JoVE Visualize What is visualize?
Stop Reading. Start Watching.
Advanced Search
Stop Reading. Start Watching.
Regular Search
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
Show Abstract
Hide Abstract
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.
Related JoVE Video
The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers.
Bioinformatics
PUBLISHED: 09-04-2014
Show Abstract
Hide Abstract
Rapid technological advances have led to an explosion of biomedical data in recent years. The pace of change has inspired new collaborative approaches for sharing materials and resources to help train life scientists both in the use of cutting-edge bioinformatics tools and databases and in how to analyse and interpret large datasets. A prototype platform for sharing such training resources was recently created by the Bioinformatics Training Network (BTN). Building on this work, we have created a centralized portal for sharing training materials and courses, including a catalogue of trainers and course organizers, and an announcement service for training events. For course organizers, the portal provides opportunities to promote their training events; for trainers, the portal offers an environment for sharing materials, for gaining visibility for their work and promoting their skills; for trainees, it offers a convenient one-stop shop for finding suitable training resources and identifying relevant training events and activities locally and worldwide. Availability and implementation: http://mygoblet.org/training-portal CONTACT: manuel.corpas@tgac.ac.uk.
Related JoVE Video
Socioeconomic factors and vulnerability to outbreaks of leptospirosis in Nicaragua.
Int J Environ Res Public Health
PUBLISHED: 08-15-2014
Show Abstract
Hide Abstract
Leptospirosis is an epidemic-prone zoonotic disease that occurs worldwide, with more than 500,000 human cases reported annually. It is influenced by environmental and socioeconomic factors that affect the occurrence of outbreaks and the incidence of the disease. Critical areas and potential drivers for leptospirosis outbreaks have been identified in Nicaragua, where several conditions converge and create an appropriate scenario for the development of leptospirosis. The objectives of this study were to explore possible socioeconomic variables related to leptospirosis critical areas and to construct and validate a vulnerability index based on municipal socioeconomic indicators. Municipalities with lower socioeconomic status (greater unsatisfied basic needs for quality of the household and for sanitary services, and higher extreme poverty and illiteracy rates) were identified with the highest leptospirosis rates. The municipalities with highest local vulnerability index should be the priority for intervention. A distinction between risk given by environmental factors and vulnerability to risk given by socioeconomic conditions was shown as important, which also applies to the "causes of outbreaks" and "causes of cases".
Related JoVE Video
Omics profiles used to evaluate the gene expression of Exiguobacterium antarcticum B7 during cold adaptation.
BMC Genomics
PUBLISHED: 02-26-2014
Show Abstract
Hide Abstract
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).
Related JoVE Video
A genome-wide association study of production traits in a commercial population of Large White pigs: evidence of haplotypes affecting meat quality.
Genet. Sel. Evol.
PUBLISHED: 02-14-2014
Show Abstract
Hide Abstract
Numerous quantitative trait loci (QTL) have been detected in pigs over the past 20 years using microsatellite markers. However, due to the low density of these markers, the accuracy of QTL location has generally been poor. Since 2009, the dense genome coverage provided by the Illumina PorcineSNP60 BeadChip has made it possible to more accurately map QTL using genome-wide association studies (GWAS). Our objective was to perform high-density GWAS in order to identify genomic regions and corresponding haplotypes associated with production traits in a French Large White population of pigs.
Related JoVE Video
Where does human plague still persist in Latin America?
PLoS Negl Trop Dis
PUBLISHED: 02-01-2014
Show Abstract
Hide Abstract
Plague is an epidemic-prone disease with a potential impact on public health, international trade, and tourism. It may emerge and re-emerge after decades of epidemiological silence. Today, in Latin America, human cases and foci are present in Bolivia, Brazil, Ecuador, and Peru.
Related JoVE Video
Quality control of spliced mRNAs requires the shuttling SR proteins Gbp2 and Hrb1.
Nat Commun
PUBLISHED: 01-24-2014
Show Abstract
Hide Abstract
Eukaryotic cells have to prevent the export of unspliced pre-mRNAs until intron removal is completed to avoid the expression of aberrant and potentially harmful proteins. Only mature mRNAs associate with the export receptor Mex67/TAP and enter the cytoplasm. Here we show that the two shuttling serine/arginine (SR)-proteins Gbp2 and Hrb1 are key surveillance factors for the selective export of spliced mRNAs in yeast. Their absence leads to the significant leakage of unspliced pre-mRNAs into the cytoplasm. They bind to pre-mRNAs and the spliceosome during splicing, where they are necessary for the surveillance of splicing and the stable binding of the TRAMP complex to spliceosome-bound transcripts. Faulty transcripts are marked for their degradation at the nuclear exosome. On correct mRNAs the SR proteins recruit Mex67 upon completion of splicing to allow a quality controlled nuclear export. Altogether, these data identify a role for shuttling SR proteins in mRNA surveillance and nuclear mRNA quality control.
Related JoVE Video
Polymorphic color vision in captive Uta Hick's cuxiús, or bearded sakis (Chiropotes utahickae).
Am. J. Primatol.
PUBLISHED: 01-22-2014
Show Abstract
Hide Abstract
The pitheciines (Chiropotes, Pithecia, and Cacajao) are frugivorous Neotropical primates that specialize on the predation of seeds from unripe fruits, usually cryptic against the foliage. However, little is known about the color vision distribution within this taxon, and even less about the abilities shared by these animals regarding discrimination of chromatic targets. The aim of this study was to evaluate the color vision perception of captive Uta Hick's cuxiús, or bearded sakis (Chiropotes utahickae) through a behavioral paradigm of color visual discrimination, as well as to estimate, by genetic studies, the number and kinds of medium to long wavelength cone photopigment (opsins) encoded by this species. Among 12 cuxiús (7 males and 5 females) studied only 1 female was diagnosed as a trichromat. Results from genotyping were in line with our behavioral data and showed that cuxiús carried one (dichromat) or two (trichromat) medium to long wavelength pigments alleles, demonstrating a color vision polymorphism in C. utahickae similar to the majority of Neotropical Primates. Am. J. Primatol. © 2014 Wiley Periodicals, Inc.
Related JoVE Video
Differential transcriptional profile of Corynebacterium pseudotuberculosis in response to abiotic stresses.
BMC Genomics
PUBLISHED: 01-09-2014
Show Abstract
Hide Abstract
The completion of whole-genome sequencing for Corynebacterium pseudotuberculosis strain 1002 has contributed to major advances in research aimed at understanding the biology of this microorganism. This bacterium causes significant loss to goat and sheep farmers because it is the causal agent of the infectious disease caseous lymphadenitis, which may lead to outcomes ranging from skin injury to animal death. In the current study, we simulated the conditions experienced by the bacteria during host infection. By sequencing transcripts using the SOLiDTM 3 Plus platform, we identified new targets expected to potentiate the survival and replication of the pathogen in adverse environments. These results may also identify possible candidates useful for the development of vaccines, diagnostic kits or therapies aimed at the reduction of losses in agribusiness.
Related JoVE Video
Pregnancy-Related Obstetric and Cardiologic Problems in Women After Atrial Switch Operation for Transposition of the Great Arteries.
Circ. J.
PUBLISHED: 12-10-2013
Show Abstract
Hide Abstract
Background:?The number of women with congenital heart disease reaching reproductive age has increased due to therapeutic advances. The aim of this study was to examine obstetric and cardiac problems during pregnancy after Mustard/Senning repair for transposition of the great arteries. Methods and Results:?Sixty pregnancies in 34 women from 3 centers were studied. The women were interviewed, and their records reviewed for clinical status and diagnostic evaluation. Age range was 16-34 years during first pregnancy, and all were in a low functional class. There were 11 miscarriages and 5 abortions. Of 44 successful pregnancies, 20 were vaginal deliveries and 24, cesarean sections. A total of 25% were delivered prematurely. Thirteen babies had birth weight <2,500g. Deterioration in functional class occurred in 7 pregnancies, without recovery in 5. Deterioration in systolic function occurred in 4 of 44 echocardiographically documented pregnancies, without recovery in 75%. In 2 women resuscitation was necessary during delivery, in 1, supraventricular tachycardia occurred during labor. Conclusions:?Pregnancy is usually well-tolerated, but outcome is unforeseeable and life-threatening problems can occur. These women belong in cardiac care conducted by experienced congenital cardiologists, who systematically check for typical residua. The pregnancy should be planned and gynecologists/obstetricians with special expertise integrated into the consultations. During delivery a congenital cardiologist, and an anesthetist experienced in congenital cardiology, should be present for possible severe cardiac events.
Related JoVE Video
Leptospirosis: a silent epidemic disease.
