"Life Science Co. Blogs" via SDBN in Google Reader

Controversial study concludes that exercise may increase heart risk for some people

2012-06-02T01:21:15Z

A recent study published in the journal PLoS One claims that exercise may increase heart risk for some people. According to the study’s abstract, researchers conclude that “adverse responses to regular exercise in cardiovascular and diabetes risk factors occur,” and “identifying the predictors of such unwarranted responses and how to prevent them will provide the foundation for personalized exercise prescription.” The study was led by Claude Bouchard, Ph.D., professor of genetics and nutrition and former executive director at the Pennington Biomedical Research Center. The medical and scientific community has received the study’s findings with mixed feelings.

“It is an interesting and well-done study,” said Dr. Michael Lauer, director of the Division of Cardiovascular Sciences at the National Heart, Lung, and Blood Institute, in an interview published in the New York Times on May 30th.

Still, some experts worry about the implications of such provocative results. “There are a lot of people out there looking for any excuse not to exercise,” said William Haskell, emeritus professor of medicine at the Stanford Prevention Research Center, in a New York Times interview published on May 30th. “This might be an excuse for them to say, ‘Oh, I must be one of those 10 percent.’” Read more about this story…

23andMe to Present Data from Sarcoma Research at Oncology Conference

2012-06-01T16:17:29Z

Starting today cancer researchers will be gathering in Chicago at the meeting of the American Society of Clinical Oncology.

Researchers and doctors at the annual meeting — the world’s largest oncology conference — will hear about the most promising drugs being developed to fight cancer. They’ll spend five days learning about the new science around a vast array of cancers, and discuss the newest therapies as well as the latest and most innovative clinical trials. They’ll wrestle with broader issues on ethics and hunt out presentations about the most successful cancer prevention.

But this year we hope that a few will also take notice of a new approach to cancer research being pioneered by 23andMe.

Along with our scientific advisors — who include Drs. George Demetri, Robert Maki, Judy Garber, and Mark Robson, — our very own Dr. Kim Barnholt, the Research Project Manager for both our Sarcoma and Myeloproliferative Neoplasms (MPN) research communities, is attending. Kim will be presenting some of the highlights of our 23andMe’s work on sarcoma.

We’ve been able to recruit almost 1,000 people with these cancers that develop in bone and soft tissue, making our sarcoma research cohort one of the world’s largest. Sarcoma, which strikes about 14,000 people each year, is not one kind of cancer, but many different ones.

The complexity of what turns out to be dozens of subtypes of sarcomas makes treating and studying them difficult. But using web-based tools allows for both quick recruitment and efficient large-scale genome-wide studies of the disease. It also gives people with sarcoma, who might be geographically isolated or far away from cancer research centers, or too sick to travel, an easier way to participate in research.

Kim is most encouraged by the engagement of the community with more than 80 percent of participants having completed important surveys. Last summer, she put together an evening gathering for the community giving patients a chance to directly interact with her and other scientists at 23andMe, as well as with sarcoma researchers and advocates.

“It’s important for researchers to meet patients,” Kim said recently. “It gives more meaning to what we do. There’s more than just numbers in research. Understanding the personal stories and each person’s journey gives what we do more relevance and meaning, but it also gives us a better picture of the disease. It all goes back to the quality of measurement in research. If you can talk and interact with patients and they have a voice and that is part of the data collection, it improves the what we do. I know it does for my work.”

Kim plans to present some preliminary data in Chicago and report back over the next few days on some of the most interesting presentations.

Your Brain on Drugs: Decision or Disease?

2012-06-01T14:47:22Z

If you were around in the 1980s, you remember Nancy Regan telling us to “just say no” to drugs. That campaign focused specifically on the effect crack had on the community. In the 1990s and 2000s, we saw and increase in reports of methamphetamine and heroin overdoses. Though they are perfectly legal, nicotine and even [...]

Friday SNPpets

2012-06-01T13:07:19Z

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…

RT @moorejh: #bioinformatics MT @brainpicker TreeVersity – interactive #visualization tool lets you compare tree diagrams http://t.co/09PMu6Oo [Mary]
RT @tferriss: HUGE – “World’s largest release of human cancer genome data”: http://t.co/tnSbqE7d Partially thanks to all 4HB readers! http://t.co/dMxHiWoX [Mary]
I’m gonna hafta watch & learn about “poo tea” RT @bykriscampbell Ooh, this @tedmed talk by @phylogenomics gets me so excited! An intro to “the microbes that live in and on us”. http://ow.ly/bhfQ0 [Jennifer]
RT @emblebies: A new mirror for OMIM.org is now running from the EMBL-EBI for European users. Please visit europe.omim.org [Mary]
Think I’d like to attend: RT @WorldSciFest: RT @TomLevenson: Four out of seven total Kavli laureates this year are women. Change comes; slowly, but it comes. #wsf12 [Jennifer]
Heh–this got a bunch of re-tweets; I suspect it touched a nerve. RT @szintri: Common problem these days RT @brent_p people keep coming to me with data and without questions. #bioinformatics [Mary]
Ha ha ha: RT @milklovesu: Now I understand why biologist are such bioinformatics haters, cause comp sci people write like this. What y… [pic] — http://t.co/aHrooVYy [Mary]

