Latest news from the Tetrahymena Stock Center
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The Tetrahymena Stock Center is pleased to be a part of the Resource Identification Initiative, a project aimed at clearly identifying key research resources used in the course of scientific research. These key research resources include model organisms, antibodies and software tools. All citations for Tetrahymena stored in the Tetrahymena Stock Center can now also be found at http://scicrunch.org/resources, a portal where publishers (see list of participating journals) are directing authors during the publication process, usually at the acceptance of the publication.
In publications using Tetrahymena strains acquired from the Stock Center, authors are asked to paste the ‘cite this’ text in the methods section for each organism used in the course of research. Although not a requirement, this simple step will help to decrease ambiguity regarding the organisms used in research. These citations will also allow for straightforward aggregation of data around key resources, allowing questions like “who else used this strain” to be answered more easily. The format for citation is relatively straightforward. For example:
Tetrahymena Strains: "Strains used in this study include CU428.2 (RRID:TSC_SD00178) and SB1805 (RRID:TSC_SD01962) …"
The RRID for each strain is listed on its description page.
We are also now collecting and distributing plasmids for use in Tetrahymena. Please check out the list of plasmids now available. We are constantly looking for plasmids to add to our collection. Contact us if you have a useful plasmid that you would be willing to deposit with the Stock Center to facilitate sharing with others in the Tetrahymena community.
In addition, we now offer high purity, high molecular weight genomic DNA from any of the strains currently housed in the Stock Center. The DNA is suitable for PCR and a variety of other downstream molecular biology applications. A minimum of 10 µg of DNA is supplied in 1xTE buffer. Larger amounts can be special ordered. DNA is Rnase treated, has an OD260/OD280 ratio of 1.7 to 2.0, and is tested for low molecular weight contamination by gel electrophoresis. Samples are also tested by HindIII digestion and PCR template activity. Information and ordering are available on our website.
The Tetrahymena Stock Center is partnering with the ASSET (Advancing Secondary Science Education with Tetrahymena) program, an educational outreach program providing Tetrahymena based educational resources to teachers and students around the United States. The Stock Center is providing cells for over 20 science exploration modules for K-12 students. See the available modules and more at ASSET website. Contact Donna Cassidy-Hanley (email@example.com) to discuss ways you can use ASSET resources in your outreach efforts.
The Tetrahymena Research Advisory Board (TetTRA) put out a request in December for participation in a community-wide annotation project of the Tetrahymena genome database (see below). Strong participation in this wiki-based annotation effort will improve the search capabilities of the database, and will strengthen the upcoming Tetrahymena Stock Center grant renewal, which is the sole source of funding for TGD. Prior to opening up TGD for community annotation, only 600 genes had been assigned definitive names (i.e. btu1). As of early January, the community-based annotation effort added 150 new gene names. Our goal is to double the gene names from 600 to 1200 by early March, and get the number to 2000 by the Ciliate Molecular Biology Conference this summer.
To facilitate gene naming, TGD has currently been reconfigured to accept both 3 letter and 4 letter names. Please participate in this worthy project.
A quick primer for gene identification can be found on the front page of Tetrahymena Genome Database and a convenient optional way to store your bioinformatic searches for gene naming assignments and make them available to the community (Supra DB) is also described on the TGD front page.
This is your chance to make a meaningful contribution to the greater Ciliate Molecular Biology community. The Tetrahymena Genome Database (TGD) is a Wiki-based community run database, curated by Naomi Stover. A larger percentage of the genes in TGD are currently designated as hypothetical proteins, yet a simple BLAST analysis provides a strong indication of what these proteins do. TGD simply does not have the resources to do manual annotation of the genome and literature.
The Tetrahymena Research Advisory (TetTRA) Board [Doug Chalker, Ted Clark, Bob Coyne, Pam Geyer, Jeff Kapler, Kazufumi Mochizuki, Carolyn Price, Naomi Stover (ex officio)], is requesting that you participate in a community-wide effort to manually annotate TGD. This will serve several important purposes. (1) It will facilitate the extraction of gene information from the database for you and your colleagues, (2) it will link published papers to genes in TGD, something we sorely need, but do not have the financial resources to support, and (3) it will help secure funds to maintain and further develop TGD, which is modestly funded by an NIH Tetrahymena Stock Center grant. The renewal of the stock center grant will be submitted in the Spring of 2013. Consequently, we are asking that you make your personal contribution to updating TGD during the next three months. The number of Wiki edits, as well as the number of originating sources of those edits are recorded. The final tally at Stock Center grant renewal time will provide reviewers with an indication as to whether this unique, community-driven approach to database curation is worth investing in.
We ask that you set a manageable goal in the next two weeks, and transmit that information to Naomi Stover to avoid unwanted duplicative efforts. The main objectives are to edit TGD by (i) naming genes and (ii) annotating your own literature (and hopefully that of others working in your area of interest). For example, using BLAST, an undergraduate in my lab identified ~150 Tetrahymena genes in DNA replication and repair pathways that were previously catalogued as ‘hypothetical protein’. She will assign gene names to TGD using the simple Wiki editing functions. Paramecium researchers should get involved and annotate TGD as well, based on information they have from their own research. If the work is spread around between labs and within labs, a lot can be accomplished.
Naomi has written a concise guide for BLAST-based bioinformatic identification of Tetrahymena genes that is posted on the TGD site and is also available as a PDF file. She has also set up second website to deposit data files, so there is a record of who did the work and what the sequence alignments and e values look like. Our collective effort to populate TGD with this low hanging fruit can make a big difference. Please give as generously of your time as you can.
To help accommodate a wider variety of gene names, TGD Wiki has increased by one (from three to four) the number of letters allowed to form a Gene Name prefix. Names were previously limited to the format "ABC123". Names with the format "ABCD123" will now be accepted by the database. Please note that the additional letter must be included before the numerals; letters after the numerals (e.g. "ABC123D") are currently not accepted. We hope this modification to the published gene naming guidelines helps with the push to name as many genes as possible by the end of the month.
Thank you to all of the concerned parties who weighed in on this decision, and to the Tetrahymena Research Advisory Board (TetRA) for mediating the discussion.
TGD Wiki is a user-updatable database of information about the Tetrahymena thermophila genome sequence determined at The Institute for Genomic Research (TIGR). TGD Wiki provides information on the genome, genes, and proteins of Tetrahymena collected from the scientific literature, research community, and many other sources.
Tetrahymena researchers who wish to contribute to the community annotation effort can now register and begin editing TGD Wiki. Simply send the information requested on the User Registration page to ciliate-curator. Once your lab receives a user name and password, visit the new Wiki Edit Guide to see what kinds of annotations can be made to your favorite Tetrahymena genes.