Tuesday, October 14, 2008

The DNA Network

The DNA Network

George Palade 1912-2008 [The Daily Transcript]

Posted: 14 Oct 2008 07:05 PM CDT

Last week one of the fathers of Cell Biology died. I found out Friday during happy hour - but I just haven't had the time to write anything until now.

George Palade and Keith Porter, were the first scientists to peer into the depths of the cell using electron microscopy. This all started in 1945 when Keith Porter, a researcher at Rockefeller University, snapped the first known EM micrograph (right). A year later Palade joined Albert Claude's group to work on the electron microscopy of large structures isolated from tissue culture cells. Palade and Porter started a revolution - they were the first to see ribosomes, the endoplasmic reticulum and countless other subcellular structures. Much about what we know about the cell can be traced back to Palade's famous EM studies from the 50s and 60s.

One of Palade's greatest series of papers dealt with how secretory proteins were produced. In an early paper Palade's group investigated small vesicles derived from mashed up pancreatic cells. By using electron microscopy, they observed that these vesicles, also known as microsomes (small vessicles, get it?), are studded with tiny bodies called ribosomes. You can see these microsomes in figure A from the powerpoint slide below (it's straight from one of my talks - the image is from Redman et al., JBC 1966). If you dissolve the microsome's membranes with detergent, you could release polysomes, or ribosomes connected together by mRNA. As you all know, mRNA contains the information on how to make specific proteins that are synthesized by ribosomes.

Palade discovered that the these mRNAs encoded secreted proteins, or proteins that end up on the outside of the cell. An example of such a protein is amylase, a digestive enzyme.

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Personalized Health Care National Conference [ScienceRoll]

Posted: 14 Oct 2008 03:47 PM CDT

I wanted to let you know the Ohio State University Medical Center is hosting it’s first conference on personalized health care this week (October 16-17). It seems to be quite an interesting event so I hope we will get some live coverage from there.

A national conference focusing on topics ranging from research in personalized medicine to clinical applications in patient care. It features internationally renowned speakers in personalized medicine, as well as panel discussions by experts from academia, industry, government and non-profit organizations.

Speakers will include Linda Avey (23andMe, Inc.), Geoffrey Ginsburg (Director, Center of Genomic Medicine,
Duke Institute) or Lawrence Lesko (Director, Office of Clinical Pharmacology, Food and Drug Administration).


Webicina coverage [ScienceRoll]

Posted: 14 Oct 2008 03:39 PM CDT

While we are working hard to make our own screencasts for Webicina, a service that aims to build a bridge between physicians and e-patients, some great blogs covered our efforts.

We also plan to let visitors access the free e-courses without registering. And for some reason, instead of patients, medical professionals tend to order Personalized Medicine 2.0 Packages which are sets of tools focusing on a medical specialty or a medical condition.


Drugs to "enhance" the dying experience [Mary Meets Dolly]

Posted: 14 Oct 2008 02:22 PM CDT

PredictER News Brief - Published Today [PredictER Blog]

Posted: 14 Oct 2008 02:21 PM CDT

The most recent edition of PredictER News Brief is now online. PredictER News Brief provides a digest of news and research relevant to the ethical, legal and social implications of predictive health research. Join the PredictER News Brief listserv or view past issues in the archive.

The October 14th edition includes links to stories related to deCODE's new genetic test to screen for breast cancer risks and (as always) a list of recent journal articles on the ethical issues of predictive health and genetic research. Including:

Alpert S. Privacy issues in clinical genomic medicine, or Marcus Welby, M.D., meets the $1000 genome. Camb Q Healthc Ethics. 2008 Fall;17(4):373-84.
[View abstract or record.]

Goodman KW and Cava A. Bioethics, business ethics, and science: bioinformatics and the future of healthcare. Camb Q Healthc Ethics. 2008 Fall;17(4):361-72.
[View abstract or record.]

Hogarth S, et al. The Current Landscape for Direct-to-Consumer Genetic Testing: Legal, Ethical, and Policy Issues. Annu Rev Genomics Hum Genet. 2008 Sep 22;9:161-182.
[View abstract or record.]

Singer E, et al. Trends in U.S. Attitudes Toward Genetic Testing, 1990-2004. Public Opin Q. 2008 September 1, 2008;72(3):446-458.
[View abstract or record.]