Paul Nurse: Family Trees Can Be Dangerous

2012-06-01T02:14:52Z

One of the points that I have always made about the advent of personal genomics was that we are going to find out some family secrets that have been under wraps for a very long time. This may not always be a bad thing. But there are going to be some cases where the participants may not be quite so prepared to handle the information. Here Paul Nurse tells a tale of ancestry and genetics that illustrates some of that complexity. It’s only 10 minutes–and it’s quite funny. Have a look.

Direct to the YouTube in case you want that: http://youtu.be/X9Jktke38I8

Who Were the Parents of Jacob Youngman?

2012-05-31T17:29:19Z

During the series Finding Your Roots with Henry Louis Gates, Jr. on PBS, The Spittoon featured posts from 23andMe’s Ancestry Ambassadors. This is the last of their own stories about using DNA to dig into ancestry.

By Tim Janzen, M.D.

For over 30 years I have been trying to determine the ancestry of my great-great-great-grandfather Jacob Youngman (b. ca Aug 1823, d. 24 May 1903).

Jacob Youngman

I used traditional genealogical research techniques for much of that time, but not long ago I realized that DNA testing at 23andMe could help me solve this decades old puzzle.

No one in our family knew who Jacob Youngman’s parents were, but his son Charles Youngman (b. 1872) left a tantalizing clue in his autobiographical sketch that was published in the book “History of Harrison County, Missouri.” Charles Youngman said that Jacob Youngman’s father lived in Kentucky, moved first to Indiana, and later settled in central Missouri where he died. Not too many Youngmans fit this description.

In the past two years I have developed a theory that Jacob Youngman’s father was John Youngman (b. ca 1793), who is listed in the 1840 Census in Clay County, Missouri but is not listed there in the 1850 Census.

Photograph of the gravestone of Jacob Youngman (b. ca Aug 1823) and his second wife Rachel Cart.

I know that my ancestor Jacob Youngman is listed in Shelby Co., Indiana in the 1850 Census but the man I presume to be his father, John Youngman isn’t. Instead, I recently discovered that John Youngman didn’t die prior to 1850, but instead moved to Denton Co., Texas where he is listed in the 1850 Census with his younger children. This genealogical puzzle is complicated by the fact that John Youngman was married 3 times and was divorced from his second wife Elizabeth Reeves, his first wife having apparently died by 1822. Census records from 1820, 1830, and 1840 indicate that he had children by all three wives, but only his 5 youngest children who were living with him in 1850 are named in the census records.

John Youngman and Family Reconstructed

John Youngman (b. ca 1793 in Kentucky) married his first wife Elizabeth Marton (b. ca 1798 in Kentucky) on 23 Feb 1816 in Campbell Co., Kentucky. Elizabeth Marton appears to have died ca 1821. John and Elizabeth had three children:
1. John M. Youngman (b. 10 Jan 1818 in Kentucky)
2. William Youngman (b. ca 1818 in Kentucky)
3. Susanna Youngman (b. ca 1821 in Kentucky)

John Youngman (b. ca 1793) married his second wife Elizabeth Reeves (b. ca 1802 in Kentucky) on 20 Jul 1822 in Campbell Co., Kentucky. They were divorced on 29 Apr 1830. They had two children:
1. Jacob Youngman (b. ca 1823, KY)
2. Unknown female (b. ca 1825-30)

John Youngman (b. ca 1793) married his third wife Priscilla Clark on 10 Jun 1830 in Clermont Co., Ohio. They had seven children:
1. Sarah A. Youngman (b. ca 1830, IN)
2. Nancy Catherine Youngman (b. ca 1832,IN)
3. James C. Youngman (b. ca 1835, IN)
4. Mary Jane Youngman (b. 1835, IN)
5. Louhany Youngman (b. 1843, MO)
6. Thomas Jefferson Youngman (b. 1844, AR)
7. Joseph Youngman (b. ca 1844, AR)

Another clue is that Jacob Youngman’s granddaughter Louise Youngman (1893-1988) said that her grandfather often referred to “Uncle Stacy Reeves”, suggesting that Jacob Youngman’s mother could have been Elizabeth Reeves, the second wife of John Youngman. A Stacy T. Reeves (b. ca 1823) is listed near Jacob Youngman and his family in the 1860 Census and may be the “Uncle Stacy Reeves” that Louise Youngman was referring to.

