WormBase release WS247

by Leave a Comment

Orthology update

* Data from Inparanoid was updated to version 8
* Orthology data for all core nemtatodes and model organisms was imported from WormBase Parasite release 1
* OMA and TreeFam data was removed in preparation for an update (TreeFam accessions will remain as database crossreferences)

Expression and Picture update

* A large set of expression graphs for other nematodes produced by Yanai’s has been added

RNASeq data

The RNASeq data will become richer in WS247.

There will also be “control” mean and median FPKM values derived from the data which does not have a specific experimental condition applied.

New/updated reference genomes

This release we see a rebuild of C. elegans, B. malayi and O. volvulus. Various data classes and curational activites have been undertaken on these species since the release of WS246

WS247: Parasite Papers II

by Leave a Comment

For the upcoming WS247 release, a set of new papers have been added to the WormBase database. Some papers of interest to the parasite community are shown below.

Khor BY, Tye GJ, Lim TS, Noordin R, Choong YS. The structure and dynamics of BmR1 protein from Brugia malayi: in silico approaches. Int J Mol Sci. 2014 Jun 19;15(6):11082-99.

genes referred to: Bm10631 (other name: BmR1)

Anderson RC, Newton CL, Millar RP, Katz AA. The Brugia malayi neuropeptide receptor-4 is activated by FMRFamide-like peptides and signals via Gai. Mol Biochem Parasitol. 2014 Jun;195(1):54-8.

genes referred to: flp-18 , npr-4 , Bma-npr-4

Casper SK, Schoeller SJ, Zgoba DM, Phillips AJ, Morien TJ, Chaffee GR, Sackett PC, Peterson FC, Crossgrove K, Veldkamp CT. The solution structure of the forkhead box-O DNA binding domain of Brugia malayi DAF-16a. Proteins. 2014 Dec;82(12):3490-6.

genes referred to: daf-16 , Bma-daf-16

Kalani K, Kushwaha V, Sharma P, Verma R, Srivastava M, Khan F, Murthy PK, Srivastava SK. In vitro, in silico and in vivo studies of ursolic acid as an anti-filarial agent. PLoS One. 2014 Nov 6;9(11):e111244.

genes referred to: Bma-gst-1

Yadav M, Singh A, Rathaur S, Liebau E. Structural modeling and simulation studies of Brugia malayi glutathione-S-transferase with compounds exhibiting antifilarial activity: implications in drug targeting and designing. J Mol Graph Model. 2010 Jan;28(5):435-45.

genes referred to: Bma-gst-1

WS247: Parasite Papers I

by Leave a Comment

For the upcoming WS247 release, a set of new papers have been added to the WormBase database. Some papers of interest to the parasite community are shown below.

Rodrigo WW, Dassanayake RS, Weerasena SJ, Silva Gunawardene YI. Novel parasitic nematode-specific protein of bovine filarial parasite Setaria digitata displays conserved gene structure and ubiquitous expression. Trop Biomed. 2014 Sep;31(3):514-24.

genes referred to: Bm8739

Tiwari S, Wadhawan M, Singh N, Rathaur S. Effect of CDNB on filarial thioredoxin reductase : A proteomic and biochemical approach. J Proteomics. 2015 Jan 15;113:435-46.

genes referred to: ced-3 , ced-9 , Bma-trxr-1 , Bma-ced-3 , Bm14668

Kulke D, von Samson-Himmelstjerna G, Miltsch SM, Wolstenholme AJ, Jex AR, Gasser RB, Ballesteros C, Geary TG, Keiser J, Townson S, Harder A, Kruecken J Characterization of the Ca2+-gated and voltage-dependent K+-channel Slo-1 of nematodes and its interaction with emodepside. PLoS Negl Trop Dis. 2014 Dec 18;8(12):e3401.

genes referred to: sle-1 , slo-1 , Bma-slo-1 , Ovo-slo-1

Lustigman S, Melnikow E, Anand SB, Contreras A, Nandi V, Liu J, Bell A, Unnasch TR, Rogers MB, Ghedin E. Potential involvement of Brugia malayi cysteine proteases in the maintenance of the endosymbiotic relationship with Wolbachia. Int J Parasitol Drugs Drug Resist. 2014 Aug 26;4(3):267-77.

genes referred to: Bm1665 , Bma-cpl-6 , Bma-cpl-2 , Bma-cpl-7 , Bma-cpl-8 , Bma-cpl-4 , Bma-cpl-5 , Bma-cpl-1