Int J Environ Res Public Health
PUBLISHED: 12-09-2013
Show Abstract
Hide Abstract
This special issue of International Journal of Environmental Research and Public Health is dedicated to leptospirosis, an endemic zoonotic disease that is a cause of many acute undifferentiated fevers, especially in tropical countries [1,2]. While it can be debated whether leptospirosis is an emerging disease, it is evident that it is becoming an emerging public health problem. It is recognized as a disease of epidemic potential that has a significant health impact in many parts of the world.
Related JoVE Video
Draft Genome Sequence of the Brazilian Toxic Bloom-Forming Cyanobacterium Microcystis aeruginosa Strain SPC777.
Genome Announc
PUBLISHED: 08-03-2013
Show Abstract
Hide Abstract
Microcystis aeruginosa strain SPC777 is an important toxin-producing cyanobacterium, isolated from a water bloom of the Billings reservoir (São Paulo State, Brazil). Here, we report the draft genome sequence and initial findings from a preliminary analysis of strain SPC777, including several gene clusters involved in nonribosomal and ribosomal synthesis of secondary metabolites.
Related JoVE Video
Best practices in bioinformatics training for life scientists.
Brief. Bioinformatics
PUBLISHED: 06-25-2013
Show Abstract
Hide Abstract
The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists.
Related JoVE Video
The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability.
Brief. Bioinformatics
PUBLISHED: 06-21-2013
Show Abstract
Hide Abstract
Next-generation sequencing (NGS) is increasingly being adopted as the backbone of biomedical research. With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data. The current resources for NGS informatics are extremely fragmented. Finding a centralized synthesis is difficult. A multitude of tools exist for NGS data analysis; however, none of these satisfies all possible uses and needs. This gap in functionality could be filled by integrating different methods in customized pipelines, an approach helped by the open-source nature of many NGS programmes. Drawing from community spirit and with the use of the Wikipedia framework, we have initiated a collaborative NGS resource: The NGS WikiBook. We have collected a sufficient amount of text to incentivize a broader community to contribute to it. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.
Related JoVE Video
Exercise reduces cellular stress related to skeletal muscle insulin resistance.
Cell Stress Chaperones
PUBLISHED: 06-17-2013
Show Abstract
Hide Abstract
This study sought to evaluate the effects of a single session of exercise on the expression of Hsp70, of c-jun N-terminal kinase (JNK), and insulin receptor substrate 1 serine 612 (IRS(ser612)) phosphorylation in the skeletal muscle of obese and obese insulin-resistant patients. Twenty-seven volunteers were divided into three experimental groups (eutrophic insulin-sensitive, obese insulin-sensitive, and obese insulin-resistant) according to their body mass index and the presence of insulin resistance. The volunteers performed 60 min of aerobic exercise on a cycle ergometer at 60 % of peak oxygen consumption. M. vastus lateralis samples were obtained before and after exercise. The protein expressions were evaluated by Western blot. Our findings show that compared with paired eutrophic controls, obese subjects have higher basal levels of p-JNK (100?±?23 % vs. 227?±?67 %, p?=?0.03) and p-IRS-1(ser612) (100?±?23 % vs. 340?±?67 %, p??0.05). Exercise reduced p-JNK in obese insulin-resistant subjects (328?±?33 %, p?=?0.001), but not in controls or obese subjects. Furthermore, exercise reduced p-IRS-1(ser612) for both obese (122?±?44 %) and obese insulin-resistant (185?±?36 %) subjects. A main effect of exercise was observed in HSP70 (p?=?0.007). We demonstrated that a single session of exercise promotes changes that characterize a reduction in cellular stress that may contribute to exercise-induced increase in insulin sensitivity.
Related JoVE Video
The genome of Anopheles darlingi, the main neotropical malaria vector.
Osvaldo Marinotti, Gustavo C Cerqueira, Luiz Gonzaga Paula de Almeida, Maria Inês Tiraboschi Ferro, Élgion Lúcio da Silva Loreto, Arnaldo Zaha, Santuza M R Teixeira, Adam R Wespiser, Alexandre Almeida E Silva, Aline Daiane Schlindwein, Ana Carolina Landim Pacheco, Artur Luiz da Costa da Silva, Brenton R Graveley, Brian P Walenz, Bruna de Araujo Lima, Carlos Alexandre Gomes Ribeiro, Carlos Gustavo Nunes-Silva, Carlos Roberto de Carvalho, Célia Maria de Almeida Soares, Claudia Beatriz Afonso de Menezes, Cleverson Matiolli, Daniel Caffrey, Demetrius Antonio M Araújo, Diana Magalhaes de Oliveira, Douglas Golenbock, Edmundo Carlos Grisard, Fabiana Fantinatti-Garboggini, Fabíola Marques de Carvalho, Fernando Gomes Barcellos, Francisco Prosdocimi, Gemma May, Gilson Martins de Azevedo Junior, Giselle Moura Guimarães, Gustavo Henrique Goldman, Itácio Q M Padilha, Jacqueline da Silva Batista, Jesus Aparecido Ferro, José M C Ribeiro, Juliana Lopes Rangel Fietto, Karina Maia Dabbas, Louise Cerdeira, Lucymara Fassarella Agnez-Lima, Marcelo Brocchi, Marcos Oliveira de Carvalho, Marcus de Melo Teixeira, Maria de Mascena Diniz Maia, Maria Helena S Goldman, Maria Paula Cruz Schneider, Maria Sueli Soares Felipe, Mariangela Hungria, Marisa Fabiana Nicolás, Maristela Pereira, Martín Alejandro Montes, Mauricio E Cantão, Michel Vincentz, Míriam Silva Rafael, Neal Silverman, Patrícia Hermes Stoco, Rangel Celso Souza, Renato Vicentini, Ricardo Tostes Gazzinelli, Rogério de Oliveira Neves, Rosane Silva, Spartaco Astolfi-Filho, Talles Eduardo Ferreira Maciel, Turán P Urményi, Wanderli Pedro Tadei, Erney Plessmann Camargo, Ana Tereza Ribeiro de Vasconcelos.
Nucleic Acids Res.
PUBLISHED: 06-12-2013
Show Abstract
Hide Abstract
Anopheles darlingi is the principal neotropical malaria vector, responsible for more than a million cases of malaria per year on the American continent. Anopheles darlingi diverged from the African and Asian malaria vectors ?100 million years ago (mya) and successfully adapted to the New World environment. Here we present an annotated reference A. darlingi genome, sequenced from a wild population of males and females collected in the Brazilian Amazon. A total of 10 481 predicted protein-coding genes were annotated, 72% of which have their closest counterpart in Anopheles gambiae and 21% have highest similarity with other mosquito species. In spite of a long period of divergent evolution, conserved gene synteny was observed between A. darlingi and A. gambiae. More than 10 million single nucleotide polymorphisms and short indels with potential use as genetic markers were identified. Transposable elements correspond to 2.3% of the A. darlingi genome. Genes associated with hematophagy, immunity and insecticide resistance, directly involved in vector-human and vector-parasite interactions, were identified and discussed. This study represents the first effort to sequence the genome of a neotropical malaria vector, and opens a new window through which we can contemplate the evolutionary history of anopheline mosquitoes. It also provides valuable information that may lead to novel strategies to reduce malaria transmission on the South American continent. The A. darlingi genome is accessible at www.labinfo.lncc.br/index.php/anopheles-darlingi.
Related JoVE Video
iAnn: an event sharing platform for the life sciences.
Bioinformatics
PUBLISHED: 06-05-2013
Show Abstract
Hide Abstract
We present iAnn, an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. iAnn allows automatic visualisation and integration of customised event reports. A central repository lies at the core of the platform: curators add submitted events, and these are subsequently accessed via web services. Thus, once an iAnn widget is incorporated into a website, it permanently shows timely relevant information as if it were native to the remote site. At the same time, announcements submitted to the repository are automatically disseminated to all portals that query the system. To facilitate the visualization of announcements, iAnn provides powerful filtering options and views, integrated in Google Maps and Google Calendar. All iAnn widgets are freely available.
Related JoVE Video
High efficiency application of a mate-paired library from next-generation sequencing to postlight sequencing: Corynebacterium pseudotuberculosis as a case study for microbial de novo genome assembly.