By the fall of 2010 I had many promising hints, but I still hadn’t solved the puzzle and then I established contact with several other Youngman researchers, Debbi Youngman and Susie Brewer. Both are related to descendents of John Youngman by his first and third wives. I decided to pursue confirmation of my theory that Jacob Youngman was a son of John Youngman by his second wife Elizabeth Reeves through autosomal DNA testing done by 23andMe.

Troy McCoy, a great-grandson of John Youngman and his third wife, was the person most closely related to John Youngman who was tested. Below is a summary of the DNA data showing the amount of autosomal DNA in centimorgans (cMs) that Troy McCoy shares in common with each of the five great-grandchildren of Jacob Youngman who have been tested by 23andMe. The comparison between Troy McCoy and Jacob Youngman’s great-grandchildren is the most important because in theory they should share the most autosomal DNA in common since they are the most closely related among all of the Youngman descendents in the project. A centimorgan is a unit of crossover frequency used to measure how often DNA segments are split up by recombination as they pass through the generations.

The proper way to analyze this data is to create an average of the amount of DNA shared between Troy McCoy and Jacob Youngman’s five great-grandchildren. (See table 1.) It is reasonable to assume that all of the matching segments over 5 cMs in length came from a shared common ancestor. A threshold of around 4 to 5 cMs is necessary since it is common for random people of European ancestry to share segments that are less than 4 cMs in length even if they don’t have any ancestry in common in the past 300 years. We would expect that on average half third cousins should share about 27.8 cMs of DNA. The above averages support of my theory that Troy McCoy’s great-grandmother Mary Jane Youngman (b. ca 1836) was a half sibling to my great-great-great-grandfather Jacob Youngman (b. ca Aug 1823).

Comparison	4 cM threshold	5 cM threshold
Frederick Mock and his 1/2 3rd cousin Troy McCoy	16.2	12.1
Raymond Youngman and his 1/2 3rd cousin Troy McCoy	5.1	5.1
Marilyn Bannister and her 1/2 3rd cousin Troy McCoy	4.6	0
Darryl Youngman and his 1/2 3rd cousin Troy McCoy	72.4	67.9
Norman Youngman and his 1/2 3rd cousin Troy McCoy	71.6	67.4
Average:	34.0	30.5

*Expected amount if the relationship is a half 3rd cousin: 27.5

But I didn’t stop there. I also found results that are very close to the expected average for a comparison like the one shown above between Troy McCoy and six great-great-grandchildren of Jacob Youngman. Thus the DNA data suggest that Mary Jane Youngman and Jacob Youngman were half-siblings based on these comparisons. I am likewise seeing results that are very close to the expected average for the comparisons between two descendents of William Youngman (b. ca 1818), John Youngman’s son by his first wife and the descendents of Jacob Youngman. The DNA data therefore suggest that William Youngman and Jacob Youngman were also half-siblings based on these comparisons.

In summary, autosomal DNA analysis has provided the key evidence to solving the genealogical puzzle of the parentage of Jacob Youngman. I now feel confident that Jacob Youngman was the son of John Youngman and Elizabeth Reeves. This project demonstrates how autosomal DNA can be used as an adjunct to traditional genealogical research to confirm or refute theories about possible genealogical relationships.

Tim Janzen is a family practice doctor at South Tabor Family Physicians in Portland, Oregon. His interest in genealogical research goes back 35 years and he has particularly focused on Mennonite genealogy for the past 15 years. He has a web site that summarizes many different sources available for Mennonite genealogical research found at www.timjanzen.com and has given many presentations about Mennonite genealogy in the United States and Canada. He is the co-administrator of the Mennonite DNA project at www.mennonitedna.com. He also serves on the ISOGG Y-DNA Haplogroup Tree Committee. Tim is married to Rachel Janzen and they have four children.

What’s the Answer? Bioinformatics/cheminformatics/biology games

2012-05-31T12:53:40Z

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s question could be dangerous….

Question: Bioinformatics/cheminformatics/biology games

I know FoldIt very well and I use it for teaching (as a next step after modelling – its interface is much more suitable to explain nuances of model refinement than any other free tools). I’m aware of couple of others such as Phylo or EteRNA. The question is what other bioinformatics/cheminformatics/biology games are out there? I’m looking for games that can be used to explain basic biological and algorithmic concepts in the course of teaching bioinformatics and systems biology to undergraduates.

Citizen science aspect (like in FoldIt) isn’t neccesary, but of course it would be nice to have it.

