• A bit of a dust-up at ScienceBlogs as they added a corporate blog (Pepsi writing about nutrition science) and several of the bloggers left or threatened to leave. The Pepsi blog is no more. I hope that’s resolved, ScienceBlogs is an excellent collection of science writing. [Trey]
• Pathway Tools Workshop 2010 held by the folks from BioCyc announced for October 21-25: http://bioinformatics.ai.sri.com/ptools10/ [Mary]
• Animal portraiture against a white background. It’s been done before, this time with birds. It always reminds me how amazingly beautiful life can be. [Trey]
• VectorBase announces that they have moved to the new style Ensembl browser with their current release–Yeah!  If you are interested in “Invertebrate Vectors of Human Pathogens”, this database may have species you want to know about. [Mary]
• A good discussion about the recent ‘longevity gene’ study and it’s possible flaws by Razib Khan of Gene Expression [Trey]
• Bandwidth-heavy, but really neat movies of tumor angiogenesis. You can open the Navigator menu to see the various movies listed, or you can migrate around the tumor yourself.  Hat tip to Jill!  [Mary]
• On the GBrowse mailing list people were looking for examples of GBrowse 2.0 in action. WormBase indicated they are up to that version, and there was another research group with a species I never heard of before that also has it running: Gardnerella vaginalis.  They have compared 2 strains: one from a healthy woman, one suffering from infection. They show divergence, interestingly.  You can check out their recent publication on it from their publication tab.  A nice demonstration of how to use GBrowse for your species of interest. [Mary]

Seattle, WA (PRWEB) May 25, 2010 – OpenHelix today announced the availability of an updated tutorial suite on GeneTests.

GeneTests is an integrated resource designed to provide access to current genetic testing and other clinical genetics information. The GeneTests resource includes the Laboratory Directory database, an international directory that identifies the location of clinical laboratories offering genetic testing; and GeneReviews, a collection of up-to-date, comprehensive disease-specific overviews which include clinical descriptions, diagnosis, management, molecular genetics, current genetic testing, and genetic counseling. This tutorials, in conjunction with OpenHelix tutorials on OMIM, dbSNP, GVS, HapMap and many others will give the medical researcher or clinician a set of training resources to help be efficient and effective at accessing and analyzing genomic variation and biomedical data.

The tutorial suites, available through an annual OpenHelix subscription, contain an online, narrated, multimedia tutorial, which runs in just about any browser connected to the web, along with slides with full script, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. The scripts, handouts and other materials can also be used as a reference or for training others.

This tutorials will teach users:
*to perform disease-specific searches and navigate the GeneTests site
*to understand the GeneReviews and Laboratory Directory Displays
*to access additional searches to query the GeneReviews and Laboratory Directory databases by disease feature, gene and protein specific searches, and more
*to identify U.S. and international laboratories offering molecular genetic testing for specific disorders, use the Clinical Directory to locate genetics professionals and services, and investigate additional educational and other resources

To find out more about these and over 90 other tutorial suites visit the OpenHelix Catalog and OpenHelix. Or visit the OpenHelix Blog for up-to-date information on genomics and genomics resources.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. The OpenHelix Search portal searches hundreds of resources, tutorial suites and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs. Researchers and institutions can save time, budget and staff resources by leveraging a subscription to nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

And the “Cell Cize and Scale” interactive flash is cool.

And while I’m at it there is a good intro to Essentials of Genetics at Scitable (and we’ve had a tip of the week on Scitable Classrooms before you might to check out so you can create a class on Genetics if you so desire).

While the mainstream news is reporting on the demise (redefinition) of the ‘gene‘, some high schools kids are doing amazing things with ‘genes.’

Oh, and if, like us, you can’t wait till the annual NAR database is published officially, you can always check out the advanced online publication of the articles to find new and updated databases (like the SpBase, sea urchin, database that went public earlier this year and SuperToxic, a database of over 60,000 toxic compounds) and genome resources!

The Gordon Conference on Quantitative Genetics and Genomics will be held at the Hotel Galvez from February 22-26. 2009. Although Hurricane Ike wreaked havoc on the Texas gulf coast, the Hotel sustained minimal damage and massive repair and restoration efforts are underway across the region.
We have received a letter from the mayor of Galveston
(http://www.grc.org/Files/News/galveston_letter.pdf) urging us to keep the conference on the island. They are trying to quickly restore the tourism industry and are welcoming visitors.

