Oyster food
via Tidal Cycles - oystergen.es http://bit.ly/11ExenE
Map of Life
By bringing together all types of information about species distributions, providing model-based integration, and providing a system for users to build upon our knowledge, the Map of Life project hopes to support our community in understanding and saving the world’s biodiversity.
There is now a demo release of Map of Life!
This demo allows you to map and produce list of species anywhere for ~ 46,000 species (includingall described birds, mammals and amphibians - for info check the ‘Dashboard’).
Map species distributions : Type species name in ‘Search’ window, select layer source and type. Use controls on top left and right of screen. Video .
Below is a screenshot of an Ostrea lurida search. (There is tons of Crassostrea data too!)
via Tidal Cycles - oystergen.es http://bit.ly/159Htqv
Mac Experiments with Spiders
Scholar Alert: New citation
Scholar Alert: New citations to my articles
Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure
exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna
(BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure …
Poly I: C induces a protective antiviral immune response in the Pacific oyster (< i> Crassostrea gigas</i>) against subsequent challenge with Ostreid herpesvirus ( …
analogue (poly I: C) against Ostreid herpes virus (OsHV-1 μvar). Pacific oysters (Crassostrea
gigas) were immune-primed by intramuscular injection of 240 μg of poly I: C or sterile …
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Ever hear of Nostrasamus?
That’s not a typo. Of course everyone’s heard of that old fool Nostradamus, who was supposed to be able to predict the fate of the world (including the OJ Simpson trial!). However, I think he’s a miserable failure.
NostraSAMus (that refers to me, by the way), on the other hand, seems to actually have a good grasp on reality and the future. As reference, notice what I wrote in this 2007 Genefish post (my first post to the lab blog, in fact!): “Soon, I’m sure we’ll all be able to buy personal GPS units so that we’ll be able to post our real-time locations on Google Earth/Maps and setup an RSS feed for our blogs without having to even be at a computer. Hmmm, maybe I should get that idea notarized/patented…”
Now, another question is whether I was being sarcastic (I’m never sacastic, though [/sarcasm]) or, more likely, an amazing visionary who can see into the future. I suspect the latter (just for reference, the first iPhone wouldn’t be released until a full year after that post).
Anyway, now that I’m done fluffing my ego, I was simply reminiscing about the lab and this blog a bit and I stumbled across that amazing post from 6 years ago. Granted, I, of course, knew that I’d still be working in the lab 6 years from when I started in March 2007. You can even ask Steven what my response was to his interview question of:
SR - “Where do you see yourself in 5yrs?”
My response: “Celebrating the 5yr anniversary of you asking me that question.” (Thank you, Mitch Hedberg!)
Despite my predictive abilities, I never envisioned how the lab would evolve over these last 6 years. We started out with skyscrapers of yeast plates:
Moved on to octopus eggs:
Continued with lab “jokes”
Acquired some new personnel:
The big boss man got tenured (and he’s happy about it)!
And we’ve finally settled on bioinformatics as our lab activity of choice. We’ve had to dive head first into the world of big data acquisition, manipulation and visualization. And, as a small lab, dealing with big data sets (e.g. 120 million sequences from a single sample) has been a fun, enlightening, and frustrating learning experience. This is all particularly true since all of us our bench-trained biologists, have little-to-no “programming” experience, and are trying to discover (and rely upon) free-ware for all of this. We’ve been utilizing software like:
SQLShare - A web-based way to use SQL (good for manipulating/joining enormous tables together) without having to deal with the backend stuff, like schema and other weird tech jargon we don’t grasp.
R - Programming language geared towards data analysis (statistical) and visualization. Think command line. Ugh. R Studio is a nice “skin” that provides a nicer GUI for R.
Galaxy - A web-based means of analyzing virtually any type of “-omics” data, including basic manipulation of text files, FASTA files, BED files, etc. Has a variety of high-throughput sequencing analysis tools, too.
iPlant Discovery Environment - Similar to Galaxy but their servers are much, much faster at virtually everything. And, they also have de novo assembly software built-in (like SOAPdenovo, Trinity, and Velvet), which Galaxy does not.
BS Map - For analyzing bisulfite-treated sequences.
iPython - A notebook for tracking your programming codes that allows you to execute the codes directly in the notebook.
Integrated Genomics Viewer (IGV) - For visualizing various features annotated within a given nucleotide/protein sequence.
