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https://www.readbyqxmd.com/read/28384626/complete-genome-sequence-of-proteus-mirabilis-phage-ppm_01-isolated-from-raw-sewage
#1
Ira Aryani Wirjon, Nyok-Sean Lau, Yahya Mat Arip
OBJECTIVES: Phage pPM_01 was previously isolated from a raw sewage treatment facility located in Batu Maung, Penang, Malaysia, and it was highly lytic against Proteus mirabilis, which causes urinary tract infections in humans. In this paper, we characterize the biology and complete genome sequence of the phage. METHODS AND RESULTS: Transmission electron microscopy revealed phage pPM_01 to be a siphovirus (the first reported virus to infect P. mirabilis), with its complete genome sequence successfully determined...
April 7, 2017: Intervirology
https://www.readbyqxmd.com/read/28286707/molecular-phylogenies-confirm-the-presence-of-two-cryptic-hemimycale-species-in-the-mediterranean-and-reveal-the-polyphyly-of-the-genera-crella-and-hemimycale-demospongiae-poecilosclerida
#2
Maria J Uriz, Leire Garate, Gemma Agell
BACKGROUND: Sponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions. Hemimycale is a sponge genus (Family Hymedesmiidae, Order Poecilosclerida) with four formally described species, from which only Hemimycale columella has been recorded in the Atlanto-Mediterranean basin, on shallow to 80 m deep bottoms. Contrasting biological features between shallow and deep individuals of Hemimycale columella suggested larger genetic differences than those expected between sponge populations...
2017: PeerJ
https://www.readbyqxmd.com/read/28256468/computational-prediction-of-immunodominant-antigenic-regions-potential-protective-epitopes-for-dengue-vaccination
#3
Karthikeyan Muthusamy, Krishnasamy Gopinath, Dharmalingam Nandhini
BACKGROUND & OBJECTIVES: Epitope-based vaccines (EVs) are specific, safe and easy to produce. However, vaccine failure has been frequently reported due to variation within epitopic regions. Therefore, development of vaccines based on conserved epitopes may prevent such vaccine failure. This study was undertaken to identify highly conserved antigenic regions in the four dengue serotypes to produce an epitope-based dengue vaccine. METHODS: Polyprotein sequences of all four dengue serotypes were collected and aligned using MAFFT multiple sequence alignment plugin with Geneious Pro v6...
October 2016: Indian Journal of Medical Research
https://www.readbyqxmd.com/read/28239610/preparing-and-analyzing-expressed-sequence-tags-ests-library-for-the-mammary-tissue-of-local-turkish-kivircik-sheep
#4
Nehir Ozdemir Ozgenturk, Zehra Omeroglu Ulu, Salih Ulu, Cemal Un, Kemal Ozdem Oztabak, Kemal Altunatmaz
Kivircik sheep is an important local Turkish sheep according to its meat quality and milk productivity. The aim of this study was to analyze gene expression profiles of both prenatal and postnatal stages for the Kivircik sheep. Therefore, two different cDNA libraries, which were taken from the same Kivircik sheep mammary gland tissue at prenatal and postnatal stages, were constructed. Total 3072 colonies which were randomly selected from the two libraries were sequenced for developing a sheep ESTs collection...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28060851/molecular-evidence-of-transmission-of-influenza-a-h1n1-2009-on-a-university-campus
#5
Ramandeep Kaur Virk, Vithiagaran Gunalan, Hong Kai Lee, Masafumi Inoue, Catherine Chua, Boon-Huan Tan, Paul Anantharajah Tambyah
BACKGROUND: In the recent years, the data on the molecular epidemiology of influenza viruses have expanded enormously because of the availability of cutting-edge sequencing technologies. However, much of the information is from the temperate regions with few studies from tropical regions such as South-east Asia. Despite the fact that influenza has been known to transmit rapidly within semi-closed communities, such as military camps and educational institutions, data are limited from these communities...