J. Microbiol. Methods
PUBLISHED: 06-03-2013
Show Abstract
Hide Abstract
With the advent of high-throughput DNA sequencing platforms, there has been a reduction in the cost and time of sequencing. With these advantages, new challenges have emerged, such as the handling of large amounts of data, quality assessment, and the assembly of short reads. Currently, benchtop high-throughput sequencers enable the genomes of prokaryotic organisms to be sequenced within two hours with a reduction in coverage compared with the SOLiD, Illumina and 454 FLX Titanium platforms, making it necessary to evaluate the efficiency of less expensive benchtop instruments for prokaryotic genomics. In the present work, we evaluate and propose a methodology for the use of the Ion Torrent PGM platform for decoding the gram-positive bacterium Corynebacterium pseudotuberculosis, for which 15 complete genome sequences have already been deposited based on fragment and mate-paired libraries with a 3-kb insert size. Despite the low coverage, a single sequencing run using a mate-paired library generated 39 scaffolds after de novo assembly without data curation. This result is superior to that obtained by sequencing using libraries generated from fragments marketed by the equipments manufacturer, as well as that observed for mate-pairs sequenced by SOLiD. The generated sequence added an extra 91kb to the genome available at NCBI.
Related JoVE Video
Defining systems biology: a brief overview of the term and field.
Methods Mol. Biol.
PUBLISHED: 05-30-2013
Show Abstract
Hide Abstract
Here we provide a broad overview of the definition of the term "systems biology" as well as pinpoint specific events in biological research and beyond that are consistently cited to have contributed and led to the current science of in silico systems biology. Since there have been many reviews and historical accounts describing the term, it would be impossible to include all single references. However, we do attempt to provide a consensus vision of how the field has evolved and consequently the terminology that followed it. We also highlight the development and general acceptance, and use, of standards for model representations as being crucial to the continued success of the in silico systems biology field.
Related JoVE Video
Complete Genome of a Methanosarcina mazei Strain Isolated from Sediment Samples from an Amazonian Flooded Area.
Genome Announc
PUBLISHED: 05-25-2013
Show Abstract
Hide Abstract
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.
Related JoVE Video
Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia.
Brief. Bioinformatics
PUBLISHED: 03-29-2013
Show Abstract
Hide Abstract
The widespread adoption of high-throughput next-generation sequencing (NGS) technology among the Australian life science research community is highlighting an urgent need to up-skill biologists in tools required for handling and analysing their NGS data. There is currently a shortage of cutting-edge bioinformatics training courses in Australia as a consequence of a scarcity of skilled trainers with time and funding to develop and deliver training courses. To address this, a consortium of Australian research organizations, including Bioplatforms Australia, the Commonwealth Scientific and Industrial Research Organisation and the Australian Bioinformatics Network, have been collaborating with EMBL-EBI training team. A group of Australian bioinformaticians attended the train-the-trainer workshop to improve training skills in developing and delivering bioinformatics workshop curriculum. A 2-day NGS workshop was jointly developed to provide hands-on knowledge and understanding of typical NGS data analysis workflows. The road show-style workshop was successfully delivered at five geographically distant venues in Australia using the newly established Australian NeCTAR Research Cloud. We highlight the challenges we had to overcome at different stages from design to delivery, including the establishment of an Australian bioinformatics training network and the computing infrastructure and resource development. A virtual machine image, workshop materials and scripts for configuring a machine with workshop contents have all been made available under a Creative Commons Attribution 3.0 Unported License. This means participants continue to have convenient access to an environment they had become familiar and bioinformatics trainers are able to access and reuse these resources.
Related JoVE Video
Chromobacterium violaceum: important insights for virulence and biotechnological potential by exoproteomic studies.
Curr. Microbiol.
PUBLISHED: 02-04-2013
Show Abstract
Hide Abstract
Chromobacterium violaceum is a beta-proteobacterium with high biotechnological potential, found in tropical environments. This bacterium causes opportunistic infections in both humans and animals, that can spread throughout several tissues, quickly leading to the death of the host. Genomic studies identified potential mechanisms of pathogenicity but no further studies were done to confirm the expression of these systems. In this study 36 unique protein entries were identified in databank from a two-dimensional profile of C. violaceum secreted proteins. Chromobacterium violaceum exoproteomic preliminary studies confirmed the production of proteins identified as virulence factors (such as a collagenase, flagellum proteins, metallopeptidases, and toxins), allowing us to better understand its pathogenicity mechanisms. Biotechnologically interesting proteins (such as chitinase and chitosanase) were also identified among the secreted proteins, as well as proteins involved in the transport and capture of amino acids, carbohydrates, and oxidative stress protection. Overall, the secreted proteins identified provide us important insights on pathogenicity mechanisms, biotechnological potential, and environment adaptation of C. violaceum.
Related JoVE Video
Ion Torrent-based transcriptional assessment of a Corynebacterium pseudotuberculosis equi strain reveals denaturing high-performance liquid chromatography a promising rRNA depletion method.
Microb Biotechnol
PUBLISHED: 01-15-2013
Show Abstract
Hide Abstract
Corynebacterium pseudotuberculosis equi is a Gram-positive pathogenic bacterium which affects a variety of hosts. Besides the great economic losses it causes to horse-breeders, this organism is also known to be an important infectious agent to cattle and buffaloes. As an outcome of the efforts in characterizing the molecular basis of its virulence, several complete genome sequences were made available in recent years, enabling the large-scale assessment of genes throughout distinct isolates. Meanwhile, the RNA-seq stood out as the technology of choice for comprehensive transcriptome studies, which may bring valuable information regarding active genomic regions, despite of the still impeditive associated costs. In an attempt to increase the use of generated reads per instrument run, by effectively eliminating unwanted rRNAs from total RNA samples without relying on any commercially available kits, we applied denaturing high-performance liquid chromatography (DHPLC) as an alternative method to assess the transcriptional profile of C. pseudotuberculosis. We have found that the DHPLC depletion method, allied to Ion Torrent sequencing, allows mapping of transcripts in a comprehensive way and identifying novel transcripts when a de novo approach is used. These data encourage us to use DHPLC in future transcriptional evaluations in C. pseudotuberculosis.
Related JoVE Video
The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains.
PLoS ONE
PUBLISHED: 01-14-2013
Show Abstract
Hide Abstract
Corynebacterium pseudotuberculosis is a facultative intracellular pathogen and the causative agent of several infectious and contagious chronic diseases, including caseous lymphadenitis, ulcerative lymphangitis, mastitis, and edematous skin disease, in a broad spectrum of hosts. In addition, Corynebacterium pseudotuberculosis infections pose a rising worldwide economic problem in ruminants. The complete genome sequences of 15 C. pseudotuberculosis strains isolated from different hosts and countries were comparatively analyzed using a pan-genomic strategy. Phylogenomic, pan-genomic, core genomic, and singleton analyses revealed close relationships among pathogenic corynebacteria, the clonal-like behavior of C. pseudotuberculosis and slow increases in the sizes of pan-genomes. According to extrapolations based on the pan-genomes, core genomes and singletons, the C. pseudotuberculosis biovar ovis shows a more clonal-like behavior than the C. pseudotuberculosis biovar equi. Most of the variable genes of the biovar ovis strains were acquired in a block through horizontal gene transfer and are highly conserved, whereas the biovar equi strains contain great variability, both intra- and inter-biovar, in the 16 detected pathogenicity islands (PAIs). With respect to the gene content of the PAIs, the most interesting finding is the high similarity of the pilus genes in the biovar ovis strains compared with the great variability of these genes in the biovar equi strains. Concluding, the polymerization of complete pilus structures in biovar ovis could be responsible for a remarkable ability of these strains to spread throughout host tissues and penetrate cells to live intracellularly, in contrast with the biovar equi, which rarely attacks visceral organs. Intracellularly, the biovar ovis strains are expected to have less contact with other organisms than the biovar equi strains, thereby explaining the significant clonal-like behavior of the biovar ovis strains.
Related JoVE Video
Graphical contig analyzer for all sequencing platforms (G4ALL): a new stand-alone tool for finishing and draft generation of bacterial genomes.
Bioinformation
PUBLISHED: 01-01-2013
Show Abstract
Hide Abstract
Genome assembly has always been complicated due to the inherent difficulties of sequencing technologies, as well the computational methods used to process sequences. Although many of the problems for the generation of contigs from reads are well known, especially those involving short reads, the orientation and ordination of contigs in the finishing stages is still very challenging and time consuming, as it requires the manual curation of the contigs to guarantee correct identification them and prevent misassembly. Due to the large numbers of sequences that are produced, especially from the reads produced by next generation sequencers, this process demands considerable manual effort, and there are few software options available to facilitate the process. To address this problem, we have developed the Graphic Contig Analyzer for All Sequencing Platforms (G4ALL): a stand-alone multi-user tool that facilitates the editing of the contigs produced in the assembly process. Besides providing information on the gene products contained in each contig, obtained through a search of the available biological databases, G4ALL produces a scaffold of the genome, based on the overlap of the contigs after curation.
Related JoVE Video
Progress towards eliminating canine rabies: policies and perspectives from Latin America and the Caribbean.
Philos. Trans. R. Soc. Lond., B, Biol. Sci.