Wallace S, et al. Governance mechanisms and population biobanks: building a framework for trust. GenEdit. 2008;6(2):1-11.
[View abstract | PDF]

A broken watch and deCode's test [The Gene Sherpa: Personalized Medicine and You]

Posted: 14 Oct 2008 12:51 PM CDT

I am posting today away from home. In case you didn't know, my family is a BRCA family and a wonderful lady who was hit with not one but 2 breast cancers and metastases just passed. I am sad today....

[[ This is a content summary only. Visit my website for full links, other content, and more! ]]

My immunological fantasy [Discovering Biology in a Digital World]

Posted: 14 Oct 2008 12:44 PM CDT

Like many people I know, I suffer from allergies, and sometimes asthma. I take drugs to control the symptoms, but they don't cure the condition. Plus, I know there can be side effects that might not be so pleasant.

This is why I like hearing about sequencing projects that target the VDJ-ome.

I have this fantasy about the things we could do with that information

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When did I begin? [Mary Meets Dolly]

Posted: 14 Oct 2008 12:34 PM CDT

I am sorry for the hiatus, but a sudden illness in the family had myself, my husband and four children driving 3500 miles across country last week. This means I have also been out of the loop when it comes to all of the recent news. So while I catch up, I will leave you with this entry that has been in the back of my mind for several weeks.

My second child is in the 4th grade and her school does not do any sex education until 7th grade. So, like with my oldest, I recently took it upon myself to sit her down and give her the facts of life. (Her response was a resounding, "That is so gross!")

To facilitate our discussion, I checked out several books from the library that had the visuals of the female reproductive system I was looking for. While reading these books designed for children, I noticed something very profound.

Not one of the secular children's books on the subject of human reproduction was ambiguous about when human life begins. See, children could care less about the broad philosophical question "When does human life begin?" They want to know when they began.

No children's book on the subject of human reproduction would say to little Johnny that "no one is really sure when your life began." No parent in their right mind would tell their little Sally that "knowing when you began is above my pay grade."

Here are some of the excerpts from the very non-religious books that I got from my very public library:

"In the very beginning, you were an egg -- a special egg inside your mother's body."

"At the begining of your life, you were a tiny egg that was smaller than a grain of salt. You didn't have any arms and legs. You didn't have a head! You certainly had a lot of growing to do!"

"When you were still very small, you took an exciting journey. You needed a place to grow, so you floated down your mother's Fallopian tube and into her uterus. You attached yourself to the wall of her uterus -- your home for the next nine months."

"But nine months before, when you first began, you were just one little cell, even smaller than the dot at the end of this sentence. Half of this cell came from your mother's body, and the other half came from your father's body."

"At the very start of your your life you began as two microscopically tiny cells. These fused together and then developed inside the safety of your mother's womb."

Sounds simple because it is simple. Even a child knows when human life begins; when their life began. Even a child knows they have been a continuous organism from the moment Daddy's sperm penetrated Mommy's egg.

Once again here is more proof that the so-called debate over the abstract "when does human life begin?" is not really about that at all. The real debate is whether that life has value. Whether or not that life deserves protection under the law.

I find it more and more disturbing the ways in which adults commit verbal acts of contortion to obfuscate this issue and others like it. I truly fear for a society that can take something so simple as the moment of conception and not only deny the facts of what has occurred, but then pat themselves on the back for being intellectually honest. All the while accusing those who acknowledge the fact that a new human life is formed at the moment of conception of being "religiously biased."

If I am "religiously biased", then so is every children's book on "how babies are made" in my public library.

IA updates [Bayblab]

Posted: 14 Oct 2008 12:15 PM CDT

Y'all better check out Informationaddiction.com for your tech news. Some interesting stuff about how Google Chrome is evil and a Astrobiology Rap.

Genetics and Boldness - Keep your hair on, there’s help on the way (we hope) [deCODE You]

Posted: 14 Oct 2008 12:04 PM CDT

deCODEme genetic test includes an identification of the male pattern baldness trait.

deCODEme genetic test includes an identification of the male pattern baldness trait.

A team of scientists, led by Professor Tim Spector of King’s College, London, have been taking a closer look at the genetic coordinates for male pattern baldness or androgenic alopecia. Male pattern baldness is the most common form of hair loss in men and one that increases steadily with age. While it has been known for some time that men inherit a tendency for baldness via their x chromosomes from their maternal grandfathers, this new research has identified a region on chromosome 20 (20p11) that suggests that a susceptibility for baldness is also inherited directly from their fathers. No preventative treatment is guaranteed to work, but if you are among the 14% who are in the greatest risk group there’s more hope now the causes are being identified. Frank Geller from deCODE genetics is among the geneticists who took part in the research. The genetic scan deCODEme already includes an identification of the male pattern baldness trait.