2017: PloS One
https://www.readbyqxmd.com/read/28038368/structure-and-expression-of-dna-methyltransferase-genes-from-apomictic-and-sexual-boechera-species
#6
Kemal Melik Taşkin, Aslıhan Özbilen, Fatih Sezer, Kaan Hürkan, Şebnem Güneş
In this study, we determined the structure of DNA methyltransferase (DNMT) genes in apomict and sexual Boechera species and investigated the expression levels during seed development. Protein and DNA sequences of diploid sexual Boechera stricta DNMT genes obtained from Phytozome 10.3 were used to identify the homologues in apomicts, Boechera holboellii and Boechera divaricarpa. Geneious R8 software was used to map the short-paired reads library of B. holboellii whole genome or B. divaricarpa transcriptome reads to the reference gene sequences...
December 20, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27843724/complete-chloroplast-genome-of-a-valuable-medicinal-plant-huperzia-serrata-lycopodiaceae-and-comparison-with-its-congener
#7
Zhi-You Guo, Hong-Rui Zhang, Nawal Shrestha, Xian-Chun Zhang
PREMISE OF THE STUDY: Here we report the complete chloroplast genome of the important medicinal species Huperzia serrata (Lycopodiaceae) and compare it to the chloroplast genome of the congeneric species H. lucidula. METHODS AND RESULTS: The whole chloroplast genome of H. serrata was sequenced using an Illumina platform and assembled with Geneious version R9.0.5. The genome size of H. serrata was 154,176 bp, with 36.3% GC content. The complete chloroplast genome contained 120 unique genes, including 86 coding genes, four rRNA genes, and 30 tRNA genes...
November 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27395897/first-report-of-the-land-planarian-diversibipalium-multilineatum-makino-shirasawa-1983-platyhelminthes-tricladida-continenticola-in-europe
#8
Giuseppe Mazza, Mattia Menchetti, Ronald Sluys, Eduard Solà, Marta Riutort, Elena Tricarico, Jean-Lou Justine, Luca Cavigioli, Emiliano Mori
Introduction of alien species may significantly affect soil ecosystems, through predation or disruption of components of native ecosystems (Winsor et al. 2004; Álvarez-Presas et al. 2014; Justine et al. 2014). Land planarians have been reported as alien species in soils throughout the world and, among those, some species are considered to be successful invaders, e.g. Platydemus manokwari de Beauchamp, 1963, Arthurdendyus triangulatus (Dendy, 1894), Bipalium adventitium Hyman, 1943, Bipalium kewense Moseley, 1878 and Dolichoplana striata Moseley, 1877 (Winsor et al...
January 26, 2016: Zootaxa
https://www.readbyqxmd.com/read/27196272/the-challenges-of-implementing-next-generation-sequencing-across-a-large-healthcare-system-and-the-molecular-epidemiology-and-antibiotic-susceptibilities-of-carbapenemase-producing-bacteria-in-the-healthcare-system-of-the-u-s-department-of-defense
#9
Emil Lesho, Robert Clifford, Fatma Onmus-Leone, Lakshmi Appalla, Erik Snesrud, Yoon Kwak, Ana Ong, Rosslyn Maybank, Paige Waterman, Patricia Rohrbeck, Michael Julius, Amanda Roth, Joshua Martinez, Lindsey Nielsen, Eric Steele, Patrick McGann, Mary Hinkle
OBJECTIVE: We sought to: 1) provide an overview of the genomic epidemiology of an extensive collection of carbapenemase-producing bacteria (CPB) collected in the U.S. Department of Defense health system; 2) increase awareness of the public availability of the sequences, isolates, and customized antimicrobial resistance database of that system; and 3) illustrate challenges and offer mitigations for implementing next generation sequencing (NGS) across large health systems. DESIGN: Prospective surveillance and system-wide implementation of NGS...
2016: PloS One
https://www.readbyqxmd.com/read/26460173/reverse-vaccinology-as-an-approach-for-developing-histophilus-somni-vaccine-candidates
#10
COMPARATIVE STUDY
Claudia Avis Madampage, Neil Rawlyk, Gordon Crockford, Yejun Wang, Aaron P White, Robert Brownlie, Joyce Van Donkersgoed, Craig Dorin, Andrew Potter
Histophilosis of cattle is caused by the Gram negative bacterial pathogen Histophilus somni (H. somni) which is also associated with the bovine respiratory disease (BRD) complex. Existing vaccines for H. somni include either killed cells or bacteria-free outer membrane proteins from the organism which have proven to be moderately successful. In this study, reverse vaccinology was used to predict potential H. somni vaccine candidates from genome sequences. In turn, these may protect animals against new strains circulating in the field...