PUBLISHED: 01-01-2013
Show Abstract
Hide Abstract
Human rabies transmitted by dogs is considered a neglected disease that can be eliminated in Latin America and the Caribbean (LAC) by 2015. The aim of this paper is to discuss canine rabies policies and projections for LAC regarding current strategies for achieving this target and to critically review the political, economic and geographical factors related to the successful elimination of this deadly disease in the context of the difficulties and challenges of the region. The strong political and technical commitment to control rabies in LAC in the 1980s, started with the regional programme coordinated by the Pan American Health Organization. National and subnational programmes involve a range of strategies including mass canine vaccination with more than 51 million doses of canine vaccine produced annually, pre- and post-exposure prophylaxis, improvements in disease diagnosis and intensive surveillance. Rabies incidence in LAC has dramatically declined over the last few decades, with laboratory confirmed dog rabies cases decreasing from approximately 25 000 in 1980 to less than 300 in 2010. Dog-transmitted human rabies cases also decreased from 350 to less than 10 during the same period. Several countries have been declared free of human cases of dog-transmitted rabies, and from the 35 countries in the Americas, there is now only notification of human rabies transmitted by dogs in seven countries (Bolivia, Peru, Honduras, Haiti, Dominican Republic, Guatemala and some states in north and northeast Brazil). Here, we emphasize the importance of the political commitment in the final progression towards disease elimination. The availability of strategies for rabies control, the experience of most countries in the region and the historical ties of solidarity between countries with the support of the scientific community are evidence to affirm that the elimination of dog-transmitted rabies can be achieved in the short term. The final efforts to confront the remaining obstacles, like achieving and sustaining high vaccination coverage in communities that are most impoverished or in remote locations, are faced by countries that struggle to allocate sufficient financial and human resources for rabies control. Continent-wide cooperation is therefore required in the final efforts to secure the free status of remaining countries in the Americas, which is key to the regional elimination of human rabies transmitted by dogs.
Related JoVE Video
Complete genome sequence of Corynebacterium pseudotuberculosis strain CIP 52.97, isolated from a horse in Kenya.
J. Bacteriol.
PUBLISHED: 11-30-2011
Show Abstract
Hide Abstract
In this work, we report the whole-genome sequence of Corynebacterium pseudotuberculosis bv. equi strain CIP 52.97 (Collection Institut Pasteur), isolated in 1952 from a case of ulcerative lymphangitis in a Kenyan horse, which has evidently caused significant losses to agribusiness. Therefore, obtaining this genome will allow the detection of important targets for postgenomic studies, with the aim of minimizing problems caused by this microorganism.
Related JoVE Video
Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.
Brief. Bioinformatics
PUBLISHED: 11-22-2011
Show Abstract
Hide Abstract
Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of high-throughput biology, the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review it, respectively, to similar initiatives and collections.
Related JoVE Video
Whole-genome sequence of Corynebacterium pseudotuberculosis PAT10 strain isolated from sheep in Patagonia, Argentina.
J. Bacteriol.
PUBLISHED: 11-01-2011
Show Abstract
Hide Abstract
In this work, we report the complete genome sequence of a Corynebacterium pseudotuberculosis PAT10 isolate, collected from a lung abscess in an Argentine sheep in Patagonia, whose pathogen also required an investigation of its pathogenesis. Thus, the analysis of the genome sequence offers a means to better understanding of the molecular and genetic basis of virulence of this bacterium.
Related JoVE Video
Importance of animal/human health interface in potential Public Health Emergencies of International Concern in the Americas.
Rev. Panam. Salud Publica
PUBLISHED: 06-29-2011
Show Abstract
Hide Abstract
This study analyzed the importance of zoonoses and communicable diseases common to man and animals as potential Public Health Emergencies of International Concern to build an evidence base for future efforts to reduce risk of infection at the animal/human health interface. The events recorded in the World Health Organization (WHO) Event Management System (EMS) database for the Americas during the 18 months since the implementation of the 2005 revised version of WHOs International Health Regulations (15 June 2007-31 December 2008) were the main source for this analysis. Of the 110 events recorded by the EMS for the Americas during the study period, 86 were classified as communicable diseases-77 (70.0%) "within the animal/human health interface," 9 (8.2%) "not common to man and animals," 16 (14.5%) "syndromes with unknown etiologies," and 8 (7.3%) "product-related/ other." Of the 77 events within the animal/human health interface, 48 were "substantiated" (the presence of hazard was confirmed and/or human cases occurred clearly in excess of normal expectancy). These results confirm previous research and underscore the importance of the animal/human health interface as well as inter-sectoral collaboration.
Related JoVE Video
Comparative analysis of two complete Corynebacterium ulcerans genomes and detection of candidate virulence factors.
BMC Genomics
PUBLISHED: 06-01-2011
Show Abstract
Hide Abstract
Corynebacterium ulcerans has been detected as a commensal in domestic and wild animals that may serve as reservoirs for zoonotic infections. During the last decade, the frequency and severity of human infections associated with C. ulcerans appear to be increasing in various countries. As the knowledge of genes contributing to the virulence of this bacterium was very limited, the complete genome sequences of two C. ulcerans strains detected in the metropolitan area of Rio de Janeiro were determined and characterized by comparative genomics: C. ulcerans 809 was initially isolated from an elderly woman with fatal pulmonary infection and C. ulcerans BR-AD22 was recovered from a nasal sample of an asymptomatic dog.
Related JoVE Video
Whole genome sequencing of environmental Vibrio cholerae O1 from 10 nanograms of DNA using short reads.
J. Microbiol. Methods
PUBLISHED: 05-14-2011
Show Abstract
Hide Abstract
Multiple Displacement Amplification (MDA) of DNA using ?29 (phi29) DNA polymerase amplifies DNA several billion-fold, which has proved to be potentially very useful for evaluating genome information in a culture-independent manner. Whole genome sequencing using DNA from a single prokaryotic genome copy amplified by MDA has not yet been achieved due to the formation of chimeras and skewed amplification of genomic regions during the MDA step, which then precludes genome assembly. We have hereby addressed the issue by using 10 ng of genomic Vibrio cholerae DNA extracted within an agarose plug to ensure circularity as a starting point for MDA and then sequencing the amplified yield using the SOLiD platform. We successfully managed to assemble the entire genome of V. cholerae strain LMA3984-4 (environmental O1 strain isolated in urban Amazonia) using a hybrid de novo assembly strategy. Using our method, only 178 out of 16,713 (1%) of contigs were not able to be inserted into either chromosome scaffold, and out of these 178, only 3 appeared to be chimeras. The other contigs seem to be the result of template-independent non-specific amplification during MDA, yielding spurious reads. Extraction of genomic DNA within an agarose plug in order to ensure circularity of the extracted genome might be key to minimizing amplification bias by MDA for WGS.
Related JoVE Video
Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study.
J. Microbiol. Methods
PUBLISHED: 05-05-2011
Show Abstract
Hide Abstract
Due to the advent of the so-called Next-Generation Sequencing (NGS) technologies the amount of monetary and temporal resources for whole-genome sequencing has been reduced by several orders of magnitude. Sequence reads can be assembled either by anchoring them directly onto an available reference genome (classical reference assembly), or can be concatenated by overlap (de novo assembly). The latter strategy is preferable because it tends to maintain the architecture of the genome sequence the however, depending on the NGS platform used, the shortness of read lengths cause tremendous problems the in the subsequent genome assembly phase, impeding closing of the entire genome sequence. To address the problem, we developed a multi-pronged hybrid de novo strategy combining De Bruijn graph and Overlap-Layout-Consensus methods, which was used to assemble from short reads the entire genome of Corynebacterium pseudotuberculosis strain I19, a bacterium with immense importance in veterinary medicine that causes Caseous Lymphadenitis in ruminants, principally ovines and caprines. Briefly, contigs were assembled de novo from the short reads and were only oriented using a reference genome by anchoring. Remaining gaps were closed using iterative anchoring of short reads by craning to gap flanks. Finally, we compare the genome sequence assembled using our hybrid strategy to a classical reference assembly using the same data as input and show that with the availability of a reference genome, it pays off to use the hybrid de novo strategy, rather than a classical reference assembly, because more genome sequences are preserved using the former.
Related JoVE Video
A practical teaching course in directed protein evolution using the green fluorescent protein as a model.
Biochem Mol Biol Educ
PUBLISHED: 03-25-2011
Show Abstract
Hide Abstract
Protein engineering is a powerful tool, which correlates protein structure with specific functions, both in applied biotechnology and in basic research. Here, we present a practical teaching course for engineering the green fluorescent protein (GFP) from Aequorea victoria by a random mutagenesis strategy using error-prone polymerase chain reaction. Screening of bacterial colonies transformed with random mutant libraries identified GFP variants with increased fluorescence yields. Mapping the three-dimensional structure of these mutants demonstrated how alterations in structural features such as the environment around the fluorophore and properties of the protein surface can influence functional properties such as the intensity of fluorescence and protein solubility.