–Freesci

Go ahead, go see the answers. And I dare you not to get sucked into at least one of the games… But also, if you know of others, go over and add them. It would be nice to have a collection of them. In fact, I just remembered another and I want to go over and add it.

UPDATE: Galaxy servers are ̶d̶o̶w̶n̶ semi-up (they know). Other mirrors or sites

2012-05-31T03:44:30Z

UPDATE: Galaxy is up–but…

Be nice–don’t run giant projects right now…and it might not be entirely stable anyway. If you can wait, it might be wise.

++++++++++++++++++++++++

I saw a notice earlier, but figured it would be short term. However, just now I saw this:

You can follow the Galaxy twitter feed for updates: @GalaxyProject

Here are links to some mirrors or other servers you can use if you need one at BioStars: list of public Galaxy servers

I suspect this also means that the GenomeSpace one from today’s tip would also be down, as that’s a test server there.

This is just a PSA–I remember one time UCSC Genome Browser went down (they had a cable cut by construction work–not an earthquake that time), and the traffic to our mirrors post was astounding. So I thought people might be looking for this kind of info as well, and it’s hard to get the word out if your site is out of service…

The Fat You Wish You Had

2012-05-30T19:31:07Z

Brown fat, white fat…isn’t all adipose tissue the same? Previously thought of as the domain of infants and hibernating bears, brown adipose tissue has been identified in the adult human body as well. Two papers that appeared in The New England Journal of Medicine in 2009 reported that adult humans have brown fat, found in small [...]

Quiz Answers: Mac vs. Windows — Was Your Intuition Right?

2012-05-30T16:30:43Z

Last week we quizzed our readers on traits that differed between 23andMe customers who use Macs versus those who use Windows. Congratulations to Brenda, the winner of the quiz! She got all three answers correct and will receive a $25 Amazon gift card. So what were the correct answers? Read on…

Which of these personality traits is most strongly linked with being a Mac user? Openness.

If you had a tough time choosing which of these traits was most associated with being a Mac user, that’s totally understandable. All of them were. Yep, that’s right. Mac users were significantly more extraverted, assertive, full of ideas, and aesthetically-oriented, but where they most differed was on openness. Openness is a one of the so-called “Big Five” personality traits (five aspects of personality thought to be found across all human cultures), and it’s linked with being curious, adventurous, unconventional, intellectual, and artistic. Does this confirm the stereotype, or just underscore the value of targeted marketing campaigns? We’ll let you decide.

Which is NOT true of Mac versus Windows users? About 40% of men are Mac users, but only 29% of women.

Actually, 39% of men are Mac users, and 38% percent of women. Definitely not a big difference! Of course, this means that all the other answers are true: Mac users were more likely to report being atheist or agnostic, more likely to drink alcohol, less likely to say they were exclusively attracted to the opposite sex, and more likely to have had braces. We thought the braces finding might be related to income, but Mac users were still significantly more likely to have had braces when we controlled for household income and childhood socioeconomic status.

Which of these is true? All of the above are true.

Mac users had significantly higher incomes, were more likely to have had mono (the so-called kissing disease), more likely to have taken medication to prevent malaria (perhaps a sign of adventurousness), and less likely to be politically conservative.

Do these differences jive with the stereotypes of Mac and Windows users? Leave a comment below and let us know!

Video Tip of the Week: GenomeSpace, an integrator of integrators

2012-05-30T13:00:18Z

Recently, the Broad Institute announced a new tool: GenomeSpace. When I first looked at it, admittedly a very cursory look, I wasn’t sure how it would be much different than an integrator of tools like Galaxy or GenePattern. Obviously that cursory look was wrong at first glance since both Galaxy and GenePattern are in their list of tools that are supported. So what is GenomeSpace? Well, you can read the answer here at their “What is GenomeSpace” page . Basically, GenomeSpace has several functions. As described here, “GenomeSpace supports several bioinformatics tools, all integrated to allow easy accessibility, easy conversion, and frictionless sharing.” It is a space (in that every expanding Amazon cloud) that allows you to store your data files and, importantly, GenomeSpace allows you to seamlessly move those files between the tools to complete complex, or simple, analyses. It achieves this by automatically converting file formats and by allowing the user to attach their accounts at the tools to their account at GenomeSpace, thus alleviating the need to log in several times when using more than one tool.

To get a good idea of what GenomeSpace might be able to do for a researcher, check out the recipes on the site. As Anton states:

GenomeSpace is an integration of integrators,” Nekrutenko said. “The benefit to the user is that this brings together distinctive collections of functionalities offered by individual tools.”