Link: “Male-pattern baldness susceptibility locus at 20p11″ in Nature Genetics
Link: “Genetic test can forecast bald facts about each man’s future” in The Times
Link: “Hair loss now predictable with gene scan” in The National Business Review

deCODEme staff writer Martin Regal

deCODEme staff writer Martin Regal

Bioethicist Arthur Caplan Says Corporate Greed Drives Genetic Testing Marketplace [Eye on DNA]

Posted: 14 Oct 2008 11:59 AM CDT

price tag Fresh on the heels of the launch of the deCODE BreastCancer genetic test last week, Dr. Arthur Caplan, renowned director of the University of Pennsylvania Center for Bioethics, said in an article for MSNBC.com that breast cancer gene tests are not worth the price.

If you are worried about your risk of getting the disease, or are thinking about getting a genetic test done for any other reason, talk with your doctor or a genetic counselor who can determine whether your family history justifies the expense. You may be surprised to find that you can make changes in lifestyle and monitoring your own health that can reduce your risk without testing.

Dr. Caplan even goes so far as to accuse genetic testing companies of corporate greed which, given the current economic environment in the U.S., is bound to send shivers down their spine.

With respect to deCODE’s breast cancer genetic test, it examines seven single nucleotide polymorphisms* (SNPs) that are purportedly involved in 60 percent of all breast cancers. Results from the test are given as personal lifetime relatively risk compared to the general population (specifically people of European descent). Other risk factors such as family history, pregnancy history, etc. are not taken into consideration when calculating a deCODE BreastCancer genetic test taker’s risk.

deCODE’s Chief Scientific Officer, Dr. Jeff Gulcher, responded to Dr. Caplan on its blog, deCODE You (a member of the DNA Network) and drew analogies between the BreastCancer genetic test and LDL-cholesterol tests. Anyone who is identified to be at higher risk of breast cancer (or in the analogy, high cholesterol leading to cardiovascular disease) would benefit from greater vigilance, more intensive screening, and possibly, preventive therapy.

Another DNA Network member, Dr. Steve Murphy at Gene Sherpas calls the deCODE BreastCancer test “hype.” Cancer Research UK also believes that “it’s too early for a test of this kind to be released to the general public.” Dr. Len Lichtenfeld of the American Cancer Society does not believe the test will “advance our cause in the fight to reduce deaths from cancer in a meaningful, evidence-based and scientifically accurate way.”

Speaking of cost, though,it seems that 23andMe customers get the better deal because all of the SNPs examined in the deCODE BreastCancer genetic test are included on version 2 of the 23andMe gene chip (I checked using SNPedia) not to mention the other nearly 600,000 SNPs included in the 23andMe report. A 23andMe DNA test costs $399 while a deCODE BreastCancer genetic test costs $1,625.

deCODE’s test offers other bits and fancy algorithms for calculating risk to justify the price. But customers should be aware that there is more than one way to get the genetic data they desire. And that data’s worth can be hard to price.

*See the list of SNPs in this sample report (pdf).

via Al’s Morning Meeting at Poynter Online

NB: I am a consultant to DNA Direct, a genetic testing company.

Photo Credit: abbyladybug

Genetic determinants of Vitamin D levels among Hispanics and African Americans [Yann Klimentidis' Weblog]

Posted: 14 Oct 2008 10:37 AM CDT

This study has a large diverse sample and they look at the association between variants in three vitamin D related genes and vitamin D levels in the blood. They find an association between variants in the DBP (vitamin D Binding Protein gene) and plasma levels of 25(OH)D and 1,25(OH)2D in all three populations. I wonder how these polymorphisms differ in frequency and haplotype structure between groups.