November 2015: Biologicals: Journal of the International Association of Biological Standardization
https://www.readbyqxmd.com/read/26459873/genomic-insight-into-aquimarina-longa-sw024-t-its-ultra-oligotrophic-adapting-mechanisms-and-biogeochemical-functions
#11
Tingting Xu, Min Yu, Heyu Lin, Zenghu Zhang, Jiwen Liu, Xiao-Hua Zhang
BACKGROUND: South Pacific Gyre (SPG) is the largest and clearest gyre in the world, where the concentration of surface chlorophyll a and primary production are extremely low. Aquimarina longa SW024(T) was isolated from surface water of the SPG center. To understand how this bacterium could survive in this ultra-oligotrophic oceanic environment and its function in biogeochemical cycle, we sequenced the genome of A. longa SW024(T) and performed extensive genomic analyses. METHODS: Genomic DNA was extracted and sequenced using Illumina Hiseq 2000 and Miseq platform...
2015: BMC Genomics
https://www.readbyqxmd.com/read/26449402/the-genome-of-dasychira-pudibunda-nucleopolyhedrovirus-dapunpv-reveals-novel-genetic-connection-between-baculoviruses-infecting-moths-of-the-lymantriidae-family
#12
Martyna Krejmer, Iwona Skrzecz, Bartosz Wasag, Boguslaw Szewczyk, Lukasz Rabalski
BACKGROUND: DapuNPV (Dasychira pudibunda nucleopolyhedrovirus), presented in this report, belongs to Alphabaculovirus group Ib. Its full, newly sequenced genome shows close relationship to baculovirus OpMNPV isolated from douglas-fir tussock moth Orgyia pseudotsugata. Baculovirus DapuNPV is a natural limiter of pale tussock moth Dasychira pudibunda L. (syn. Calliteara pudibunda L.)(Lepidoptera, Lymantriidae), which can occur in a form of an outbreak on many species of deciduous trees and may cause significant economic losses in the forests...
2015: BMC Genomics
https://www.readbyqxmd.com/read/26446890/phylogenetic-and-geographic-analysis-of-fowl-adenovirus-field-strains-isolated-from-poultry-in-poland
#13
Jowita Samanta Niczyporuk
Fowl adenoviruses (FAdVs) are widely distributed in chickens in Poland and throughout the world. FAdV infections have been reported in the United States, Australia, Europe, and the Mediterranean basin. Detection of FAdVs strains is very important from the epidemiological point of view and for monitoring disease outbreaks and developing strategies for vaccine development. Several molecular epidemiology and phylogenetic studies have been performed, but the results obtained are still limited, because FAdV strains, even of the same serotype, have very diverse characteristics...
January 2016: Archives of Virology
https://www.readbyqxmd.com/read/26220837/islands-within-islands-diversification-of-tailless-whip-spiders-amblypygi-phrynus-in-caribbean-caves
#14
Lauren A Esposito, Trevor Bloom, Laura Caicedo-Quiroga, Angela M Alicea-Serrano, Jose A Sánchez-Ruíz, Laura J May-Collado, Greta J Binford, Ingi Agnarsson
Islands have played a key role in understanding species formation ever since Darwin's work on the Galapagos and Wallace's work in the Malay Archipelago. Like oceanic islands, habitat 'islands', such as mountaintops and caves similarly may drive diversification. Here we examine patterns of diversification in the tailless whip spider genus Phrynus Larmarck, 1809 (Amblypygida: Phrynidae) a system that shows evidence of diversification under the influence of 'islands within islands'. We estimate phylogeographic history and measure genetic diversity among representatives of three nominal Phrynus species from epigean and cave systems of Puerto Rico and nearby islands...