The site is new, and only in beta. They only recently opened up registration from their invite-only stage. As such, there are some bugs and some features that aren’t quite at full capacity. For example, the Galaxy and UCSC Table Browser integration is with the test versions of those tools during beta. Thus, for example, your account at Galaxy will not be recognized when trying to link that account with GenomeSpace. I had to create a new one on the test site. And, if you go to the public version of the Table Browser, it will look different (no link to GenomeSpace as there is on the test site). Currently there are seven tools, more to come.

All that aside, it’s definitely a tool to get acquainted with. And with that in mind, take a quick introductory spin with me in this week’s video tip to get an idea of what you might be able to do.

Quick Links:

GenomeSpace
UCSC Table Browser (OH tutorial)
Galaxy (OH Tutorial)
Cytoscape (OH Tutorial)
Genomica
GenePattern
IGV
InSilicoDB

Broad Institute
NHGRI

Pathway Genomics Selected as a “Cool Company” by San Diego Venture Group

2012-05-30T00:18:43Z

Pathway Genomics has been selected by San Diego Venture Group as one of 30 “cool companies“ to be featured at its 10th Annual Venture Summit on June 6. Selected from a field of over 150 applicants, Pathway Genomics and the other 29 companies will be a prominent part of the event, which draws more than 100 venture capitalists and 500 attendees.

What We Do
Looking at millions of characters of genetic data is not typically thought of as, “Cool.” But, it’s what we provide that’s cool. Partially funded by Founders Fund (Facebook, SpaceX), Pathway screens genes associated with the propensity for drug responses, life-altering conditions, as well as food and exercise responses. We decode that information and turn it into easy-to-read reports for physicians and their patients, and in some cases, we give actionable advice they can use to optimize their health and wellness. Learn more about Pathway…

23andMe Partnering with Patients

2012-05-29T22:35:42Z

By Meghan Mullins

Before joining 23andMe, I worked at a more traditional genetic research lab. Like virtually all research centers, we didn’t return genetic results to our research participants.

I occasionally thought about what that meant, that I knew more about an anonymous stranger’s DNA than he or she ever would. These people had variants that scientists had never seen before, but the research participants would never learn of this.

Last fall I moved back to the Bay Area and joined the research team at 23andMe. I suddenly found myself in a completely different environment – not only do we return data to research participants, but they play an active role in the research process. 23andMe partners with patients who work side-by-side with us to dramatically accelerate genetic discovery.

We recently launched a 23andMe Research Ambassador program, where research participants have volunteered to help more formally spread awareness of and expand our Sarcoma, Myeloproliferative Neoplasms (MPN), and Parkinson’s research initiatives. In honor of National Cancer Research Awareness month, we asked some of our newly minted Sarcoma and MPN Ambassadors to share their cancer stories.

Each of these ambassadors — Tracy, Ruth Ann, Natalie, Greg, and Cheryl-Anne — describe the uncertainty he or she faced when being diagnosed with a rare cancer. Tracy says her doctors at first did not know if her tumor “was a chondrosarcoma or a chordoma. Apparently [it was] one in a million.” For many, the simple lack of information available feels like hitting a wall. Ruth Ann joined our Sarcoma Community because “having been so discouraged in my own journey with the lack of information about sarcomas, I was more than willing to sign up to start a project that might provide some real answers.”

• Do you have sarcoma, or know someone who does? Learn how to join our Sarcoma research community today.

• Do you have an MPN, or know someone who does? Learn how to join our MPN research initiative today.

Cheryl-Anne agrees, saying that “the more we know, the more we will be able to make sure the right patient gets the right drug at the right dose at the right time.” A sense of community and support also drew many to our research initiatives. Greg says that “connecting with others who have a similar interest in fighting sarcoma was my initial motivator in joining 23andMe.” When asked what advice he would give to someone who was just diagnosed, he said to “connect with others who have been in similar situations. Learn from their successes and mind their shortcomings.”

Our research Ambassadors also desire to look at the big picture when studying cancer risk. Greg notes that it’s currently unknown how different risk factors, like “radiation or chemical exposure, a virus or genetic factors,” interact to cause sarcomas. He wants “to help the scientists come closer to solving these questions.” Ruth Ann adds that “since it is so rare, there have to be many more factors than genetics alone that affect the occurrence of sarcoma. But, that doesn’t mean there isn’t a genetic component.” 23andMe wants to learn more about those different factors, too, so we combine our genetic data with survey responses to study all aspects of cancer risk.

Cheryl-Anne has enjoyed exploring her own 23andMe data, saying that “it is fascinating to learn about myself, my own biology. This is me, my chromosomes, my DNA, and it helps me to make better choices for myself.” Natalie’s advice to someone else with an MPN is to “get a 23andMe spit kit. Find out your risks, and go back to your doctor and share that information. You learn a lot about yourself. . . I am very glad that I went through with that decision.”