There are others that we have tried (and continue to try) that often serve a fringe purpose and there are others that we’d like to continue using that we just need more time using and practicing. Unfortunately, time is probably one of the most precious commodities in the lab and it’s difficult to set aside serious chunks of time to really learn, and apply, tools like Perl, Python, BioPerl, BioPython, Quadrigram, and Orange Canvas. We know these tools are immensely powerful and useful, but it’s hard to sit at the computer learning these things from the beginning while your data is just sitting around waiting to be dealt with in some fashion.
Additionally, in order to handle all this data, we’ve purchased our own server! Keeping with a trend of computer naming in the lab (most of our computers are named after birds, which should be obvious, since we do all of our work on shellfish), we call it The Eagle. It’s a Synology DS413 and it’s been one of the best purchases the lab has ever made. It has (temporarily) resolved multiple issues:
- Data storage capacity (8TB!)
- Automated “backup” (RAIDed hard drives ensure that when one HDD fails, we don’t lose any data)
- Data hosting for generating URLs for our files. Additionally, the Synology also helps to replace Dropbox, which the sizes of our data had finally outgrown.
- Direct downloads to the server eliminate the need to download large files to a desktop, only to then upload them to the server.
All in all, the last 6yrs have been pretty awesome over here in Fisheries Teaching & Research at the University of Washington. The lab is never short on exciting new work and approaches to science. Plus, we really have had (and continue to have) great people in the lab (personality-wise and scientific-mind-wise), which is critical to a fun, stimulating, creative laboratory.
Well, enough of the brown nosing. Time for you grad students to stop wasting time reading this blog and get back to work!
In the mean time, I think I’ll walk up to Big Time for lunch and a beer before I leave early today to play softball…
Top 20 Articles (related to: Immune response and mechanical stress susceptibility in diseased oysters)
List 1: Top 20 Articles, in the Domain of Article 21853237, Since its Publication (2012)
1. Immune response and mechanical stress susceptibility in diseased oysters, Crassostrea virginica.
Roberts SB, Sunila I, Wikfors GH.
J Comp Physiol B; 2012 Jan;182(1):41-8.
2. Water-quality parameters and total aerobic bacterial and Vibrionaceae loads in Eastern oysters (Crassostrea virginica) from oyster-gardening sites.
Fay JP, Richards GP, Ozbay G.
Arch Environ Contam Toxicol; 2012 May;62(4):628-37.
3. Immunomodulation in eastern oysters, Crassostrea virginica, exposed to a PAH-contaminated, microphytobenthic diatom.
Croxton AN, Wikfors GH, Schulterbrandt-Gragg RD.
Aquat Toxicol; 2012 Aug 15;118-119:27-36.
4. Interactive effects of salinity and elevated CO2 levels on juvenile eastern oysters, Crassostrea virginica.
Dickinson GH, Ivanina AV, Matoo OB, Pörtner HO, Lannig G, Bock C, Beniash E, Sokolova IM.
J Exp Biol; 2012 Jan 1;215(Pt 1):29-43.
5. Expression of candidate genes related to metabolism, immunity and cellular stress during massive mortality in the American oyster Crassostrea virginica larvae in relation to biochemical and physiological parameters.
Genard B, Moraga D, Pernet F, David E, Boudry P, Tremblay R.
Gene; 2012 May 10;499(1):70-5.
6. Mutation in promoter region of a serine protease inhibitor confers Perkinsus marinus resistance in the eastern oyster (Crassostrea virginica).
He Y, Yu H, Bao Z, Zhang Q, Guo X.
Fish Shellfish Immunol; 2012 Aug;33(2):411-7.
7. Quantitative PCR assay to determine prevalence and intensity of MSX (Haplosporidium nelsoni) in North Carolina and Rhode Island oysters Crassostrea virginica.
Wilbur AE, Ford SE, Gauthier JD, Gomez-Chiarri M.
Dis Aquat Organ; 2012 Dec 27;102(2):107-18.
8. Effective reduction of Vibrio vulnificus in the Eastern oyster (Crassostrea virginica) using high salinity depuration.
Larsen AM, Scott Rikard F, Walton WC, Arias CR.
Food Microbiol; 2013 May;34(1):118-22.
9. Pilot study on effects of nanoparticle exposure on Crassostrea virginica hemocyte phagocytosis.
Abbott Chalew TE, Galloway JF, Graczyk TK.
