Tag Archives: GenBank

SNPpets_2

Friday SNPpets

This week I left the “call to action” tweet at the top–you could vote for GenBank every day until the end of the competition. Today’s the last day. Vote once more. And remember how resources like GenBank let us have foundations for other important resources as well. There are new resources in this week’s SNPpets that are definitely descendants of GenBank. Also, more tit-for-tat on the Venter paper privacy issue drama. A very personal genome story from a personal genome researcher. Makes you think about the policy issues in new ways. Also, policy on gene editing in plants. The first species to have every members’ genome data. Gene counts via RNAseq in a new resource, and a new cancer gene repository.


SNPpets_2Welcome 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…


SNPpets_2

Friday SNPpets

This week I left the “call to action” tweet at the top–you could vote for GenBank every day until the end of the competition. On other fronts, there’s big media on Venter’s DNA re-identification article–but there’s also significant blowback on that. A series of tweets in there gets to that. Otherwise, more of the other cool things in genomics around the tools available and around other species.


SNPpets_2Welcome 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…


https://twitter.com/david_a_knowles/status/905203427931602944

https://twitter.com/clairemcwhite/status/905445932094939136

 

SNPpets_2

Friday SNPpets

This week I left the “call to action” tweet at the top–you can vote for GenBank every day in August. The cut is coming soon, so go vote again. In other news this week, a story about big data for assessing biodiversity across time and space. And a Big Photo. Whole-genome sequencing in primary care–not ready yet. #CRISPR ethics–not ready yet. Animal breeding, plant bioinformatics, and horizontal gene transfer round out the week.


SNPpets_2Welcome 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…


https://twitter.com/FloridaMuseum/status/898293371814330368

SNPpets_2

Friday SNPpets

This week I left the “call to action” tweet at the top–you can vote for GenBank every day. But the other tweets are new this week. First, don’t fall for the fake grant scam. A catalog of museum samples (I love the data from sequencing projects using those), genotyping arrays vs. sequencing debate and a lot of new data that’s been released, fungi and E. coli data, a terrible DNA joke, and a terrible use of DNA testing to see how white a White Nationalist is.


SNPpets_2Welcome 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…


https://twitter.com/surt_lab/status/897187105495019520

SNPpets_2

Friday SNPpets

This week there’s an actual call to action in the tweets. See Steven Salzberg’s tweet about the 2017 Service to America award and GenBank is nominated–you can vote every day! The rest of the week’s intriguing tweets include yeast diversity, British historical diversity, non-coding regulatory stuff, computer-coding DNA hackers, and setting standards for information of uncultured samples of organisms and for personal data.


SNPpets_2Welcome 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…


SNPpets_2

Friday SNPpets

This week there’s an actual call to action in the tweets. See Steven Salzberg’s tweet about the 2017 Service to America award. You can vote for Genbank. Really–try to imagine the last couple of decades without it. And it’s time to celebrate government science in front of the public. Go vote. After that, come back for the cheese and pomegranite genome. Most intriguing chatter this week was the ancient plant genome stuff at the bottom. I keep trying to tell people how far ahead agriculture is in genomics applications. Human researchers: ZZZZzzzzzzzzz.


SNPpets_2Welcome 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…


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.

Tip of the Week: NCBI Makeover!

NCBI_interface_movieThe two earliest web-based bioinformatics resources that I can remember relying on in my career were Pedro’s List and NCBI.  (For those of you who need a little nostalgia trip you can see a copy of Pedro’s list here.) There are plenty of descendants of Pedro’s list in various forms–including our recently launched resource search tool.  But the National Center for Biotechnology Information (NCBI) interface has kinda been…well…comfortingly stable–for a really long time.  I looked in the Wayback Machine to see what the older interfaces used to look like.   I was able to find one variant from 1997 which I had forgotten about until I saw it.  But then I kept looking and found the version I am most familiar with starting in 1999.  If you compare 1999 to 2009 you will see essentially the same layout.  Here is a comparison of the previous interfaces, and then the new one:

NCBI interfaces through the years

NCBI interfaces through the years

ncbi_new_2009

Well, that’s all changing now!  The NCBI is doing a MAJOR overhaul of the interfaces.  You can examine the homepage look at the  Preview site here (link may break when they move over to production with it), and you can look at the PubMed changes here, and even start using the PubMed preview site here.