Genetic and environmental determinants of 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D levels in Hispanic and African Americans.
Corinne D. Engelman, Tasha E. Fingerlin, Carl D. Langefeld, Pamela J. Hicks, Stephen S. Rich, Lynne E. Wagenknecht, Donald W. Bowden and Jill M. Norris
The Journal of Clinical Endocrinology & Metabolism Vol. 93, No. 9 3381-3388
Context: Vitamin D deficiency is associated with many adverse health outcomes, yet little is known about the genetic epidemiology of vitamin D or its metabolites. Objective: Our objective was to examine the relationship among three vitamin D-related genes and levels of 25-hydroxyvitamin D [25(OH)D] and 1,25-dihydroxyvitamin D [1,25(OH)2D] in Hispanics (HAs) and African Americans (AAs). Design and Setting: The cross-sectional Insulin Resistance Atherosclerosis Family Study recruited and examined subjects in: Los Angeles, California (AAs; 513 individuals from 42 families); San Luis Valley (SLV), Colorado (HAs; 513 individuals from 30 families); and San Antonio (SA), Texas (HAs; 504 individuals from 58 families). Main Outcome Measures: Plasma levels of 25(OH)D and 1,25(OH)2D were measured. Results: Levels of 25(OH)D were highest in SLV-HAs [18.3 ± 7.7 ng/ml (45.7 ± 19.2 nmol/liter)], lower in SA-HAs [14.6 ± 6.4 ng/ml (36.4 ± 16.0 nmol/liter)], and lowest in AAs [11.0 ± 5.4 ng/ml (27.5 ± 13.5 nmol/liter)]. Levels of 1,25(OH)2D were similar in AAs [43.5 ± 13.9 pg/ml (113.1 ± 36.1 pmol/liter)] and SLV-HAs [43.2 ± 13.3 pg/ml (112.3 ± 34.6 pmol/liter)], but higher in SA-HAs [48.6 ± 17.0 pg/ml (126.4 ± 44.2 pmol/liter)]. After adjusting for gender and age within the site, two single nucleotide polymorphisms (SNPs) in the vitamin D binding protein gene (DBP), rs4588 and rs7041, were associated with 25(OH)D, and one SNP in the DBP, rs4588, was associated with 1,25(OH)2D at all three study centers. Conclusions: SNPs in the DBP are associated with levels of 25(OH)D and 1,25(OH)2D in HA and AA participants in the Insulin Resistance Atherosclerosis Family Study.

DNA Could Reveal Your Surname, Of Course [The Genetic Genealogist]

Posted: 14 Oct 2008 07:08 AM CDT

allelic length variation among 6 individuals

Image via Wikipedia

New research from Mark Jobling’s lab at the University of Leicester suggests that Y-DNA can be used to determine a male’s surname.

I know, I know, this is obvious to anyone who is familiar with genetic genealogy.  Just check out the many instances of this type of determination at ISOGG’s Success Stories website, for example.  However, as you’ll see below, this research has resulted in some new and interesting information.


Dr. Turi King, who conducted the research, recruited over 2,500 men with roughly 500 different surnames to submit Y-DNA samples.  The sample set included a group not sharing surnames as well as sets of men (between 2 and 180) who shared a surname (including recognized variants).  She then typed 9 SNPs and 17 STRs.  There’s much more information about this research at the Jobling lab’s website regarding this project.


Although this research may seem obvious, what makes it interesting are the actual statistics.  According to Dr. King’s research, there is a 24% chance that two men who share the same surname share a common ancestor through that name, and this increases to nearly 50% if the surname they share is rare. Keep in mind, of course, that this study was conducted solely in the U.K., so it is unclear how it applies to other countries.  From the press release:

“Dr King then went on to look at 40 surnames in depth by recruiting many different men all bearing the same surname, making sure that she excluded known relatives. Surnames such as Attenborough and Swindlehurst showed that over 70% of the men shared the same or near identical Y chromosome types whereas surnames such as Revis, Wadsworth and Jefferson show more than one group of men sharing common ancestry but unrelated to other groups.”


The implications of Dr. King’s research have strong significance for genetic genealogists, but the press release focused only on forensic science, stating that “the fact that such a strong link exists between surname and Y chromosome type has a potential use in forensic science, since it suggests that, given large databases of names and Y chromosome profiles, surname prediction from DNA alone may be feasible.”

For more analysis, see Anthropology.net.

