WS248: Parasite Papers II

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For the upcoming WS248 release, a set of new papers have been added to the WormBase database. Some papers of interest to the parasite community are shown below.

Doharey PK, Suthar MK, Verma A, Kumar V, Yadav S, Balaramnavar VM, Rathaur S, Saxena AK, Siddiqi MI, Saxena JK. Molecular cloning and characterization of Brugia malayi thymidylate kinase. Acta Trop. 2014 May;133:83-92. doi:10.1016/j.actatropica.2014.02.003. Epub 2014 Feb 17.

genes referred to: Bm5401

Singh VK, Doharey PK, Kumar V, Saxena JK, Siddiqi MI, Rathaur S, Narender T.
Synthesis, molecular docking and Brugia malayi thymidylate kinase (BmTMK) enzyme inhibition study of novel derivatives of [6]-shogaol. Eur J Med Chem. 2015 Mar 26;93:74-82. doi: 10.1016/j.ejmech.2015.01.035. Epub 2015 Jan 20.

genes referred to: Bm5401

Bulman CA, Bidlow CM, Lustigman S, Cho-Ngwa F, Williams D, RascĂłn AA Jr, Tricoche N, Samje M, Bell A, Suzuki B, Lim KC, Supakorndej N, Supakorndej P, Wolfe AR, Knudsen GM, Chen S, Wilson C, Ang KH, Arkin M, Gut J, Franklin C,
Marcellino C, McKerrow JH, Debnath A, Sakanari JA. Repurposing auranofin as a lead candidate for treatment of lymphatic filariasis and onchocerciasis. PLoS Negl Trop Dis. 2015 Feb 20;9(2):e0003534. doi: 10.1371/journal.pntd.0003534. eCollection 2015 Feb.

genes referred to: Bma-trxr-1

WS248: Parasite Papers I

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For the upcoming WS248 release, a set of new papers have been added to the WormBase database. Some papers of interest to the parasite community are shown below.

Singh AR, Joshi S, Arya R, Kayastha AM, Srivastava KK, Tripathi LM, Saxena JK. Molecular cloning and characterization of Brugia malayi hexokinase. Parasitol Int. 2008 Sep;57(3):354-61. doi: 10.1016/j.parint.2008.03.004. Epub 2008 Apr 9.

genes referred to: Bm4678

Poole CB, Davis PJ, Jin J, McReynolds LA. Cloning and bioinformatic identification of small RNAs in the filarial nematode, Brugia malayi. Mol Biochem Parasitol. 2010 Feb;169(2):87-94. doi: 10.1016/j.molbiopara.2009.10.004. Epub 2009 Oct 27.

linked miRNA genes can be found at the WBPaper00046326 page

Singh N, Heneberg P, Singh N, Singh SK, Rathaur S. Identification of a novel stress regulated FERM domain containing cytosolic protein having PTP activity in Setaria cervi, a bovine filarial parasite. Biochem Biophys Res Commun. 2015 Feb 27;458(1):194-200. doi: 10.1016/j.bbrc.2015.01.100. Epub 2015 Jan 31.

genes referred to: Bma-ptp-1 , ptp-1

Devarajan E, Mishra PK, Thirugnanam S, Mehta K, Chandrashekar R, Perumal K. Molecular characterization of a Brugia malayi transglutaminase. Parasitol Res. 2004 Jun;93(2):145-50. Epub 2004 May 1.

genes referred to: Bma-pdi-3

WormBase Workshop at International Worm Meeting 2015

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Thursday, June 25 – 1pm -2:30pm
Saturday, June 27 – 1pm – 2:30pm

For the 2015 International C. elegans meeting, WormBase will present two identical workshops to cover some of WormBase’s newer tools and data as well as ways in which the nematode research community may contribute data and annotations to the database. We will cover basics of data mining with WormMine (the WormBase instance of Intermine), introduce our instantiation of the JBrowse genome browser, and demo the new ParaSite website which hosts genome sequences for parasitic nematode species. We will discuss WormBase sequence data available in complementary resources such as Ensembl Genomes and the UCSC Assembly Hub for C. elegans. We will also provide a number of options for users to submit their own data using sequence variation data, gene concise descriptions and Gene Ontology annotations as examples.

CRISPR workshop at the 2015 C.elegans meeting

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CRISPR-based Strategies for Genome Engineering
Announcing the “CRISPR revolution” workshop to be held during the final plenary session of the 2015 International C. elegans Meeting,
June 28th, 10:30am – 12:00pm, Royce Hall Auditorium
Organizers: Mike Boxem, Daniel Dickinson, Alexandre Paix

CRISPR is a rapidly evolving technology that is quickly becoming an essential tool for every C. elegans lab. We would like to bring together representatives of the various groups that are developing CRISPR-based approaches for C. elegans to discuss current strategies for genome modifications. Specific topics to be discussed will include screening strategies, improving efficiency, target site selection, and guidelines for making different kinds of modifications. The workshop will conclude with an overview by Geraldine Seydoux of the status of CRISPR-based methods in C. elegans, based on previous reports and current methods presented in the workshop or elsewhere at the meeting.

For members of the community who are actively developing CRISPR methods, the workshop will serve as an opportunity to compare notes, share ideas, and stay current on the efforts of others. For those who are “end users” of these methods, it will be an opportunity to learn the latest approaches, obtain protocols, ask questions and seek advice.

Researchers who actively develop CRISPR-based approaches or are making technical improvements are invited to share their results and experiences. If you would like to speak at this workshop, please submit your abstract under the category “V, Gene Regulation and Genomics, Novel Genetic Technologies” to the 2015 C. elegans Meeting.

If you have questions about this workshop, contact Mike Boxem.

WS247: C. briggsae genes have descriptions!

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In the previous WS246 release we introduced automated gene descriptions for C. elegans genes that lacked a manually written one. These gene descriptions include information related to orthology, process, function and sub-cellular localization (when these data-types have been curated in the WormBase database), giving the user a quick overview of the gene. The current WS247 release includes automated descriptions for over 18,000 C. briggsae genes.  Check out the C. briggase gene pages to view these descriptions under ‘Overview’!  In future releases, we will add genes from many more species!  Also, WormBase is working on user-friendly forms which you can use to edit these descriptions and make them better.