Tag Archives: refseq

Friday SNPpets

This week’s SNPpets include an interactive timeline of cancer research, NIH’s statement on cloud-stored genomics data, Facebook and genomics data, hilarious typos in some published equations, and more….


Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Video Tip of the Week: VnD Resource for Genetic Variation and Drug Information


In today’s tip I am going to feature a resource that I found recently. I’ve been updating our dbSNP tutorial, which Mary & Trey will be presenting at workshops in Morocco, and also our free PDB tutorial, which is sponsored by the RCSB PDB team. I have therefore been thinking about protein structures and small sequence variations a lot lately. As I explored the latest Database issue of NAR looking for resources to do a tip on, I found an article describing the VnD (genetic Variation and Drug) resource, which can also be accessed at the URL www.vandd.org, according to the NAR article. The article is “VnD: a structure-centric database of disease-related SNPs and drugs“, and figure one shows a veritable Who’s Who of protein, variation and disease resources, so I had to investigate.

What I found at VnD made me sure that this was a resource that I wanted to feature in a tip. VnD is from the Korean Bioinformation Center, or KOBIC, who has a list of databases and tools that they provide. I’ll save the rest of the KOBIC resources for another post & concentrate on VnD here. Compiling data from resources such as RefSeq, OMIM, UniProt, PDB, DrugBank, dbSNP, GAD and more might have been cool enough, depending on how it was done, but the VnD also does their own structure modeling analysis on how the variation affects the protein structure and drug/ligand binding.

This tip movie isn’t long enough to really show you the breadth of what is available from the VnD, but I hope it will be enough to encourage you to read the NAR article (listed below), and to check out VnD. One thing to note: don’t expect to find every dbSNP rs# over there – one that I’ve been using in our tutorial isn’t over there. They are specifically interested in variations within genes that might effect drug binding. But hey, you can’t query DrugBank with rs#s, and I’ve never seen the structure modeling done like VnD, so it is a worthy resource that you may want to investigate if you are interested in how genetic variations connect with disease and drug therapies.

Quick links:

VnD: Variations and Drugs resource -  http://vnd.kobic.re.kr:8080/VnD/index.jsp

Korean Bioinformation Center (KOBIC) – http://www.kobic.re.kr/

RCSB PDB – http://www.pdb.org

OpenHelix Tutorial on the RCSB PDB – http://www.openhelix.com/pdb

dbSNP: Short Genetic Variations, from NCBI -  http://www.ncbi.nlm.nih.gov/projects/SNP/

OpenHelix Tutorial on NCBI’s dbSNP – http://www.openhelix.com/cgi/tutorialInfo.cgi?id=39

For links to other resources and OpenHelix tutorials mentioned in this post, please see our catalog of resources – http://www.openhelix.com/cgi/tutorials.cgi

Reference:
Yang, J., Oh, S., Ko, G., Park, S., Kim, W., Lee, B., & Lee, S. (2010). VnD: a structure-centric database of disease-related SNPs and drugs Nucleic Acids Research, 39 (Database) DOI: 10.1093/nar/gkq957

Picnics in Peril: Bees, Mosquitoes and Zombie Ants!

My husband loves spending time on our deck & mosquitoes love spending time chewing on me. Maybe that’s why I’ve been taking notice of research on the “Bugs of Summer” a bit more lately. Or maybe there’s just a bunch more of it right now, but I’ve seen what seems like an unusually large number of articles on bees, mosquitoes, and even “zombie ants”.

It’s a given that I’ve got to begin with the zombie ants. I mean, look how much traffic the CDC’s “Zombie Apocalypse” generated. The article is entitled “Behavioral mechanisms and morphological symptoms of zombie ants dying from fungal infection” and it is in the May 9th issue of BMC Ecology, which is open access & therefore free to read. (amusing side note is that the ad on the abstract page when I looked was for Terminix.) The article is an “extended phenotype” study in which ants (Camponotus leonardi) infected by a fungus (Ophiocordyceps unilateralis s.l.) display altered phenotypes – namely they descend from a Thai rain forest canopy, bite leaf veins, and then dying lock-jawed on the vein. The authors explain their use of the term zombies:

The term zombie ants underlines that, while the manipulated individual may look like an ant, it represents a fungal genome expressing fungal behavior through the body of an ant.

