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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...
2016: Zootaxa
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
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
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
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
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
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
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
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 Here, we present version 3...
July 1, 2015: Nucleic Acids Research
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
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
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
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
Shorash Amin, Peter J Prentis, Edward K Gilding, Ana Pavasovic
BACKGROUND: The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species...
2014: BMC Research Notes
Sherryn Ciavaglia, Stephen Donnellan, Julianne Henry, Adrian Linacre
In this paper we report on the identification of a section of mitochondrial DNA that can be used to identify the species of protected and illegally traded pythons of the genus Morelia. Successful enforcement of wildlife laws requires forensic tests that can identify the species nominated in the relevant legislation. The potentially degraded state of evidentiary samples requires that forensic investigation using molecular genetic species identification is optimized to interrogate small fragments of DNA. DNA was isolated from 35 samples of Morelia spilota from which the complete cytochrome b was sequenced...
September 2014: Forensic Science, Medicine, and Pathology
Andargachew Mulu, Melanie Maier, Uwe Gerd Liebert
BACKGROUND: Helminth infections as well as structural alternations in the long-terminal repeat (LTR) regions of HIV-1 are known to contribute to elevated HIV RNA level and enhance HIV-1 diseases progression. However, the impact of helminths infections on the occurrences of triple NF-κB and genetic variability in LTR region of HIV-1C isolates is not known. We aimed to examine the presence of genetic variability in the LTR region of HIV-1C isolates during chronic HIV-helminth co-infection...
2014: Parasites & Vectors
Hui-juan Yang, Jian-sheng Liu, Yun-kun Zhang, Zhong-fei Ma, Wei-zhong Zhao, Yue Pan, Jun-ying Chen, Cong-wen Shao, Shao-hui Ma
OBJECTIVE: To analyze the genetic characterization of the complete genome from a human coxsackievirus B3 strain A103/KM/09 isolated in Yunnan province, 2009. METHODS: By using RT-PCR, all the eight fragments which containing about 1000 nucleotides and covering full viral genome, were sequenced. By using Mega 5.05,Geneious, RDP 3 and SimPlot 3.5.1 software, sequences were aligned with other enterovirus reference sequences. Phylogenetic and recombination analysis were also carried out...
December 2013: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
Sureshnee Pillay, Ruth M Bland, Richard J Lessells, Justen Manasa, Tulio de Oliveira, Sivapragashini Danaviah
BACKGROUND: Better understanding of drug resistance patterns in HIV-infected children on antiretroviral therapy (ART) is required to inform public health policies in high prevalence settings. The aim of this study was to characterise the acquired drug resistance in HIV-infected children failing first-line ART in a decentralised rural HIV programme. METHODS: Plasma samples were collected from 101 paediatric patients (≤15 yrs of age) identified as failing ART. RNA was extracted from the plasma, reverse transcribed and a 1...
2014: AIDS Research and Therapy
W K Yu, Y F Shi, C C Fong, Y Chen, J P van de Merwe, Alice K Y Chan, F Wei, J Bo, R Ye, Doris W T Au, Rudolf S S Wu, M S Yang
Marine medaka (Oryzias melastigma) were exposed to 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) to investigate the gender-specific transcriptional profiles of liver tissue in response to this flame retardant. A cDNA library of O. melastigma was constructed, and 2304 clones were amplified from the library to fabricate a cDNA microarray. Sequences of these genes were assembled into 1800 sequences using Geneious, a bioinformatics software. Corresponding expressed sequence tags were blasted against the National Centre for Biotechnology Information non-redundant database and further classified into various biological categories according to the Gene Ontology project...
September 2013: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Luke Hecht, Anton Dormer
In silico tools are employed to examine the evolutionary relationship to possible vaccine peptide candidates' development. This perspective sheds light on the proteomic changes affecting the creation of HLA specific T-cell stimulating peptide vaccines for HIV. Full-length sequences of the envelope protein of the HIV subtypes A, B, C and D were obtained through the NCBI Protein database were aligned using CLUSTALW. They were then analyzed using RANKPEP specific to Human Leukocyte Antigen A*02 and B*27. Geneious was used to catalogue the collected gp160 sequences and to construct a phylogenic tree...
2013: Bioinformation
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