Tracy was able “to provide the raw data to a genetic counselor for hereditary cancer testing for a condition called Ollie’s disease, where tumors mutate into sarcomas.” Ruth Ann has “enjoyed filling out the surveys, and getting the results about ordinary things. Who knew there was an asparagus pee gene?” We also make sure to share new discoveries with our research participants who helped us find them. Greg is grateful for 23andMe’s “sincere partnership in making strides to identifying the root cause of this life threatening disease.”

Scientists may have the best in technology and theory at their disposal, but they cannot move forward without research participants who are willing to give their time and energy to scientific pursuit. Natalie hopes that scientists and those with rare disease can “help each other, hand in hand.” I feel so incredibly lucky to interact with these generous individuals on a daily basis, to see their desire to give back so that others do not have to face the fear and uncertainty that they felt.

Meghan Mullins is a research assistant at 23andMe and works with our Research Communities. Meghan studied Human Biology at Stanford University. She spent a few years studying the genetics of obesity and diabetes in the Pima Indians as part of a NIH Postbaccalureate Intramural Research Training program, and played a key role in a large sequencing project that discovered several variants of interest in the MC4R gene.

Transcriptomes in space. Sweet.

2012-05-29T15:59:34Z

I know a lot of sci-geeks were lured into the field by space. Rockets, space travel, great science fiction–I understand the appeal. But as it seemed much more physics oriented, space wasn’t my primary fascination. But the effects of space travel on organisms (humans, of course, but others as well)–that’s something I can find pretty intriguing. And I was always really pleased to hear about the various cells and organisms that were on the trips and undergoing experimentation.

But until last week, had never gone to the primary literature that resulted from these studies to have a look. I had seen an article in Wired that talked about the work, though, and I had to see it. Have a look at the piece How Plants Deal With Space Travel for their take on it. Coincidentally on Fascination of Plants Day a piece appeared in SciAm as well, on other Plants! In! Space! (Moon trees were totally new to me in that piece, but I was previously familiar with Space Beer barley.)

What does happen to gene expression in space? It changes in some expected ways: the structural features of the cytoskeleton can be affected, as can metabolism. These had been previously described. But with new technologies now they can look more broadly across the genome to see further details.

This is not your average experiment, though. One set needs to be run on the ground as a control, while the other one needs to be loaded on to spacecraft, monitored for all sorts of external conditions, and run in the shuttle. They spent a bit of time explaining how they coordinated those to be sure they were making as direct comparisons as possible. But they get all that under control, and have a look at the Arabidopsis plants in a couple of ways.

They have seedlings to look at, but they also used tissue culture cells. I think that’s an interesting thing to do–it gets at some of the differences between structural features that might be more affected by gravity in an intact plant vs. a dish. And you can also think about the differences in tissue types.

The space seedlings had a lot of upregulation of pathogen/wound response genes. Other stress-response genes were up as well. Downregulated genes were curious to me: a lot of transcription factors went down, but cell wall metabolism and elongation ones did too. I might have expected the cell walls to have to try harder if the cytoskeleton was misbehaving. Gravitropism genes were down, which seems sensible.

The cultured cells were different. They ramped up their heat shock genes more, but also did have some stress-responses for wounding and other conditions too. But of course, all of the scenarios included lots of things that would have to be characterized in more detail to fully understand. The general features are interesting and informative, but some specific genes might provide interesting clues too.

One of the things that struck me was that the tissue cultures cells could be more prepared to just throw some “on” switches because they are more undifferentiated–or at least not under the same tissue-specific constraints that seedlings are. That could explain some of the transcription factor differences. And they go into that a bit in the discussion.

They go into more details and offer lists of the genes to examine, and in the discussion they speculate about some of the differences between the conditions. But I imagine it’s important to examine both scenarios. If I was on a long space flight I’d want some fresh veggies to eat, but maybe also some cultured cells in a vat to produce various things–including oxygen.

I don’t imagine this information is anything I need to know soon–I have no plans for flight myself, although I think recently Trey bought a lottery ticket for that… I’m glad someone is looking at it.

When I contacted the team with a question about the paper, Anna-Lisa Paul also pointed me to this video. You can see her trying to work on a sample project like it would happen in space. Funny, just the other day I posted about that guy who needed to get genome samples from dangerous critters–now there’s this. Genomics can be a lot more physically challenging than you might think–it’s not all done on keyboards!

