu
Cytogenetic maps of Gossypium hirsutum (Linnaeus, 1753) homoeologous chromosomes Ah01 and Dh01 were constructed by fluorescence in situ hybridization (FISH), using eleven homoeologous-chromosomes-shared bacterial artificial chromosomes (BACs) clones and one chromosome-specific BAC clone respectively. We compared the cytogenetic maps with the genetic linkage and draft genome assembly maps based on a standardized map unit, relative map position (RMP), which allowed a global view of the relationship of genetic and physical distances along each chromosome, and assembly quality of the draft genome assembly map...
2017: Comparative Cytogenetics
https://www.readbyqxmd.com/read/28916450/capsule-switching-of-neisseria-meningitidis-sequence-type-7-serogroup-a-to-serogroup-x
#13
Xuemeng Ji, Ping-Ping Yao, Le-Yi Zhang, Yi Li, Fang Xu, Ling-Ling Mei, Shui-Rong Zhu, Yan-Jun Zhang, Han-Ping Zhu, Stijn van der Veen
OBJECTIVES: The bacterial pathogen Neisseria meningitidis is able to escape the currently available capsule-based vaccines by undergoing capsule switching. In this study, we investigated whether capsule switching has occurred in a recently emerged sequence type (ST) 7 serogroup X isolate in China, for which currently no vaccine is available. METHODS: To identify capsule switching breakpoints, the capsule locus and flanking regions of the ST-7 serogroup X isolate and three endemic ST-7 serogroup A isolates were sequenced and compared...
September 12, 2017: Journal of Infection
https://www.readbyqxmd.com/read/28914880/tremblaya-phenacola-pper-an-evolutionary-beta-gammaproteobacterium-collage
#14
Rosario Gil, Carlos Vargas-Chavez, Sergio López-Madrigal, Diego Santos-García, Amparo Latorre, Andrés Moya
Many insects rely on bacterial endosymbionts to obtain nutrients that are scarce in their highly specialized diets. The most surprising example corresponds to the endosymbiotic system found in mealybugs from subfamily Pseudococcinae in which two bacteria, the betaproteobacterium 'Candidatus Tremblaya princeps' and a gammaproteobacterium, maintain a nested endosymbiotic consortium. In the sister subfamily Phenacoccinae, however, a single beta-endosymbiont, 'Candidatus Tremblaya phenacola', has been described...
September 15, 2017: ISME Journal
https://www.readbyqxmd.com/read/28912838/phylogenomics-of-colombian-helicobacter-pylori-isolates
#15
Andrés Julián Gutiérrez-Escobar, Esperanza Trujillo, Orlando Acevedo, María Mercedes Bravo
BACKGROUND: During the Spanish colonisation of South America, African slaves and Europeans arrived in the continent with their corresponding load of pathogens, including Helicobacter pylori. Colombian strains have been clustered with the hpEurope population and with the hspWestAfrica subpopulation in multilocus sequence typing (MLST) studies. However, ancestry studies have revealed the presence of population components specific to H. pylori in Colombia. The aim of this study was to perform a thorough phylogenomic analysis to describe the evolution of the Colombian urban H...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/28912769/adaptation-of-surface-associated-bacteria-to-the-open-ocean-a-genomically-distinct-subpopulation-of-phaeobacter-gallaeciensis-colonizes-pacific-mesozooplankton
#16
Heike M Freese, Anika Methner, Jörg Overmann
The marine Roseobacter group encompasses numerous species which occupy a large variety of ecological niches. However, members of the genus Phaeobacter are specifically adapted to a surface-associated lifestyle and have so far been found nearly exclusively in disjunct, man-made environments including shellfish and fish aquacultures, as well as harbors. Therefore, the possible natural habitats, dispersal and evolution of Phaeobacter spp. have largely remained obscure. Applying a high-throughput cultivation strategy along a longitudinal Pacific transect, the present study revealed for the first time a widespread natural occurrence of Phaeobacter in the marine pelagial...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28912766/environmental-bacteriophages-of-the-emerging-enterobacterial-phytopathogen-dickeya-solani-show-genomic-conservation-and-capacity-for-horizontal-gene-transfer-between-their-bacterial-hosts
#17
Andrew Day, Jiyoon Ahn, Xinzhe Fang, George P C Salmond
Dickeya solani is an economically important phytopathogen widespread in mainland Europe that can reduce potato crop yields by 25%. There are no effective environmentally-acceptable chemical systems available for diseases caused by Dickeya. Bacteriophages have been suggested for use in biocontrol of this pathogen in the field, and limited field trials have been conducted. To date only a small number of bacteriophages capable of infecting D. solani have been isolated and characterized, and so there is a need to expand the repertoire of phages that may have potential utility in phage therapy strategies...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28912069/generation-of-a-novel-human-cytomegalovirus-bacterial-artificial-chromosome-tailored-for-transduction-of-exogenous-sequences
#18
William L Close, Amit Bhandari, Marwa Hojeij, Philip E Pellett
The study of herpesviruses, including human cytomegalovirus (HCMV), is complicated by viral genome complexity and inefficient methods for genetic manipulation in tissue culture. Reverse genetics of herpesviruses has been facilitated by propagating their genomes in E. coli as bacterial artificial chromosomes (BACs), which enables complex and precise genetic manipulation using bacterial recombinational systems. Internal capsid volume imposes a strict limit on the length of genome that can be packaged efficiently...
September 11, 2017: Virus Research
https://www.readbyqxmd.com/read/28910967/identification-and-characterization-of-domesticated-bacterial-transposases
#19
Frederic Bertels, Jenna Gallie, Paul B Rainey
Selfish genetic elements, such as insertion sequences and transposons are found in most genomes. Transposons are usually identifiable by their high copy number within genomes. In contrast, REP-associated tyrosine transposases (RAYTs), a recently described class of bacterial transposase, are typically present at just one copy per genome. This suggests that RAYTs no longer copy themselves and thus they no longer function as a typical transposase. Motivated by this possibility we interrogated thousands of fully sequenced bacterial genomes in order to determine patterns of RAYT diversity, their distribution across chromosomes and accessory elements, and rate of duplication...
August 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28910288/genomics-enabled-analysis-of-the-emergent-disease-cotton-bacterial-blight
#20
Anne Z Phillips, Jeffrey C Berry, Mark C Wilson, Anupama Vijayaraghavan, Jillian Burke, J Imani Bunn, Tom W Allen, Terry Wheeler, Rebecca S Bart
Cotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistant germplasm for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Here, we report analysis of cotton variety planting statistics that indicate a steady increase in the percentage of susceptible cotton varieties grown each year since 2009. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv...
September 14, 2017: PLoS Genetics
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