Related JoVE Video
Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains.
PLoS ONE
PUBLISHED: 03-11-2011
Show Abstract
Hide Abstract
Corynebacterium pseudotuberculosis, a gram-positive, facultative intracellular pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL mainly affects small ruminants, such as goats and sheep; it also causes infections in humans, though rarely. This species is distributed worldwide, but it has the most serious economic impact in Oceania, Africa and South America. Although C. pseudotuberculosis causes major health and productivity problems for livestock, little is known about the molecular basis of its pathogenicity.
Related JoVE Video
Omics technologies, data and bioinformatics principles.
Methods Mol. Biol.
PUBLISHED: 03-04-2011
Show Abstract
Hide Abstract
We provide an overview on the state of the art for the Omics technologies, the types of omics data and the bioinformatics resources relevant and related to Omics. We also illustrate the bioinformatics challenges of dealing with high-throughput data. This overview touches several fundamental aspects of Omics and bioinformatics: data standardisation, data sharing, storing Omics data appropriately and exploring Omics data in bioinformatics. Though the principles and concepts presented are true for the various different technological fields, we concentrate in three main Omics fields namely: genomics, transcriptomics and proteomics. Finally we address the integration of Omics data, and provide several useful links for bioinformatics and Omics.
Related JoVE Video
Microbial diversity of an anoxic zone of a hydroelectric power station reservoir in Brazilian Amazonia.
Microb. Ecol.
PUBLISHED: 02-28-2011
Show Abstract
Hide Abstract
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.
Related JoVE Video
A molecular phylogeny of living primates.
PLoS Genet.
PUBLISHED: 02-16-2011
Show Abstract
Hide Abstract
Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (~8 Mb) from 186 primates representing 61 (~90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.
Related JoVE Video
Elimination of neglected diseases in latin america and the Caribbean: a mapping of selected diseases.
PLoS Negl Trop Dis
PUBLISHED: 01-12-2011
Show Abstract
Hide Abstract
In Latin America and the Caribbean, around 195 million people live in poverty, a situation that increases the burden of some infectious diseases. Neglected diseases, in particular, are often restricted to poor, marginalized sections of the population. Tools exist to combat these diseases, making it imperative to work towards their elimination. In 2009, the Pan American Health Organization (PAHO) received a mandate to support the countries in the Region in eliminating neglected diseases and other poverty-related infections. The objective of this study is to analyze the presence of selected diseases using geo-processing techniques. Five diseases with information available at the first sub-national level (states) were mapped, showing the presence of the disease ("hotspots") and overlap of diseases ("major hotspots"). In the 45 countries/territories (approximately 570 states) of the Region, there is: lymphatic filariasis in four countries (29 states), onchocerciasis in six countries (25 states), schistosomiasis in four countries (39 states), trachoma in three countries (29 states), and human rabies transmitted by dogs in ten countries (20 states). Of the 108 states with one or more of the selected diseases, 36 states present the diseases in overlapping areas ("major hotspots"). Additional information about soil-transmitted helminths was included. The analysis suggests a majority of the selected diseases are not widespread and can be considered part of an unfinished agenda with elimination as a goal. Integrated plans and a comprehensive approach, ensuring access to existing diagnostic and treatment methods, and establishing a multi-sectoral agenda that addresses social determinants, including access to adequate water and sanitation, are required. Future studies can include additional diseases, socio-economic and environmental variables.
Related JoVE Video
Analysis of quality raw data of second generation sequencers with Quality Assessment Software.
BMC Res Notes
PUBLISHED: 01-06-2011
Show Abstract
Hide Abstract
Second generation technologies have advantages over Sanger; however, they have resulted in new challenges for the genome construction process, especially because of the small size of the reads, despite the high degree of coverage. Independent of the program chosen for the construction process, DNA sequences are superimposed, based on identity, to extend the reads, generating contigs; mismatches indicate a lack of homology and are not included. This process improves our confidence in the sequences that are generated.
Related JoVE Video
Complete genome sequence of Corynebacterium pseudotuberculosis I19, a strain isolated from a cow in Israel with bovine mastitis.
J. Bacteriol.
PUBLISHED: 10-29-2010
Show Abstract
Hide Abstract
This work reports the completion and annotation of the genome sequence of Corynebacterium pseudotuberculosis I19, isolated from an Israeli dairy cow with severe clinical mastitis. To present the whole-genome sequence, a de novo assembly approach using 33 million short (25-bp) mate-paired SOLiD reads only was applied. Furthermore, the automatic, functional, and manual annotations were attained with the use of several algorithms in a multistep process.
Related JoVE Video
Nesprin-2 interacts with {alpha}-catenin and regulates Wnt signaling at the nuclear envelope.
J. Biol. Chem.
PUBLISHED: 08-26-2010
Show Abstract
Hide Abstract
Nesprins and emerin are structural nuclear envelope proteins that tether nuclei to the cytoskeleton. In this work, we identified the cytoskeleton-associated ?-N/E-catenins as novel nesprin-2-binding partners. The association involves the C termini of nesprin-2 giant and ?-N/E-catenins. ?-E/T/N-catenins are known primarily for their roles in cadherin-mediated cell-cell adhesion. Here, we show that, in addition, ?-catenin forms complexes with nesprin-2 that include ?-catenin and emerin. We demonstrate that the depletion of nesprin-2 reduces both the amount of active ?-catenin inside the nucleus and T-cell factor/lymphoid-enhancing factor-dependent transcription. Taken together, these findings suggest novel nesprin-2 functions in cellular signaling. Moreover, we propose that, in contrast to emerin, nesprin-2 is a positive regulator of the Wnt signaling pathway.
Related JoVE Video
Genetic structure of red-handed howler monkey populations in the fragmented landscape of Eastern Brazilian Amazonia.
Genet. Mol. Biol.
PUBLISHED: 07-13-2010
Show Abstract
Hide Abstract
We genotyped 15 microsatellite loci in order to evaluate the effects of habitat fragmentation, caused by flooding of the Tucuruí reservoir, on the genetic structure of Alouatta belzebul in eastern Amazonia. The analysis included two populations sampled in 1984, representing both margins of the Tocantins river, and three populations sampled 18 years later. Minimal differences in the diversity levels between present-day (Ho = 0.62-0.69 and A(R) = 6.07-7.21) and pre-flooding (Ho = 0.60-0.62 and A (R) = 6.27-6.77) populations indicated there was no significant loss of genetic variability, possibly because of successful management strategies applied during the flooding. The changes observed were limited to shifts in the composition of alleles, which presumably reflect the admixture of subpopulations during flooding. Given this, there were significant differences in the Rst values (p = 0.05) in all but one between-site comparison. Both present-day and original populations showed a deficit of heterozygotes, which suggests that this may be typical of the species, at least at a local level, perhaps because of specific ecological characteristics. The relatively large number of private alleles recorded in all populations may be a consequence of the Wahlund effect resulting from population admixture or a process of expansion rather than the loss of rare alleles through genetic drift. Additionally, the levels of genetic variability observed in this study were higher than those reported for other species of Neotropical primates, suggesting good fitness levels in these A. belzebul populations. Regular genetic monitoring of remnant populations, especially on islands, should nevertheless be an integral component of long-term management strategies.
Related JoVE Video
Bioinformatics training: selecting an appropriate learning content management system--an example from the European Bioinformatics Institute.
Brief. Bioinformatics
PUBLISHED: 07-02-2010
Show Abstract
Hide Abstract
Todays molecular life scientists are well educated in the emerging experimental tools of their trade, but when it comes to training on the myriad of resources and tools for dealing with biological data, a less ideal situation emerges. Often bioinformatics users receive no formal training on how to make the most of the bioinformatics resources and tools available in the public domain. The European Bioinformatics Institute, which is part of the European Molecular Biology Laboratory (EMBL-EBI), holds the worlds most comprehensive collection of molecular data, and training the research community to exploit this information is embedded in the EBIs mission. We have evaluated eLearning, in parallel with face-to-face courses, as a means of training users of our data resources and tools. We anticipate that eLearning will become an increasingly important vehicle for delivering training to our growing user base, so we have undertaken an extensive review of Learning Content Management Systems (LCMSs). Here, we describe the process that we used, which considered the requirements of trainees, trainers and systems administrators, as well as taking into account our organizational values and needs. This review describes the literature survey, user discussions and scripted platform testing that we performed to narrow down our choice of platform from 36 to a single platform. We hope that it will serve as guidance for others who are seeking to incorporate eLearning into their bioinformatics training programmes.
