J. Craig Venter Institute

About: J. Craig Venter Institute is a nonprofit organization based out in La Jolla, California, United States. It is known for research contribution in the topics: Genome & Gene. The organization has 1268 authors who have published 2300 publications receiving 304083 citations. The organization is also known as: JCVI & The Institute for Genomic Research.

Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana

Abstract: It is believed that intracellular carbonic anhydrases (CAs) are essential components of carbon concentrating mechanisms in microalgae. In this study, putative CA-encoding genes were identified in the genome sequences of the marine diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. Subsequently, the subcellular localizations of the encoded proteins were determined. Nine and thirteen CA sequences were found in the genomes of P. tricornutum and T. pseudonana, respectively. Two of the β-CA genes in P. tricornutum corresponded to ptca1 and ptca2 identified previously. Immunostaining transmission electron microscopy of a PtCA1:YFP fusion expressed in the cells of P. tricornutum clearly showed the localization of PtCA1 within the central part of the pyrenoid structure in the chloroplast. Besides these two β-CA genes, P. tricornutum likely contains five α- and two γ-CA genes, whereas T. pseudonana has three α-, five γ-, four δ-, and one ζ-CA genes. Semi-quantitative reverse transcription PCR performed on mRNA from the two diatoms grown in changing light and CO2 conditions revealed that levels of six putative α- and γ-CA mRNAs in P. tricornutum did not change between cells grown in air-level CO2 and 5% CO2. However, mRNA levels of one putative α-CA gene, CA-VII in P. tricornutum, were reduced in the dark compared to that in the light. In T. pseudonana, mRNA accumulation levels of putative α-CA (CA-1), ζ-CA (CA-3) and δ-CA (CA-7) were analyzed and all levels found to be significantly reduced when cells were grown in 0.16% CO2. Intercellular localizations of eight putative CAs were analyzed by expressing GFP fusion in P. tricornutum and T. pseudonana. In P. tricornutum, CA-I and II localized in the periplastidial compartment, CA-III, VI, VII were found in the chloroplast endoplasmic reticulum, and CA-VIII was localized in the mitochondria. On the other hand, T. pseudonana CA-1 localized in the stroma and CA-3 was found in the periplasm. These results suggest that CAs are constitutively present in the four chloroplastic membrane systems in P. tricornutum and that CO2 responsive CAs occur in the pyrenoid of P. tricornutum, and in the stroma and periplasm of T. pseudonana.

Phylogenomics and the dynamic genome evolution of the genus Streptococcus.

Abstract: The genus Streptococcus comprises important pathogens that have a severe impact on human health and are responsible for substantial economic losses to agriculture. Here, we utilize 46 Streptococcus genome sequences (44 species), including eight species sequenced here, to provide the first genomic level insight into the evolutionary history and genetic basis underlying the functional diversity of all major groups of this genus. Gene gain/loss analysis revealed a dynamic pattern of genome evolution characterized by an initial period of gene gain followed by a period of loss, as the major groups within the genus diversified. This was followed by a period of genome expansion associated with the origins of the present extant species. The pattern is concordant with an emerging view that genomes evolve through a dynamic process of expansion and streamlining. A large proportion of the pan-genome has experienced lateral gene transfer (LGT) with causative factors, such as relatedness and shared environment, operating over different evolutionary scales. Multiple gene ontology terms were significantly enriched for each group, and mapping terms onto the phylogeny showed that those corresponding to genes born on branches leading to the major groups represented approximately one-fifth of those enriched. Furthermore, despite the extensive LGT, several biochemical characteristics have been retained since group formation, suggesting genomic cohesiveness through time, and that these characteristics may be fundamental to each group. For example, proteolysis: mitis group; urea metabolism: salivarius group; carbohydrate metabolism: pyogenic group; and transcription regulation: bovis group.

Submission of microarray data to public repositories.