The authors followed 21 zombies, all with confirmed fungal infections, and observed changes in their activity and morphological changes in their head cavities. I generally don’t read ecology research but I think I’ve seen the process featured in nature programs that I’ve watched & the paper explained it well. I would like to read further research on the changes in gene expression, etc. that would help complete the story of the process.

I’ve been aware of bee issues, such as Colony Collapse Disorder, for a while now – it is hard not to be when even popular television such as Dr. Who reference it – but it was an article in an alumni magazine that really got me interested in the subject. Turns out last fall a tornado hit Ohio State’s Ohio Agricultural Research and Development Center (OARDC) and did thousands of dollars of damage to the honey bee program’s inventory and equipment, including a comprehensive collection of hive and queen bee production boxes. Today I came across an article describing the Honey Bee PeptidAtlas. I mentioned the PeptideAtlas as an item in a Friday SNPets post, but didn’t go into it further. The article is in BMC Genomics, is free to read, and has the title: “A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues.” It has been a long time since I spent much time with a genome that isn’t associated with a fairly well established proteome, but that was the state (according to the authors) of the bee genome before they built the bee PeptidAtlas.  The authors have built the Honey Bee PeptideAtlas on the backbone of the PeptideAtlas, which they describe as providing

a central, stable resource for mass spectrometry data supporting protein identification information for several species.”

They collected a large set of MS/MS data from A. mellifera, matched peaks to peptides & peptides to a comprehensive protein set compiled from RefSeq, GenBank and Gnomon predictions. The atlas was then constructed & functional predictions were made using BLAST2GO. The Honey Bee PeptideAtlas contains over 3000 proteins and 27,000 peptides, and should be a valuable resource for be proteogenomic studies.

The third “Bug of Summer”, the mosquito, is one that I experience often but do not understand well. My husband & I can be sitting next to each other & he can apparently not get a single bite while I am covered with big itchy bumps – why do they like me so well? I’ve always assumed that it was because of temperature – my skin often feels warmer than his. According to two articles in Nature: “Malaria: Mosquitoes bamboozled” (editor’s summary) and “Ultra-prolonged activation of CO2-sensing neurons disorients mosquitoes” (both require a subscription), there may be another reason – carbon dioxide. Apparently exhaled carbon dioxide is the most important cue for guiding the long-distance host-seeking flight of blood-feeding female mosquitoes, so perhaps my breathing somehow creates a higher CO2 trail. The authors used Drosophila melanogaster as a model organism to study compounds that might inhibit the CO2 detection machinery in mosquitoes. They were able to identify a cocktail of compounds that so overactivated the CO2-sensing neurons of three disease-causing mosquitoes (Anopheles gambiae, A. aegypti and Culex quinquefasciatus) that it greatly reduced their ability to navigate the CO2 train to a potential blood meal. Unfortunately according to the authors the volatile odorants reported in the paper

“…have undesirable safety profiles at high concentrations and are not ideal for human use without further testing.”

I also think such “long range” repellents will need to be paired with nearer-range effectors as well. They may find you through the CO2 in your breath, but once they are in range they seem to no longer need that cue and will bite you anywhere that will itch massively – like around your toenails, on your ankles & at the back of your knees – I’m might be biased from experience though…

PS, here’s another mosquito paper for you: Dissecting gene expression in mosquito

PSS, anyone know if the chemicals that commercial treatment “mosquito removal” companies use harm “good bugs”, humming birds, etc? Inquiring, concerned & itchy minds would like to know…

For good results, try several databases

Just wanted to point out this paper recently published in BMC Genomics: Integrating multiple genome annotation databases i… [BMC Genomics. 2010]

Often in our trainings we are asked which annotations or databases are best. Our stock and, frankly, accurate answer is that it depends on what you are looking for, your personal preferences and more. This paper concludes, at least when it comes to zebrafish transcript data, that pulling annotations from several databases instead of one increases the ability to get full data. Might sound obvious to some, but it’s always good to see the data.. and to point it out.