Related JoVE Video
Bioinformatics training: a review of challenges, actions and support requirements.
Brief. Bioinformatics
PUBLISHED: 06-18-2010
Show Abstract
Hide Abstract
As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics services, and discuss successful training strategies shared by a diverse set of bioinformatics trainers. We also identify steps that trainers in bioinformatics could take together to advance the state of the art in current training practices. The ideas presented in this article derive from the first Trainer Networking Session held under the auspices of the EU-funded SLING Integrating Activity, which took place in November 2009.
Related JoVE Video
Vaginal microbiome of reproductive-age women.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 06-03-2010
Show Abstract
Hide Abstract
The means by which vaginal microbiomes help prevent urogenital diseases in women and maintain health are poorly understood. To gain insight into this, the vaginal bacterial communities of 396 asymptomatic North American women who represented four ethnic groups (white, black, Hispanic, and Asian) were sampled and the species composition characterized by pyrosequencing of barcoded 16S rRNA genes. The communities clustered into five groups: four were dominated by Lactobacillus iners, L. crispatus, L. gasseri, or L. jensenii, whereas the fifth had lower proportions of lactic acid bacteria and higher proportions of strictly anaerobic organisms, indicating that a potential key ecological function, the production of lactic acid, seems to be conserved in all communities. The proportions of each community group varied among the four ethnic groups, and these differences were statistically significant [?(2)(10) = 36.8, P < 0.0001]. Moreover, the vaginal pH of women in different ethnic groups also differed and was higher in Hispanic (pH 5.0 ± 0.59) and black (pH 4.7 ± 1.04) women as compared with Asian (pH 4.4 ± 0.59) and white (pH 4.2 ± 0.3) women. Phylotypes with correlated relative abundances were found in all communities, and these patterns were associated with either high or low Nugent scores, which are used as a factor for the diagnosis of bacterial vaginosis. The inherent differences within and between women in different ethnic groups strongly argues for a more refined definition of the kinds of bacterial communities normally found in healthy women and the need to appreciate differences between individuals so they can be taken into account in risk assessment and disease diagnosis.
Related JoVE Video
Molecular mechanisms of centrosome and cytoskeleton anchorage at the nuclear envelope.
Cell. Mol. Life Sci.
PUBLISHED: 05-18-2010
Show Abstract
Hide Abstract
Cell polarization is a fundamental process underpinning organismal development, and tissue homeostasis, which requires an orchestrated interplay of nuclear, cytoskeletal, and centrosomal structures. The underlying molecular mechanisms, however, still remain elusive. Here we report that kinesin-1/nesprin-2/SUN-domain macromolecular assemblies, spanning the entire nuclear envelope (NE), function in cell polarization by anchoring cytoskeletal structures to the nuclear lamina. Nesprin-2 forms complexes with the kinesin-1 motor protein apparatus by associating with and recruiting kinesin light chain 1 (KLC1) to the outer nuclear membrane. Similar to nesprin-2, KLC1 requires lamin A/C for proper NE localization. The depletion of nesprin-2 or KLC1, or the uncoupling of nesprin-2/SUN-domain protein associations impairs cell polarization during wounding and dislodges the centrosome from the NE. In addition nesprin-2 loss has profound effects on KLC1 levels, the cytoskeleton, and Golgi apparatus organization. Collectively these data show that NE-associated proteins are pivotal determinants of cell architecture and polarization.
Related JoVE Video
Contraception in women with congenital heart disease.
Am. J. Cardiol.
PUBLISHED: 03-03-2010
Show Abstract
Hide Abstract
The present study reports on contraceptive use, methods used, and counseling received on contraceptive issues for women with congenital heart disease and provides a brief review of current knowledge of the risks in relation to the different cardiac situations encountered with these specific patients. A total of 536 consecutive adult women with congenital heart disease (median age 29 years) were recruited from 2 tertiary care centers. They underwent a clinical assessment and completed a questionnaire regarding their contraceptive use. Oral contraceptives, condoms, and intrauterine devices were the most commonly used methods. Pregnancy occurred in almost every tenth woman despite the use of contraception. We identified a substantial number of women (20%) who were presently using contraceptive methods that were contraindicated for their specific cardiac condition. Additionally, a high proportion of patients (28%), in the group with high pregnancy-associated risks, were not using contraception despite having a sexual relationship. In our study, 43% of the women had not been counseled about contraception, and 48% had not been informed of the pregnancy-related risks by their treating physician. In conclusion, timely and competent counseling about contraception is important for women with congenital heart disease. Collaboration between cardiologists and gynecologists should be strengthened. Failure to give adequate family planning advice to this patient group could have hazardous consequences, causing an unnecessary risk to mother and child.
Related JoVE Video
Comparison of self-collected and physician-collected vaginal swabs for microbiome analysis.
J. Clin. Microbiol.
PUBLISHED: 03-03-2010
Show Abstract
Hide Abstract
To our knowledge, no data are available on whether the microbial species composition and abundance sampled with self-collected vaginal swabs are comparable to those of swabs collected by clinicians. Twenty healthy women were recruited to the study during a routine gynecological visit. Eligible women were between 18 and 40 years old with regular menstrual cycles. Participants self-collected a vaginal swab using a standardized protocol and then were examined by a physician, who collected an additional five swabs from the lateral wall of the mid-vagina. In this study, the self-collected and three physician-obtained swabs were analyzed and compared using terminal restriction fragment length polymorphism and sequence analyses of the 16S rRNA genes. Vaginal microbial community comparative statistical analyses of both T-RFLP and 16S rRNA gene sequence datasets revealed that self-collected vaginal swabs sampled the same microbial diversity as physician collected swabs of the mid-vagina. These findings enable large-scale, field-based studies of the vaginal microbiome.
Related JoVE Video
Comparative genetic diversity of wild and captive populations of the bare-faced curassow (Crax fasciolata) based on cross-species microsatellite markers: implications for conservation and management.
Biochem. Genet.
PUBLISHED: 01-20-2010
Show Abstract
Hide Abstract
The bare-faced curassow (Crax fasciolata) is a large Neotropical bird that suffers anthropogenic pressure across much of its range. A captive population is maintained for conservation management, although there has been no genetic screening of stocks. Based on the six microsatellite markers developed for Crax globulosa, the genetic variability of C. fasciolata and possible differences between a wild and a captive population were investigated. Only three loci were polymorphic, with a total of 27 alleles. More than half of these alleles were private to the wild (n = 8) or captive (n = 7) populations. Significant deviations from Hardy-Weinberg equilibrium were restricted to the captive population. Despite the number of private alleles, genetic drift has probably promoted differentiation between populations. Our results indicate that wild C. fasciolata populations are genetically impoverished and structured, but species-specific microsatellite markers will be necessary for a more reliable assessment of the species genetic diversity.
Related JoVE Video
Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009-31 July 2009.
, Glenn R Almany, Maurício P DE Arruda, Wolfgang Arthofer, Z K Atallah, Steven R Beissinger, Michael L Berumen, S M Bogdanowicz, S D Brown, Michael W Bruford, C Burdine, Jeremiah W Busch, Nathan R Campbell, D Carey, Bryan C Carstens, K H Chu, Marc A Cubeta, J P Cuda, Zhaoxia Cui, L E Datnoff, J A Dávila, Emily S Davis, R M Davis, Onno E Diekmann, Eduardo Eizirik, J A Fargallo, Fabiano Fernandes, Hideo Fukuda, L R Gale, Elizabeth Gallagher, Yongqiang Gao, Philippe Girard, Anna Godhe, Evonnildo C Gonçalves, Licinia Gouveia, Amber M Grajczyk, M J Grose, Zhifeng Gu, Christer Hallden, Karolina Härnström, Amanda H Hemmingsen, Gerald Holmes, C H Huang, Chuan-Chin Huang, S P Hudman, Geoffrey P Jones, Loukas Kanetis, Iddya Karunasagar, Indrani Karunasagar, Nusha Keyghobadi, S J Klosterman, Page E Klug, J Koch, Margaret M Koopman, Kirsten Köppler, Eriko Koshimizu, Susanne Krumböck, T Kubisiak, J B Landis, Mario L Lasta, Chow-Yang Lee, Qianqian Li, Shou-Hsien Li, Rong-Chien Lin, M Liu, Na Liu, W C Liu, Yuan Liu, A Loiseau, Weisha Luan, K K Maruthachalam, Helen M McCormick, Rohan Mellick, P J Monnahan, Eliana Morielle-Versute, Tomás E Murray, Shawn R Narum, Katie Neufeld, P J G De Nova, Peter S Ojiambo, Nobuaki Okamoto, Ahmad Sofiman Othman, W A Overholt, Renata Pardini, Ian G Paterson, Olivia A Patty, Robert J Paxton, Serge Planes, Carolyn Porter, Morgan S Pratchett, Thomas Püttker, Gordana Rasić, Bilal Rasool, O Rey, Markus Riegler, C Riehl, John M K Roberts, P D Roberts, Elisabeth Rochel, Kevin J Roe, Maurizio Rossetto, Daniel E Ruzzante, Takashi Sakamoto, V Saravanan, Cladinara Roberts Sarturi, Anke Schmidt, Maria Paula Cruz Schneider, Hannes Schuler, Jeanne M Serb, Ester T A Serrão, Yaohua Shi, Artur Silva, Y W Sin, Simone Sommer, Christian Stauffer, Carlos Augusto Strüssmann, K V Subbarao, Craig Syms, Feng Tan, Eugenio Daniel Tejedor, Simon R Thorrold, Robert N Trigiano, María I Trucco, Mirian Tieko Nunes Tsuchiya-Jerep, P Vergara, Mirjam S Van De Vliet, Phillip A Wadl, Aimin Wang, Hongxia Wang, R X Wang, Xinwang Wang, Yan Wang, Andrew R Weeks, Fuwen Wei, William J Werner, E O Wiley, D A Williams, Richard J Wilkins, Samantha M Wisely, Kimberly A With, Danhua Wu, Cheng-Te Yao, Cynthia Yau, Beng-Keok Yeap, Bao-Ping Zhai, Xiangjiang Zhan, Guo-Yan Zhang, S Y Zhang, Ru Zhao, Lifeng Zhu.