Due to the generous support from many sponsors, we are able to fund several scholarships for graduate students and postdocs to partially defray registration costs for attending the conference. Depending on interest, we are currently expecting to fund at least 10 scholarships of at least $500 each. To apply, please email the following by October 27 to
grc2009@gmail.com:

a) A one page letter stating the reasons why you would like to attend the conference.
b) Your current CV

We already have over 100 applicants for the conference, and space is limited. I urge you to register as early as possible:
http://www.grc.org/application.aspx?id=8785

See you in Galveston,
Daniel Pomp , Chair
Peter Visscher, Vice-Chair

(emails removed for web post, go to the web page).

Hat tip to David Threadgill for forwarding that along to the MGI mailing list to draw attention to it.

View a live webcast of the Kaiser Family Foundation’s series, Today’s Topics In Health Disparities, which will discuss the potential of race-based medical solutions for improving healthcare and reducing racial/ethnic health disparities. The webcast will take a closer look at efforts to study the interaction between race, genetics and health.

Panelists will discuss the efforts underway to develop medications to treat diseases that disproportionately affect certain racial and ethnic groups, as well as the benefits and drawbacks of using genetic markers for race in medical decisions. Other topics covered include which genetic factors are being used to personalize medicine and what pharmaceutical companies are doing to target the drugs and treatments they offer to certain groups.

Details about the technology and setup are here: Today’s Topics In Health Disparities – Race and Genetics: The Future of Personalized Medicine

I’m not sure how research-oriented it will be. But if you are interested in the future directions of personal genomics this is an area that might be worth learning more about. A new focus at NIH includes the NICGHD, that we talked about here.

OpenHelix today announced the availability of new tutorial suites on two genetic disease resources: GeneTests and Genetic Home Reference. GeneTests is an integrated resource designed to provide access to current genetic testing and other clinical genetics information for clinicians, biomedical professionals and researchers. Genetic Home Reference is an extensive collection of data that describe the effects of genetic variability on human health and disease written in lay language for both the general public and researchers.

The tutorial suites, available for single purchase or through a low-priced yearly subscription to all OpenHelix tutorials, contain a narrated, self-run, online tutorial, slides, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. These tutorials will teach users:

GeneTests

• to perform disease-specific searches and navigate the GeneTests site
• to understand the GeneReviews and Laboratory Directory Displays
• to access additional searches to query the GeneReviews and Laboratory Directory databases by disease feature, gene and protein specific searches, and more
• to identify U.S. and international laboratories offering molecular genetic testing for specific disorders, use the Clinical Directory to locate genetics professionals and services, and investigate additional educational and other resources

Genetic Home Reference (GHR)

• How to search by genetic disease, condition, or syndrome, gene or chromosome
• To access more general or more specific information on genetic conditions, genes or chromosomes
• To browse GHR and explore its resources like the genetic handbook and glossary
• Methods to stay current in the latest developments in genetics

To find out more about these and other tutorial suites visit OpenHelix or the OpenHelix blog for up-to-date information on genomics. About OpenHelix
OpenHelix, LLC, (http://www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix currently provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.

… dedicated to performing innovative basic research on the brain and distributing its discoveries to researchers around the world. Through its efforts, the Institute aims to advance a new understanding of brain diseases and disorders.

The result of this research is disseminated through some excellent tools at the Allen Brain Atlas. This research and tool focuses on the mouse brain and determining which genes are expressed in different parts of the brain.

Well, it was recently announced that not only are they planning to extend this map to the mouse spinal chord and another atlas of brain development from fetus to adult mouse, they have launched a project to do a similar atlas of the human brain. This project is expected to take four years.

btw, the “brain explorer” tool is just cool. My expertise isn’t mouse or brain science, but I like roaming around the brain as much as the next guy .

We’ll keep you up-to-date on the progress .

First me: I am a walking recessive. A cipher. The ‘uncommon’ allele. In everything. Blond hair, blue eyes, no hair on my mid-digit of my fingers, right thumb on top when clasping hands, unbent little finger and the list goes on. So what do you think the taste test showed?