Abstract: A fundamental principle guiding the publication of scientific results is that the data supporting any scholarly work must be made fully available to the research community, in a form that allows the basic conclusions to be evaluated independently. In the context of molecular biology, this has typically meant that authors of a paper describing a newly sequenced genome, gene, or protein must deposit the primary data in a permanent, public data repository, such as the sequence databases maintained by the DNA Data Bank of Japan (DDBJ), European Bioinformatics Institute (EBI), and National Center for Biotechnology Information (NCBI). Similarly, we, members of the Microarray Gene Expression Data Society (MGED; http://www.mged.org), believe that all scholarly scientific journals should now require the submission of microarray data to public repositories as part of the process of publication. While some journals have already made this a condition of acceptance, we feel that submission requirements should be applied consistently and that journals should recognize ArrayExpress (Brazma et. al. 2003), Gene Expression Omnibus (GEO) (Edgar et. al 2002), and the Center for Information Biology Gene Expression Database (CIBEX) (Ikeo et. al. 2003) as acceptable public repositories. To this end, the members of MGED propose the following as a new paradigm for the publication of microarray-based studies. (1) Authors should continue to take primary responsibility for ensuring that all data collected and analyzed in their experiments adhere to the “Minimum Information about a Microarray Experiment” (MIAME) guidelines and should continue to use the MIAME checklist (www.mged.org/Workgroups/MIAME/miame_checklist.html) as a means of achieving this goal. (2) Scientific journals should require that all primary microarray data are submitted to one of the public repositories—ArrayExpress, GEO, or CIBEX—in a format that complies with the MIAME guidelines. (3) Public databases should work with authors and scientific journals to establish data submission and release protocols to assure compliance with MIAME guidelines. (4) To assist with the review process, the databases should continue to work in collaboration with publishers to provide qualified referees with secure means of accessing prepublication data. Authors should be strongly encouraged to submit data to the databases during review. Naturally, data should be protected from general release prior to either publication or authorization from the data submitters, whichever comes first. At a minimum, journals should require valid accession numbers for microarray data as a requirement for publication, and these accession numbers should be included in the text of the manuscript to allow members of the community to find and access the underlying data. Since its inception in 1999, MGED has been working with the broader scientific community to establish standards for the exchange and annotation of microarray data. In December 2001, we proposed the MIAME guidelines (Brazma et al. 2001) and requested that interested parties provide feedback on its relevance and utility. The feedback from both researchers and scientific journals was overwhelmingly positive, yet almost everyone who responded also asked for help in implementing these guidelines. Subsequently, in the summer of 2002, we submitted an open letter to various journals (e.g., Ball et al. 2002a, 2002b) urging the community to adopt the MIAME requirements for microarray data publication. We provided a checklist so that authors could ensure that sufficient information to allow their data to be re-analyzed by others would be available. Again, the response from the community was extremely positive, and most of the major scientific journals now require publications describing microarray experiments to comply with the MIAME standards. While the adoption of these standards has greatly improved the accessibility of microarray data, much of it remains on individual authors' websites in a variety of formats; consequently, obtaining and comparing datasets remains a significant challenge. Clearly we need additional requirements for publication that include submission of expression data to public data repositories. Though one might ask why this requirement was not part of the original MIAME recommendation, the answer is quite simple—MIAME was ahead of its time. While NCBI and the EBI had developed nascent microarray data repositories, and work was underway to create a similar database at the DDBJ, submitting data to these databases was a considerable burden for authors. However, since that time, improvements in the data-entry utilities available for GEO (www.ncbi.nlm.nih.gov/geo), ArrayExpress (www.ebi.ac.uk/arrayexpress), and CIBEX (cibex.nig.ac.jp), as well as a growing number of commercial and academic software packages capable of writing MAGE-ML documents (Spellman et al. 2002) that can be directly submitted to these public databases, have lowered the barriers for data submission to the point where we as a community must now reconsider that submission to one of these databases be a requirement. Requiring authors to submit microarray data to a public database will provide a number of distinct advantages to the entire research community. (1) These established repositories have a commitment to continued community service and to providing some level of assurance that published gene expression datasets will continue to be available into the future. (2) Having the data available in these public repositories in a standardized format will not only make them more accessible, but it will allow expression data to be integrated with other relevant data, including the available genome sequences, single nucleotide polymorphism and haplotype mapping information, the literature, and other resources that can aid in further interpretation of expression patterns. Although many authors now provide some or all of this information, the established databases are much more likely to assure that these links are maintained and current. (3) Curation of data submitted to public data repositories will assist authors, reviewers, and publishers in assuring that the data comply with the MIAME requirements, further enhancing their utility. (4) The standardization of microarray data formats will enable the development of additional data analysis and integration tools and makes it easier for scientists to access, query, and share data. (5) Finally, submission prior to publication will make it easier for referees to access the data confidentially, facilitating the review and publication process. In the same way that availability of sequence data had a profound impact on a wide range of disciplines, we believe that requiring that microarray data be deposited in public repositories as a necessity for publication will accelerate the rate of scientific discovery. What this proposal requires is a change in the way in which we approach the publication of microarray-based studies. Both authors and journals have a responsibility to assure that the requisite data are available, and because submitting MIAME-compliant data can take considerable time and effort, this process should be factored into review and publication timelines. However, while this process may be time consuming and painful at first, we believe that the benefits of building an open repository of microarray data will far outweigh any initial disadvantages. As always, it is our sincere hope that these suggestions stimulate discussion within the community and that together we can arrive at a consensus that ensures that microarray data are widely and easily accessible. Finally we would like to urge the DDBJ, EBI, and NCBI to work together towards exchanging all MIAME-compliant microarray data.