Mol Ecol Resour
PUBLISHED: 09-29-2009
Show Abstract
Hide Abstract
This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.
Related JoVE Video
Bacterial succession in a glacier foreland of the High Arctic.
ISME J
PUBLISHED: 07-09-2009
Show Abstract
Hide Abstract
Succession is defined as changes in biological communities over time. It has been extensively studied in plant communities, but little is known about bacterial succession, in particular in environments such as High Arctic glacier forelands. Bacteria carry out key processes in the development of soil, biogeochemical cycling and facilitating plant colonization. In this study we sampled two roughly parallel chronosequences in the foreland of Midre Lovén glacier on Svalbard, Norway and tested whether any of several factors were associated with changes in the structure of bacterial communities, including time after glacier retreat, horizontal variation caused by the distance between chronosequences and vertical variation at two soil depths. The structures of soil bacterial communities at different locations were compared using terminal restriction fragment length polymorphisms of 16S rRNA genes, and the data were analyzed by sequential analysis of log-linear statistical models. Although no significant differences in community structure were detected between the two chronosequences, statistically significant differences between sampling locations in the surface and mineral soils could be demonstrated even though glacier forelands are patchy and dynamic environments. These findings suggest that bacterial succession occurs in High Arctic glacier forelands but may differ in different soil depths.
Related JoVE Video
Rabies transmitted by vampire bats to humans: an emerging zoonotic disease in Latin America?
Rev. Panam. Salud Publica
PUBLISHED: 05-21-2009
Show Abstract
Hide Abstract
Human rabies transmitted by vampire bats reached new heights in Latin America in 2005. A total of 55 human cases were reported in several outbreaks, 41 of them in the Amazon region of Brazil. Peru and Brazil had the highest number of reported cases from 1975 to 2006. In Peru, outbreaks involving more than 20 cases of bat-transmitted human rabies were reported during the 1980s and 1990s. During this period, a smaller number of cases were reported from outbreaks in Brazil. A comparison of data from field studies conducted in Brazil in 2005 with those from the previous decade suggests similar bat-bite situations at the local level. The objective of this study was to review the epidemiological situation and, on the basis of this information, discuss possible factors associated with the outbreaks. Prevention and control measures already recommended for dealing with this problem are also reviewed, and some further suggestions are provided.
Related JoVE Video
Molecular identification of rapidly growing mycobacteria isolates from pulmonary specimens of patients in the State of Pará, Amazon region, Brazil.
Diagn. Microbiol. Infect. Dis.
PUBLISHED: 05-01-2009
Show Abstract
Hide Abstract
We isolated 44 strains of rapidly growing mycobacteria (RGM) from 19 patients with pulmonary infections assisted at the Instituto Evandro Chagas (Pará, Brazil) from 2004 to 2007. Identification at the species level was performed by PCR restriction fragment length polymorphism analysis (PRA) of a 441 bp hsp65 fragment and partial 16S rRNA, hsp65, and rpoB gene sequencing. Genotyping by PRA yielded 3 digestion patterns: one identical to Mycobacterium abscessus type I (group I); another to M. abscessus type II, Mycobacterium bolletii, and Mycobacterium massiliense (group II); and a third typical for Mycobacterium fortuitum type I (group III). When comparing analysis of the 3 genes, more discrimination was obtained by rpoB gene sequence, which allowed good distinction between group I, II, and III strains and subclassification of group II strains in SG IIa (M. bolletii) and SG IIb (M. massiliense). In this study, we show that the description of new RGM species requires the establishment of standardized procedures for RGM identification and the alert of the clinician about their involvement in pulmonary disease and the necessity of treatment for control and cure.
Related JoVE Video
An alternative genotyping method using dye-labeled universal primer to reduce unspecific amplifications.
Mol. Biol. Rep.
PUBLISHED: 04-28-2009
Show Abstract
Hide Abstract
We proposed a modification the procedure of genotyping based in labeled universal primer and tailed primer. In the standard protocol, three primers are used in the same PCR reaction, a forward primer with tail added at the 5 end of the identical sequence to labeled universal primer with dye-fluorescent and a reverse primer. Unfortunately, the choice of a labeled primer characterized by a large number of complementary sequences in target genomes (which is more probable in larger genomes) result in unspecific amplifications (false positive) can cause absence or decrease amplification of the locus of interest and also false interpretation of the analysis. However, identification of possible homologies between the primer chosen for labelling and the genome is rarely possible from the available DNA data bases. In our approach, cycling is interrupted for the addition of the labeled primer only during the final cycles, thus minimizing unspecific amplification and competition between primers, resulting in the more fidelity amplification of the target regions.
Related JoVE Video
Floating caval thrombus arising from the ovarian vein.
Ann Vasc Surg
PUBLISHED: 02-20-2009
Show Abstract
Hide Abstract
We describe the case of a 37-year-old pregnant woman, who was admitted to hospital for suspicion of chorioamnionitis. An emergency C-section was performed. Four days later, the patient suffered from abdominal pain and fever. Computed tomographic scanning demonstrated only a thrombosis of the right ovarian vein. Anticoagulation and antibiotic therapy was started immediately. Color duplex imaging performed 3 days later revealed a free-floating caval thrombus reaching the confluence of hepatic veins while the patient was fully anticoagulated. Emergency thrombectomy was performed by laparotomy, and the thrombus was removed by caval incision during suprahepatic clamping of the inferior vena cava. The patient recovered rapidly from surgery and was discharged on the tenth postoperative day.
Related JoVE Video
Genetic diversity of red-bellied Titis (Callicebus moloch) from Eastern Amazonia based on microsatellite markers.
Biochem. Genet.
PUBLISHED: 01-25-2009
Show Abstract
Hide Abstract
The titi monkeys (Callicebus spp.) are a large, diverse genus of platyrrhines, widely distributed in tropical South America. The genetic variability of these monkeys is still relatively poorly known, especially at the population level. In the present study, four heterologous microsatellite markers were used to investigate genetic diversity in 23 individuals from a wild population of red-bellied titis (Callicebus moloch) in eastern Amazonia. An unexpectedly low level of diversity was found. The average number of alleles was 8.75 (range: 5-15), and the average heterozygosity was 0.33 (range: 0.09-0.65). This preliminary information suggests a reduction of the potential for long-term survival of the population and indicates the putative necessity of implementation of a species conservation program.
Related JoVE Video
Complete genome sequence of Corynebacterium pseudotuberculosis biovar ovis strain P54B96 isolated from antelope in South Africa obtained by rapid next generation sequencing technology.
Stand Genomic Sci
Show Abstract
Hide Abstract
The Actinobacteria, Corynebacterium pseudotuberculosis strain P54B96, a nonmotile, non-sporulating and a mesophile bacterium, was isolated from liver, lung and mediastinal lymph node lesions in an antelope from South Africa. This strain is interesting in the sense that it has been found together with non-tuberculous mycobacteria (NTMs) which could nevertheless play a role in the lesion formation. In this work, we describe a set of features of C. pseudotuberculosis P54B96, together with the details of the complete genome sequence and annotation. The genome comprises of 2.34 Mbp long, single circular genome with 2,084 protein-coding genes, 12 rRNA, 49 tRNA and 62 pseudogenes and a G+C content of 52.19%. The analysis of the genome sequence provides means to better understanding the molecular and genetic basis of virulence of this bacterium, enabling a detailed investigation of its pathogenesis.