Reference:
Paul, A., Zupanska, A., Ostrow, D., Zhang, Y., Sun, Y., Li, J., Shanker, S., Farmerie, W., Amalfitano, C., & Ferl, R. (2012). Spaceflight Transcriptomes: Unique Responses to a Novel Environment Astrobiology, 12 (1), 40-56 DOI: 10.1089/ast.2011.0696

Announcing 23andMe’s First Patent

2012-05-29T04:38:52Z

[Ed: A clarifying addendum has been added to the end of this post. - 6/01/12]

23andMe has a substantial research arm with more than 20 scientists dedicated to making meaningful discoveries that will improve the lives of all of us. We’ve made a number of discoveries that we’ve published in peer reviewed journals and on our website. As we make these discoveries, we have often debated: what is the best way to make sure that genetic breakthroughs translate into real-world benefits? We want to make discoveries that will impact your life and the lives of everyone on the planet. We do not want our discoveries to just be an academic pursuit — we want to meaningfully improve lives.

Our patent, “Polymorphisms Associated With Parkinson’s Disease” is expected to issue on Tuesday, May 29, 2012. This relates to our discovery of a variant in the SGK1 gene that may be protective against Parkinson’s disease in individuals who carry the rare risk-associated LRRK2 G2019S mutation. Our patent is an important step in ensuring that we’ve done all we can towards successful translation of this discovery. If the follow up work we are now doing with the Scripps Research Institute and the Michael J. Fox Foundation looks promising and moves towards drug development, the patent will be important for a biotech or pharmaceutical company to pursue drug development.

We believe patents should not be used to obstruct research or prevent individuals from knowing what’s in their genome. We believe that everyone has a right to know their genomes — their sequence of As, Ts, Cs, and Gs — and should be able to access them should they want to. This has been our guiding principle since day one, and 23andMe has pioneered the ability for individuals to have unfettered access to their genomes.

We recognize that patents are complicated and can be controversial. Patents were created to protect innovation. Is discovering the function of a gene an innovation? The question of whether innovations related to genetics can be patented is in hot debate as evidenced by recent rulings related to Prometheus and Myriad patents.

We want to emphasize that we are firm in our belief that individuals should have access to their own genetic data. We will continue to pursue patents that we believe will eventually benefit us all. The majority of our customers have opted to participate in research. Thanks to that community, we have been able to make an incredible number of novel discoveries. We want those discoveries to move from the realm of academic publishing to the world of impacting lives by preventing, treating or curing disease.

Addendum — June 1, 2012:

The patent announcement has generated a lot of discussion. In addition to reiterating our core beliefs I’d like to clarify a few points about our perspective:

23andMe will not prevent others from accessing their genetic data or its interpretation specific to our patents. Other entities can present information about the genetic associations covered in our patents without licensing fees. As has always been the case, 23andMe customers can freely apply their raw genetic data to other interpretation tools whenever they wish.

23andMe is a business with a mission to improve lives. We sell a service to our customers and we conduct research, on our own and with partners, that we believe will lead to better treatments, diagnostics, and prevention of disease. We aim for these discoveries to benefit everyone.

Patents give organizations researching and developing new drugs confidence that their significant investments will be commercially viable. Developing new drugs and treatments costs time and money. A lot of time and money. Often the only way a company will even think about pursuing a drug lead is if they have assurance that they can recoup their investment. Having patent protection over the entire line of discovery gives a company confidence to invest in this resource-intensive process.

Many of you, especially in the Parkinson’s community, saw this as a major milestone and the first step in potentially having a meaningful impact on the lives of Parkinson’s patients. Our ultimate goal is to make discoveries that will benefit everyone.

Forgot Something? Maybe Your Diet, not Your Age, is to Blame

2012-05-25T14:19:29Z

Have trouble finding your car keys this morning because you forgot where you left them? Or maybe you can’t remember the name of the new person who just joined the department down the hall? Before you blame age for your faulty memory, take a look at your diet. New research suggests that low levels of [...]

Friday SNPpets

2012-05-25T13:18:03Z

Heh. RT @davidmam: #filmquotebioinformatics The first rule about bioinformatics in grants is that nobody talks about bioinformatics in grants. [Mary]
RT @widdowquinn: #filmquotebioinformatics ‘Homology!’
‘You keep using that word. I do not think it means what you think it means.’ [Mary]
Note–those two film quotes were part of a hilarious meme recently, which was captured in a storify by Casey Bergman: Bioinformatics Film Quotes
Hey Hopkins folks–do this if you have been wanting to pick up some programming skills: RT @jiffyclub: Help spread the word about our upcoming Johns Hopkins Software Carpentry bootcamp! Lots of room still. It’s free! http://t.co/iLIp2JZ5 [Mary]
From a LinkedIn discussion for the International Society for Biocuration group: “American Society for Cell Biology (ASCB) 2012 Annual Meeting Travel Awards now available http://bit.ly/Jj1YFA“ [Jennifer]
RT @NCBI: Try the new 1,000 Genomes Browser which displays graphics and tables for Project data as well as NCBI annotations: http://t.co/QPTe59J6 [Mary]
Amen. I wish curation got the respect it deserves: RT @GenomeMedicine: John Hawks’ blog puts genomic data into perspective http://t.co/kziT7zvV. New generation of data curators needed? [Mary]
From a LinkedIn discussion at the American Association for the Advancement of Science (AAAS) group: “Its time for the 2012 Dance Your PhD Contest!!! Enter for a chance to win $1,000, a trip to TEDx in Brussels and be featured in Science Mag! Details at http://gonzolabs.org/dance/ …” [Jennifer]
RT @iGenomics: Just about to finish teaching a fun 2-day RNA-Seq workshop.The teaching materials are at http://t.co/vqhp304z [Mary]
From The Wall Street Journal: “Making Gene Mapping Part of Everyday Care” HT: Bio SmartBrief [Jennifer]