This is a huge break with the past, and like all new interfaces will take a little time to get used to.  But I have to say I like the organization.  The left navigation will make finding the tools easier.  The “Popular” box will be quick access to the most frequently used items.  Highlights and news are available still as well.  There are some things I’ll miss. We liked the site map layout to explain the features in an overview sort of way, and the preview page doesn’t link to that–it links to the alphabetical list.  Might change, though.

Anyway–I think the new look is nice and effective.  Of course we’ll have to update all of our NCBI tutorials with new shots of the interfaces.  But it looks like the underlying tools don’t change much conceptually–but they may move the location of the items (like the PubMed filters).  So as soon as the interface becomes the main site and appears to be stable we’ll make our changes.

This short Tip of the Week introduces the new interface briefly to get you starting to think about how to navigate around.  Check it out!

NCBI: http://www.ncbi.nlm.nih.gov/

A Tree is Barcoded in Brooklyn

Figure 1 of the Plant Barcoding paperScrolling through some of my regular podcasts the other day I came across this tidbit about bioinformatics growing in New York (among other things, or course!):

Barcoding Plant DNA (I hope the embed of the audio file works, first time I’m trying that…)

It is a discussion with Dr. Damon Little, a curator of bioinformatics from the New York Botanical Garden.  The focus of the discussion is the recent publication of the CBOL Plant Working Group which has settled on the regions that will be used for barcoding plants.

If you aren’t familiar with barcoding efforts yet, you can check out Jennifer’s prior post with some background and great links.  Essentially a small snippet of DNA sequence is used to (hopefully) uniquely identify a given species.  This can be stored in a database–Dr. Little of the NY Botanical Garden refers to GenBank at NCBI, but there are other sites as well.  I was just reading about the web interface for barcoding called iBarcode.org for analyzing and managing this sort of data.

The Consortium for the Barcode Of Life Plant Working Group summary press release of this work can be found here.   The paper that describes the work is Open Access in PNAS here.  The paper describes the genes that had been candidates for the barcode, and the ones that were selected (rbcL + matK).  They described primer selection and sequencing results for the series they examined.  They evaluate which ones meet the barcoding standard criteria and provide the selections.  They use MUSCLE to examine the sequence alignments.

This is an excellent effort on many fronts.  Just assessing and cataloging biodiversity is useful itself, but this can also help to identify plants that are claimed to be used in food or medicine products to see if that is what’s really in there.  It can help combat poaching of protected species–for example, it can identify wood harvested that shouldn’t have been taken for lumber.

Glad to see this work moving forward and getting out in front of the public!

Related links

Podcast direct page: http://www.wnyc.org/shows/lopate/episodes/2009/07/29/segments/137623

NYBG: http://www.nybg.org/

Barcode blog: http://phe.rockefeller.edu/barcode/blog/

Scientific American article on the topic: http://www.scientificamerican.com/blog/60-second-science/post.cfm?id=botanists-agree-on-dna-barcode-for-2009-07-29

Consortium for the Barcode of Life (CBOL): http://www.barcoding.si.edu/

References
CBOL Plant Working Group (2009). A DNA barcode for land plants PNAS, 106 (31), 12794-12797 : 10.1073/pnas.0905845106

Singer, G., & Hajibabaei, M. (2009). iBarcode.org: web-based molecular biodiversity analysis BMC Bioinformatics, 10 (Suppl 6) DOI: 10.1186/1471-2105-10-S6-S14

Edgar, R. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Research, 32 (5), 1792-1797 DOI: 10.1093/nar/gkh340