Related JoVE Video
Teaching the fundamentals of biological data integration using classroom games.
PLoS Comput. Biol.
Show Abstract
Hide Abstract
This article aims to introduce the nature of data integration to life scientists. Generally, the subject of data integration is not discussed outside the field of computational science and is not covered in any detail, or even neglected, when teaching/training trainees. End users (hereby defined as wet-lab trainees, clinicians, lab researchers) will mostly interact with bioinformatics resources and tools through web interfaces that mask the user from the data integration processes. However, the lack of formal training or acquaintance with even simple database concepts and terminology often results in a real obstacle to the full comprehension of the resources and tools the end users wish to access. Understanding how data integration works is fundamental to empowering trainees to see the limitations as well as the possibilities when exploring, retrieving, and analysing biological data from databases. Here we introduce a game-based learning activity for training/teaching the topic of data integration that trainers/educators can adopt and adapt for their classroom. In particular we provide an example using DAS (Distributed Annotation Systems) as a method for data integration.
Related JoVE Video
Simplifier: a web tool to eliminate redundant NGS contigs.
Bioinformation
Show Abstract
Hide Abstract
Modern genomic sequencing technologies produce a large amount of data with reduced cost per base; however, this data consists of short reads. This reduction in the size of the reads, compared to those obtained with previous methodologies, presents new challenges, including a need for efficient algorithms for the assembly of genomes from short reads and for resolving repetitions. Additionally after abinitio assembly, curation of the hundreds or thousands of contigs generated by assemblers demands considerable time and computational resources. We developed Simplifier, a stand-alone software that selectively eliminates redundant sequences from the collection of contigs generated by ab initio assembly of genomes. Application of Simplifier to data generated by assembly of the genome of Corynebacterium pseudotuberculosis strain 258 reduced the number of contigs generated by ab initio methods from 8,004 to 5,272, a reduction of 34.14%; in addition, N50 increased from 1 kb to 1.5 kb. Processing the contigs of Escherichia coli DH10B with Simplifier reduced the mate-paired library 17.47% and the fragment library 23.91%. Simplifier removed redundant sequences from datasets produced by assemblers, thereby reducing the effort required for finalization of genome assembly in tests with data from Prokaryotic organisms.
Related JoVE Video
Leptospirosis outbreaks in Nicaragua: identifying critical areas and exploring drivers for evidence-based planning.
Int J Environ Res Public Health
Show Abstract
Hide Abstract
Leptospirosis is an epidemic-prone zoonotic disease that occurs worldwide. In Central America, leptospirosis outbreaks have been reported in almost all countries; Nicaragua in particular has faced several outbreaks. The objective of this study was to stratify the risk and identify "critical areas" for leptospirosis outbreaks in Nicaragua, and to perform an exploratory analysis of potential "drivers". This ecological study includes the entire country (153 municipalities). Cases from 2004 to 2010 were obtained from the countrys health information system, demographic and socioeconomic variables from its Census, and environmental data from external sources. Criteria for risk stratification of leptospirosis were defined. Nicaragua reported 1,980 cases of leptospirosis during this period, with the highest percentage of cases (26.36%) in León, followed by Chinandega (15.35%). Among the 153 municipalities, 48 were considered critical areas, 85 were endemic and 20 silent. Using spatial and statistical analysis, the variable presenting the most evident pattern of association with critical areas defined by top quintile of incidence rate is the percentage of municipal surface occupied by the soil combination of cambisol (over pyroclastic and lava bedrock) and andosol (over a volcanic ashes foundation). Precipitation and percentage of rural population are also associated with critical areas. This methodology and findings could be used for Nicaraguas Leptospirosis Intersectoral Plan, and to identify possible risk areas in other countries with similar drivers.
Related JoVE Video
Genome sequence of Exiguobacterium antarcticum B7, isolated from a biofilm in Ginger Lake, King George Island, Antarctica.
J. Bacteriol.
Show Abstract
Hide Abstract
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.
Related JoVE Video
Complete genome sequence of Corynebacterium pseudotuberculosis Cp31, isolated from an Egyptian buffalo.
J. Bacteriol.
Show Abstract
Hide Abstract
Corynebacterium pseudotuberculosis is of major veterinary importance because it affects many animal species, causing economically significant livestock diseases and losses. Therefore, the genomic sequencing of various lines of this organism, isolated from different hosts, will aid in the development of diagnostic methods and new prevention and treatment strategies and improve our knowledge of the biology of this microorganism. In this study, we present the genome of C. pseudotuberculosis Cp31, isolated from a buffalo in Egypt.
Related JoVE Video
Genome sequence of the Corynebacterium pseudotuberculosis Cp316 strain, isolated from the abscess of a Californian horse.
J. Bacteriol.
Show Abstract
Hide Abstract
The bacterium Corynebacterium pseudotuberculosis is of major veterinary importance because it affects livestock, particularly sheep, goats, and horses, in several countries, including Australia, Brazil, the United States, and Canada, resulting in significant economic losses. In the present study, we describe the complete genome of the Corynebacterium pseudotuberculosis Cp316 strain, biovar equi, isolated from the abscess of a North American horse.
Related JoVE Video
Whole-genome sequence of Corynebacterium pseudotuberculosis strain Cp162, isolated from camel.
J. Bacteriol.
Show Abstract
Hide Abstract
Corynebacterium pseudotuberculosis is a pathogen of great veterinary and economic importance, since it affects livestock, mainly sheep and goats, worldwide, together with reports of its presence in camels in several Arabic, Asiatic, and East and West African countries, as well as Australia. In this article, we report the genome sequence of Corynebacterium pseudotuberculosis strain Cp162, collected from the external neck abscess of a camel in the United Kingdom.
Related JoVE Video
Campylobacter fetus subspecies: comparative genomics and prediction of potential virulence targets.
Gene
Show Abstract
Hide Abstract
The genus Campylobacter contains pathogens causing a wide range of diseases, targeting both humans and animals. Among them, the Campylobacter fetus subspecies fetus and venerealis deserve special attention, as they are the etiological agents of human bacterial gastroenteritis and bovine genital campylobacteriosis, respectively. We compare the whole genomes of both subspecies to get insights into genomic architecture, phylogenetic relationships, genome conservation and core virulence factors. Pan-genomic approach was applied to identify the core- and pan-genome for both C. fetus subspecies and members of the genus. The C. fetus subspecies conserved (76%) proteome were then analyzed for their subcellular localization and protein functions in biological processes. Furthermore, with pathogenomic strategies, unique candidate regions in the genomes and several potential core-virulence factors were identified. The potential candidate factors identified for attenuation and/or subunit vaccine development against C. fetus subspecies contain: nucleoside diphosphate kinase (Ndk), type IV secretion systems (T4SS), outer membrane proteins (OMP), substrate binding proteins CjaA and CjaC, surface array proteins, sap gene, and cytolethal distending toxin (CDT). Significantly, many of those genes were found in genomic regions with signals of horizontal gene transfer and, therefore, predicted as putative pathogenicity islands. We found CRISPR loci and dam genes in an island specific for C. fetus subsp. fetus, and T4SS and sap genes in an island specific for C. fetus subsp. venerealis. The genomic variations and potential core and unique virulence factors characterized in this study would lead to better insight into the species virulence and to more efficient use of the candidates for antibiotic, drug and vaccine development.
Related JoVE Video
Complete genome sequences of Corynebacterium pseudotuberculosis strains 3/99-5 and 42/02-A, isolated from sheep in Scotland and Australia, respectively.
J. Bacteriol.
Show Abstract
Hide Abstract
Here, we report the whole-genome sequences of two ovine-pathogenic Corynebacterium pseudotuberculosis isolates: strain 3/99-5, which represents the first C. pseudotuberculosis genome originating from the United Kingdom, and 42/02-A, the second from Australia. These genome sequences will contribute to the objective of determining the global pan-genome of this bacterium.
Related JoVE Video
Complete genome sequence of Corynebacterium pseudotuberculosis strain 1/06-A, isolated from a horse in North America.
J. Bacteriol.
Show Abstract
Hide Abstract
Corynebacterium pseudotuberculosis causes disease in several animal species, although distinct biovars exist that appear to be restricted to specific hosts. In order to facilitate a better understanding of the differences between biovars, we report here the complete genome sequence of the equine pathogen Corynebacterium pseudotuberculosis strain 1/06-A.
Related JoVE Video

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.