Special video SNPpet–this story had a link to a video about obtaining samples for genome sequence from unusual species. Makes those mouse bites I got way back seem pretty tame. And makes you think about your choices of species for sequencing. Choose wisely, young grad student:

RT @DNAday: Mapping the crocodile genome is not for the faint of heart http://t.co/hAXJRsow

UCSC Table Browser webinar follow-up post (May 24)

2012-05-24T16:19:11Z

We’ll be having our May 24th webinar today, and we find there are questions to follow up afterwards that are often better handled in discussions on the blog.

If there are questions we didn’t have time to get to–or things we want to expand on with more detail–we can discuss them in this thread.

Or if you have other things you’ve been meaning to ask, let us know.

If you can’t make the webinar, the same material is covered in the training movie, slides, and exercises that are freely available, sponsored by the UCSC team: http://www.openhelix.com/ucscadv. You can also sign up to be informed of future webinars coming up on these topics, Galaxy, ENCODE and others.

SNPwatch: Novel Genetic Factors for Crohn’s Disease Identified for Ashkenazi Jewish Ancestry

2012-05-24T13:00:51Z

Crohn’s disease develops when the immune system mistakenly attacks the body’s own gut cells.

Although most people with European ancestry are pretty genetically similar, some sub-groups like Ashkenazi Jews have distinct genetic characteristics that carry important implications for health. For instance, people with Ashkenazi ancestry have higher rates of numerous rare genetic disorders like Tay-Sachs disease and are at increased risk for certain multi-gene conditions like Crohn’s disease.

The exact cause of Crohn’s disease isn’t known, but this inflammatory bowel disease may result from a case of mistaken identity — the immune system mounts a reaction to an invader and ends up attacking the body’s own cells, too. At least 12 genetic factors have been associated with Crohn’s disease in Europeans. Although researchers don’t know why people with Ashkenazi ancestry are two to four times more likely to develop Crohn’s disease, they suspect that the genetic “uniqueness” of this group may have something to do with it.

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To investigate this intriguing idea, a research team led by scientists at Columbia University and Mount Sinai carried out a study looking at nearly 2,000 people with Crohn’s disease and roughly 4,500 people without it, all of Ashkenazi descent. The results, published in PLoS Genetics earlier this year, replicate previously reported associations for people of European descent and also identify novel factors specific to those with Ashkenazi ancestry.

In the new study by lead author Eimear Kenny, individuals with the C version of rs11229030 and the G version of rs7705924 had slightly higher odds of developing Crohn’s disease. Two other factors seemed to be protective. People with the T version of rs6545946 and the G version of rs12677663 had slightly lower odds of developing Crohn’s disease. More research is needed to understand how these genetic variants influence the biology of the disease.

These new findings confirm that genetics likely has something to do with the higher rates of Crohn’s disease in people with Ashkenazi ancestry. All of the newly discovered factors appeared to be specific to Ashkenazi ancestry as they weren’t found in previous studies carried out with broader European study groups.

May is Jewish American Heritage Month. Read about the “uniqueness” of Ashkenazi Jewish ancestry and how it’s important for health. Read more about Jewish ancestry in guest posts by 23andMe’s Ancestry Ambassadors, Tim Janzen, CeCe Moore and Andrea Badger.

What’s the Answer? (Bioinformatics Tools on Biostar)

2012-05-24T13:00:57Z

Just about a month ago, BioStar added a tool section as a place to announce and update new and old bioinformatics tools. So, in a sense, today’s post is are answers in search of your questions :

We just added a new section to the site called **Tools** We designate this section to announcements regarding bioinformatics software tools, both new and old.

There are about 10 tools listed currently for various areas of analysis. This dovetails nicely with a the “obituary” section Mary created at Biostar for no longer supported tools and databases she discussed earlier this week. Circle of life and all that .