You guessed it.

I couldn’t taste anything on any paper. Nada. This walking recessive still walks recessively even in taste.

When I gave the PTC paper to my almost 6-year-old daughter (who is adopted btw, of African heritage), the reaction her facial expression seemed to say was “Why in the world would you, the parent who loves and cares for me, give me something so vile and disgusting as that?” To make matters worse, I laughed at the reaction. She was not pleased. But to this day, it still strikes me as odd that other people taste something so drastically strong when I don’t taste anything at all. I find it amusing in a strange way. I apologized and explained it was all for the good of science. I’m not sure she’ll like science much any more.

She also thought the thiourea paper tasted like paint and the sodium benzoate tasted like the sugar “Papa likes” (that’d be the artificial sweetener I put in my tea).

The other OH bloggers?

Mary: SB, sweet (like nutrasweet. PTC, burnt tires (w a lingering aftertaste that keeps on giving). Th, nothing.

Jennifer: SB, mildly sweet. PTC, quite bitter. Th, moderately bitter.

We tested a some others. Scott and Neeraj, the two who post to the OH news and some friends and family, here are our results:

As you see, we got some diverse answers and and all the controls were given a ‘no taste’ rating so we know no one was having any phantom tastes. I also find it interesting that the PTC tastes seem to fall into two main categories (other than the nontasting of the walking recessive): very bitter and metallic.

Well, that was the phenotype. What about the genotype?

Though the genetics of sodium benzoate taste aren’t well described, those of PTC are.

The taste of PTC is affected by the a gene in the TR2 family of “G-protein-coupled receptors” (GPCR). In fact it is TAS2R38 (the link opens a session of the UCSC Genome Browser with that gene). In fact, there are three non-synonymous coding SNPs in this region that form 5 distinct haplotypes in various populations. You can see those three SNPs at HapMap and explore them more at the Genome Variation Server and learn more at OMIM (all link directly to the TAS2R38 gene record at those resources).

The basic conclusion is that the genotypes of these three SNPs affect how PTC is experienced. Homozygotes for the common alleles for each of these three variations taste PTC strongly, heterozygotes not so strongly and homozygous rare alleles not at all. But with five haplotypes, the variation in taste for PTC will be quite diverse and not quite as simple as ‘dominant/recessive,’ but it’s a good lesson in the connection between genotype and phenotype.

As to the evolutionary whys and hows of taste (PTC and otherwise)? There’s lots interesting research there too.

Now all we need to do here at OH is genotype ourselves .

Well, not all mice–not like the project that studied the history of cats (I can haz domesticashun?). This project examined the ancestry of the laboratory inbred mouse. This poster (small section on the left) is one of those cool nearly-secret things you come across once in a while that just make you go: whew–I’m glad somebody knows this… This work was underway when I was at the Jackson Lab and I often think back to it when I read mouse papers, and you can print up the whole document as a poster (it’s a big PDF). I’m not going to link to the PDF itself, please go to this page at Jax: Genealogy Chart of Inbred Strains and click the downloadable Portable Document Format (PDF) file link for to examine this whole mouse pedigree chart.

From the paper:

We describe the origins and relationships of inbred mouse strains, 90 years after the generation of the first inbred strain.

The paper is actually quite a nice description of the how we got to the mice you probably know and love if you have ever worked with them in the lab. It describes important phenotypic considerations around aging and breeding that could impact your work–even if those topics are not the focus of your work.

Of course, this paper is not recent–but it is classic, and I wanted to highlight it for that classic nature. Even if some of the individual inbred strains shifted around with more molecular analysis, the fundamentals of the history of inbred mice are important to know about.

If you are working with mice, trying to select mice for experiments, or trying to interpret different results on different strains of mice this might be useful to think about. Another thing that people often ask about are known SNPs among strains. Jax has a very useful form to query for that. From their brand-new-just-released-today homepage: http://www.informatics.jax.org/ if you click the link for Strains and SNPs you will access tools that can show you exactly which alleles appear in which species. Good stuff.
Fisher, E.M., Beck, J.A., Lloyd, S., Hafezparast, M., Lennon-Pierce, M., Eppig, J.T., Festing, M.F. (2000). . Nature Genetics, 24(1), 23-25. DOI: 10.1038/71641