Mar Pollut Bull; 2012 Oct;64(10):2251-3.
10. Integration of Vibrio vulnificus into marine aggregates and its subsequent uptake by Crassostrea virginica oysters.
Froelich B, Ayrapetyan M, Oliver JD.
Appl Environ Microbiol; 2013 Mar;79(5):1454-8.
11. Effects of temperature and cadmium exposure on the mitochondria of oysters (Crassostrea virginica) exposed to hypoxia and subsequent reoxygenation.
Ivanina AV, Kurochkin IO, Leamy L, Sokolova IM.
J Exp Biol; 2012 Sep 15;215(Pt 18):3142-54.
12. Diseases of oysters Crassostrea ariakensis and C. virginica reared in ambient waters from the Choptank River, Maryland and the Indian River Lagoon, Florida.
Dungan CF, Carnegie RB, Hill KM, McCollough CB, Laramore SE, Kelly CJ, Stokes NA, Scarpa J.
Dis Aquat Organ; 2012 Nov 19;101(3):173-83.
13. Bioaccumulation and depuration of brevetoxins in the eastern oyster (Crassostrea virginica) and the northern quahog (= hard clam, Mercenaria mercenaria).
Griffith AW, Shumway SE, Volety AK.
Toxicon; 2013 May;66:75-81.
14. Identification of a novel metal binding protein, segon, in plasma of the eastern oyster, Crassostrea virginica.
Xue Q, Gauthier J, Schey K, Li Y, Cooper R, Anderson R, La Peyre J.
Comp Biochem Physiol B Biochem Mol Biol; 2012 Sep;163(1):74-85.
15. Comparison of haemocytic parameters among flat oyster Ostrea edulis stocks with different susceptibility to bonamiosis and the Pacific oyster Crassostrea gigas.
Comesaña P, Casas SM, Cao A, Abollo E, Arzul I, Morga B, Villalba A.
J Invertebr Pathol; 2012 Mar;109(3):274-86.
16. First report of the protozoan parasite Perkinsus marinus in South America, infecting mangrove oysters Crassostrea rhizophorae from the Paraíba River (NE, Brazil).
da Silva PM, Vianna RT, Guertler C, Ferreira LP, Santana LN, Fernández-Boo S, Ramilo A, Cao A, Villalba A.
J Invertebr Pathol; 2013 May;113(1):96-103.
17. Expression, tissue localization and synergy of antimicrobial peptides and proteins in the immune response of the oyster Crassostrea gigas.
Schmitt P, de Lorgeril J, Gueguen Y, Destoumieux-Garzón D, Bachère E.
Dev Comp Immunol; 2012 Jul;37(3-4):363-70.
18. A hemocyte gene expression signature correlated with predictive capacity of oysters to survive Vibrio infections.
Rosa RD, de Lorgeril J, Tailliez P, Bruno R, Piquemal D, Bachère E.
BMC Genomics; 2012;13:252.
19. A restoration suitability index model for the eastern oyster (Crassostrea virginica) in the Mission-Aransas Estuary, TX, USA.
Beseres Pollack J, Cleveland A, Palmer TA, Reisinger AS, Montagna PA.
PLoS One; 2012;7(7):e40839.
20. Microarray analysis highlights immune response of pacific oysters as a determinant of resistance to summer mortality.
Fleury E, Huvet A.
Mar Biotechnol (NY); 2012 Apr;14(2):203-17.
Gluten
What’s the problem with gluten? Gluten is a sticky protein composite found in cereal grains. Hank gives us some insight into the importance of gluten in history, as well as its impact on health in our own time.
Like SciShow? Want to help support us, and also get things to put on your walls, cover your torso and hold your liquids? Check out our awesome products over at DFTBA Records: http://dftba.com/artist/52/SciShow
References for this episode can be found in the Google document here: http://dft.ba/-5E72
Scholar Alert: New citation
Scholar Alert: New citations to my articles
Genetic and epigenetic variation in mass selection populations of Pacific oyster Crassostrea gigas
phenotypic change within a species is a consequence of genetic variation. However, there is
growing evidence for phenotypic change even in the absence of DNA sequence …
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Find out more about the ‘Food Exploration’ Community in the new Mercer Court buildings - launching in autumn 2013! [link for more information]