The Genetics of Voting [Bayblab]

Posted: 14 Oct 2008 06:26 AM CDT

This past weekend was Canadian Thanksgiving and with my family all together and elections on both side of the border, the conversation naturally turned to politics. One person almost proudly claimed that they had never voted (and not for lack of opportunity). It's not uncommon to see families with similar political views, but what about similar political participation? Again, I wouldn't be surprised if there were familial trends in voter engagement but my first inclination would be to chalk it up to nurture over nature. According to Wikipedia parental turnout is a strong predictor of youth turnout, and recently published twin studies of voting trends in Los Angeles showed that while the choice of a particular candidate don't appear to be heritable, "genes account for a significant proportion of the variation in voter turnout." A follow-up paper published in the Journal of Politics attempts to identify genes involved, though they stress that they work shows association, but nothing about causality. From the abstract:
Using data from the National Longitudinal Study of Adolescent Health, we show that a polymorphism of the MAOA gene significantly increases the likelihood of voting. We also find evidence of a gene-environment interaction between religious attendance and a polymorphism of the 5HTT gene that significantly increases voter turnout.
Both of those genes are involved in serotonin pathways. I haven't looked at the paper in detail, so I don't know if their methods are valid (they use a mixed-effects logistic regression model) or their conclusions are sound - or how reliable the Journal of Politics is as a source of genetic knowledge so take it with a grain of salt until you check it out for yourself.

Inspirational Talks at TED [Bitesize Bio]

Posted: 14 Oct 2008 05:20 AM CDT

Imagine bringing some of the world’s greatest talkers and thinkers in a conference and challenging them to give the best talk of their life, on whatever they want to talk about. Wouldn’t that be an amazing event?

And if someone videoed all of the talks and put them on a website, what a great resource that would be.

If you agree, you’d better take a look at the TED website. TED, which stands for Technology Entertainment and Design, is an annual conference that was first held in in 1984 bringing together thinkers in these three areas. Since then the variety of subjects covered in the conference has mushroomed and eminent thinkers from a whole gamut of disciplines are now invited to talk each year.

The talks are are available on the TED website and are a real feast. They are concise, informative and inspiring but also generally entertaining - the speakers are giving the talks of their lives remember. More often than not they are also very profound and give a real insight into the thinking of some of the greatest thinkers in the world.

Some science highlights include:

…and many more in the science section.

But it’s not just science. Some more great talks include:

As well as a feast of entertainment and information this is a great opportunity to see some of the world’s greatest presenters speaking and maybe pick up some tips!

Let us know what you think of TED in the comments section.

Highlight HEALTH Goes Mobile [Highlight HEALTH]

Posted: 14 Oct 2008 05:00 AM CDT

As more and more people use cell phones, the Mobile Web — accessing the World Wide Web using a mobile device such as a cell phone, PDA or other portable device — is increasingly being used to access online information. According to AdMob, the world’s largest mobile advertising marketplace, in August 2008 mobile worldwide traffic grew 12.8% to 5.1 billion web page requests [1].

New smartphones like the iPhone are accelerating this use in the mobile web. Indeed, in August 2008 the iPhone saw the largest share increase of any smartphone [1]. With healthcare consumers and professionals increasingly relying on handheld devices to access the web, I’m pleased to announce that a mobile version of Highlight HEALTH is now available.

Standard mobile phones, Blackberries and 3G devices such as the iPhone and iTouch are fully supported. The site is powered by MoFuse, short for Mobile Fusion, an application that provides content publishers the ability to publish to the mobile web. Optimized for the mobile web, http://m.highlighthealth.com enables readers to access all the articles on Highlight HEALTH while on the go.

At the bottom of every article, you can show and post comments. Additionally, there are links to “Email” the full HTML article link, “Bookmark on delicious” or “Share on Twitter”.

According to a study last year, 75% of people who access the mobile web conduct searches [2]. As consumers use the Internet more than any other media source to research health information [3], I anticipate an increasing number of health-related searches to be done using the mobile web. I hope the mobile version of Highlight HEALTH will enhance its appeal to readers who have busy schedules and frequently don’t have time to read on a computer.

Mobile web users, please give the mobile version of Highlight HEALTH a try and let me know what you think.


  1. AdMob Mobile Metrics Report. AdMob. 2008 August
  2. Consumers Stick with Big Search Engines, Demand Mobile Optimized Content. iCrossing press release. 2007 Apr 25.
  3. Research Reveals That Internet Has Become Primary Means by Which Consumers Access Health Information. WebMD press release. 2003 Feb 10.
Thank you for subscribing by RSS or email. I work hard to make the articles on Highlight HEALTH engaging and I truly appreciate your interest and readership!

This article was published on Highlight HEALTH.