December 2015: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/26063445/sequence-analysis-of-lip-r-a-good-method-for-molecular-epidemiology-of-clinical-isolates-of-mycobacterium-tuberculosis
#15
Samaneh Saedi, Masoud Youssefi, Hadi Safdari, Saman Soleimanpour, Parviz Marouzi, Kiarash Ghazvini
Advances in DNA sequencing have greatly enhanced the molecular epidemiology studies. In order to assess evolutionary and phylogenetic relation of Mycobacterium tuberculosis isolates several gene targets were evaluated. In this study, appropriate fragments of 5 highly variable genes (rpsL, mprA, lipR, katG, and fgd1 genes) were sequenced. The sequence data were analyzed with neighbor-joining method using mega and Geneious software. The phylogenetic trees analyzes revealed that the discriminatory power of lipR is much stronger than that observed in the other genes...
October 2015: Current Microbiology
https://www.readbyqxmd.com/read/25948579/antismash-3-0-a-comprehensive-resource-for-the-genome-mining-of-biosynthetic-gene-clusters
#16
Tilmann Weber, Kai Blin, Srikanth Duddela, Daniel Krug, Hyun Uk Kim, Robert Bruccoleri, Sang Yup Lee, Michael A Fischbach, Rolf Müller, Wolfgang Wohlleben, Rainer Breitling, Eriko Takano, Marnix H Medema
Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3...
July 1, 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/25896365/whole-genome-sequence-comparison-of-ten-diagnostic-brucellaphages-propagated-on-two-brucella-abortus-hosts
#17
Ekaterine Tevdoradze, Jason Farlow, Adam Kotorashvili, Natia Skhirtladze, Irina Antadze, Sophio Gunia, Nana Balarjishvili, Leila Kvachadze, Mzia Kutateladze
BACKGROUND: Recently the genome sequences of two brucellaphages, isolated in Georgia (Tb) and Mexico (Pr) were reported revealing pronounced sequence homogeneity and the presence of two major indels discriminating the two phages. Subsequent genome sequencing of six diagnostic brucellaphages: Tbilisi (Tb), Firenze (Fz), Weybridge (Wb), S708, Berkeley (Bk) and R/C phages identified three major genetic groups. However, the propensity for fine-scale genetic variability of diverse brucellaphages grown on multiple hosts within a single Brucella species remains unknown...
2015: Virology Journal
https://www.readbyqxmd.com/read/25826378/mixturetree-annotator-a-program-for-automatic-colorization-and-visual-annotation-of-mixturetree
#18
Shu-Chuan Chen, Aaron Ogata
The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information...
2015: PloS One
https://www.readbyqxmd.com/read/25793402/evidence-of-long-lived-founder-virus-in-mother-to-child-hiv-transmission
#19
Sivapragashini Danaviah, Tulio de Oliveira, Ruth Bland, Johannes Viljoen, Sureshnee Pillay, Edouard Tuaillon, Philippe Van de Perre, Marie-Louise Newell
Exposure of the infant's gut to cell-associated and cell-free HIV-1 trafficking in breast milk (BM) remains a primary cause of mother-to-child transmission (MTCT). The mammary gland represents a unique environment for HIV-1 replication and host-virus interplay. We aimed to explore the origin of the virus transmitted during breastfeeding, and the link with quasi-species found in acellular and cellular fractions of breast-milk (BM) and in maternal plasma. The C2-V5 region of the env gene was amplified, cloned and sequenced from the RNA and DNA of BM, the RNA from the mother's plasma (PLA) and the DNA from infant's dried blood spot (DBS) in 11 post-natal mother-infant pairs...
2015: PloS One
https://www.readbyqxmd.com/read/25506521/geneious-simplified-genome-skimming-methods-for-phylogenetic-systematic-studies-a-case-study-in-oreocarya-boraginaceae
#20
Lee A Ripma, Michael G Simpson, Kristen Hasenstab-Lehman
UNLABELLED:PREMISE OF THE STUDY: As systematists grapple with how to best harness the power of next-generation sequencing (NGS), a deluge of review papers, methods, and analytical tools make choosing the right method difficult. Oreocarya (Boraginaceae), a genus of 63 species, is a good example of a group lacking both species-level resolution and genomic resources. The use of Geneious removes bioinformatic barriers and makes NGS genome skimming accessible to even the least tech-savvy systematists...
December 2014: Applications in Plant Sciences
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