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Find video protocols related to scientific articles indexed in Pubmed.
Genome Sequence of Corynebacterium pseudotuberculosis MB20 bv. equi Isolated from a Pectoral Abscess of an Oldenburg Horse in California.
Genome Announc
PUBLISHED: 11-15-2014
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The genome of Corynebacterium pseudotuberculosis MB20 bv. equi was sequenced using the Ion Personal Genome Machine (PGM) platform, and showed a size of 2,363,089 bp, with 2,365 coding sequences and a GC content of 52.1%. These results will serve as a basis for further studies on the pathogenicity of C. pseudotuberculosis bv. equi.
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Draft Genome Sequence of Non-O1 and Non-O139 Vibrio cholerae Strain VCC19.
Genome Announc
PUBLISHED: 11-08-2014
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Vibrio cholerae O1 is the causative agent of cholera and is ubiquitous in the aquatic environment, while V. cholerae strains non-O1 and non-O139 are recognized as causative agents of sporadic and localized outbreaks of diarrhea. Here, we report the complete sequence of a non-O1 and non-O139 V. cholerae strain (VCC19), which was isolated from the environment in Brazil. The sequence includes the integrative conjugative element (ICE). This paper is the first report of the presence of such an element in a V. cholerae strain isolated in Brazil.
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Omics profiles used to evaluate the gene expression of Exiguobacterium antarcticum B7 during cold adaptation.
BMC Genomics
PUBLISHED: 02-26-2014
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Exiguobacterium antarcticum strain B7 is a Gram-positive psychrotrophic bacterial species isolated in Antarctica. Although this bacteria has been poorly studied, its genome has already been sequenced. Therefore, it is an appropriate model for the study of thermal adaptation. In the present study, we analyzed the transcriptomes and proteomes of E. antarcticum B7 grown at 0[degree sign]C and 37[degree sign]C by SOLiD RNA-Seq, Ion Torrent RNA-Seq and two-dimensional difference gel electrophoresis tandem mass spectrometry (2D-DIGE-MS/MS).
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Draft Genome Sequence of Corynebacterium ulcerans FRC58, Isolated from the Bronchitic Aspiration of a Patient in France.
Genome Announc
PUBLISHED: 01-11-2014
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Corynebacterium ulcerans is a bacterial species with high importance because it causes infections in animals and, rarely, in humans. Its virulence mechanisms remain unclear. The current study describes the draft genome of C. ulcerans FRC58, which was isolated from the bronchitic aspiration of a patient in France.
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Draft Genome Sequence of Serratia fonticola UTAD54, a Carbapenem-Resistant Strain Isolated from Drinking Water.
Genome Announc
PUBLISHED: 11-29-2013
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Serratia fonticola UTAD54 is an environmental isolate that is resistant to carbapenems due to the presence of a class A carbapenemase and a metallo-?-lactamase that are unique to this strain. Its draft genome sequence was obtained to clarify the molecular basis of its carbapenem resistance and identify the genomic context of its carbapenem resistance determinants.
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Draft Genome Sequence of Serratia fonticola LMG 7882T Isolated from Freshwater.
Genome Announc
PUBLISHED: 11-23-2013
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Serratia fonticola is a Gram-negative bacterium with a wide distribution in aquatic environments. On some occasions, it has also been regarded as a significant human pathogen. In this work, we report the first draft genome sequence of an S. fonticola strain (LMG 7882(T)), which was isolated from freshwater.
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Complete Genome of a Methanosarcina mazei Strain Isolated from Sediment Samples from an Amazonian Flooded Area.
Genome Announc
PUBLISHED: 05-25-2013
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Methanosarcina mazei is a strictly anaerobic methanogen from the Methanosarcinales order, which is known for its broad catabolic range among methanogens and is widespread throughout diverse environments. The draft genome of the strain presented here was cultivated from sediment samples collected from the Tucuruí hydroelectric power station reservoir.
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Microbial diversity of an anoxic zone of a hydroelectric power station reservoir in Brazilian Amazonia.
Microb. Ecol.
PUBLISHED: 02-28-2011
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Microbial diversity was evaluated in an anoxic zone of Tucuruí Hydroelectric Power Station reservoir in Brazilian Amazonia using a culture-independent approach by amplifying and sequencing fragments of the 16S rRNA gene using metagenomic DNA as a template. Samples obtained from the photic, aphotic (40 m) and sediment (60 m) layers were used to construct six 16S rDNA libraries containing a total of 1,152 clones. The sediment, aphotic and photic layers presented 64, 33 and 35 unique archaeal operational taxonomic units (OTUs). The estimated richness of these layers was evaluated to be 153, 106 and 79 archaeal OTUs, respectively, using the abundance-based coverage estimator (ACE) and 114, 83 and 77 OTUs using the Chao1 estimator. For bacterial sequences, 114, 69 and 57 OTUs were found in the sediment, aphotic and photic layers, which presented estimated richnesses of 1,414, 522 and 197 OTUs (ACE) and 1,059, 1,014 and 148 OTUs (Chao1), respectively. Phylogenetic analyses of the sequences obtained revealed a high richness of microorganisms which participate in the carbon cycle, namely, methanogenic archaea and methanotrophic proteobacteria. Most sequences obtained belong to non-culturable prokaryotes. The present study offers the first glimpse of the huge microbial diversity of an anoxic area of a man-made lacustrine environment in the tropics.
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Genome sequence of Exiguobacterium antarcticum B7, isolated from a biofilm in Ginger Lake, King George Island, Antarctica.
J. Bacteriol.
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Exiguobacterium antarcticum is a psychotropic bacterium isolated for the first time from microbial mats of Lake Fryxell in Antarctica. Many organisms of the genus Exiguobacterium are extremophiles and have properties of biotechnological interest, e.g., the capacity to adapt to cold, which make this genus a target for discovering new enzymes, such as lipases and proteases, in addition to improving our understanding of the mechanisms of adaptation and survival at low temperatures. This study presents the genome of E. antarcticum B7, isolated from a biofilm sample of Ginger Lake on King George Island, Antarctic peninsula.
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FunSys: Software for functional analysis of prokaryotic transcriptome and proteome.
Bioinformation
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The vast amount of data produced by next-generation sequencing (NGS) has necessitated the development of computational tools to assist in understanding the myriad functions performed by the biological macromolecules involved in heredity. In this work, we developed the FunSys programme, a stand-alone tool with an user friendly interface that enables us to evaluate and correlate differential expression patterns from RNA sequencing and proteomics datasets. The FunSys generates charts and reports based on the results of the analysis of differential expression to aid the interpretation of the results.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.