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Happy Open Access Day: Back to Genome Biology for Me [The Tree of Life]

Posted: 14 Oct 2008 03:03 AM CDT

Well, good timing on this one. A new paper from Martin Wu in my lab has recently been accepted to Genome Biology and the provisional PDF was posted online 10/13. The paper ( A simple, fast, and accurate method of phylogenomic inference ) describes a new program Martin wrote called AMPHORA and shows how it can be used to build phylogenetic trees based on concatenated alignments of housekeeping proteins and also for metagenomic phylotyping using a diversity of protein markers. As today is Open Access Day I thought I would just put in a plug for this OA paper and thank Martin for his great work and commitment to Open Access.

I should note - I really really like Genome Biology as a journal - even though they have been rejecting many of my papers lately (or maybe in part because of this). I am really glad this one got in there. I published my first fully OA paper in Genome Biology in 2000 (on symmetric genome inversions in bacteria and archaea -- a paper co-authored with Steven Salzberg, Owen White and John Heidelberg - see Evidence for symmetric chromosomal inversions around the replication origin in bacteria). It is one of my favorite papers from my entire career, as in it we report on a pattern that turns out to appear to be one of the few rules of bacterial and archaeal genome evolution. Anyway - glad to be back in Genome Biology.

Open Access Day: Video of a Talk I Gave About OA [The Tree of Life]

Posted: 14 Oct 2008 02:30 AM CDT

Well, I was going to write all this blather about OA. But I realized it would be easier to share a video of a talk I gave at U. Washington on Open Access as part of their Biomedical Research Integrity Series (U. Washington Program). I cannot figure out how to download/embed the video so instead I am just posting the links. If someone has software for downloading it and wants to help me embed it and/or upload to YouTube and SciVee that would be great ((NOTE - VIDEO IS NOW EMBEDDED BELOW THANKS TO FRANCOIS MICHONNEAU) . Here are the links:

Lecture #2, Responsible Authorship:

Thursday, August 7, 2008; Speaker: Jonathan Eisen, Ph.D., "Responsible Authorship and the Ownership of Scientific Knowledge: Thoughts on Open Access Publishing"
To view the lecture, click here: Flash Player version, Windows Media Player version, or QuickTime Player version (for QuickTime players you may have to open the player and paste the url: rtsp://media.depts.washington.edu/uwbri/BRI_Eisen_2008.mov)

Open Access Day: Thanks to OA Journals Staff [The Tree of Life]

Posted: 14 Oct 2008 02:10 AM CDT

Well, today is a big day for Open Access, as it is, well, Open Access Day. And one thing I really wanted to put out there is that I think we all should say a big thanks to all of those who have worked tirelessly at various OA journals to help move OA into the mainstream and to produce a vast collection of fully open biomedical and scientific literature.

As I am involved in PLoS journals in many ways, I want to thank all of the staff who work behind (and sometimes in front) of the scenes there. There is a relatively full list of these people here. And I am publishing that list here too, with, along with a heartfelt thank you. Thank you. You all rock. And we should also thank all the staff at other OA Publishers (e.g., BMC). You rock too.

PLoS Staff

Finance/Administration Team

Strategic Alliances/Development

IT/Web Team

Publishing Teams

Marketing Team

Production Team

PLoS Biology Team

PLoS Medicine Team

PLoS Community Journals Team


Open Access Day [The Tree of Life]

Posted: 14 Oct 2008 02:01 AM CDT

Today is Open Access Day.  For more information see here.  It is a big celebration of, well, Open Access to scientific and medical literature.

We are going to have a little shindig at Davis (organized by a grad. student Collin Ellis who is also starting a new organization here on Campus - the UCD-SSOA (Society of Scientists for Open Access).  The shindig will include a live WebCast of OA Day presentations by Richard Roberts (who has one of them Nobel Prize thingies) and Phil Bourne (Editor in Chief of PLoS Computational Biology, and creative mind behind a ton of OA initiatives).  The meeting will be in the Genome Center, GBSF 4202.  FIrst showing of the webcast at 4.  Second showing at 7.  In between I will give a little talk on "Why Open Access is Good for Scientists and the World".

Hope others will enjoy the day too.  More later ...

Open Access and me [business|bytes|genes|molecules]

Posted: 13 Oct 2008 11:20 PM CDT

So today is Open Access day. I am writing this late in the evening, following a busy day at work and away from the computer.

Writing this as late as I am, there have been some great posts already, none better than that by Neil. Tough to add to what he wrote.

Open Access has taken a special meaning for me as I have moved away from science. I come from a heritage where the favorite journals included journals by the ACS, an organization that has come to epitomize closed access to me. Back in the day, sitting in universities with free access to papers and journals, that journal access wasn’t democratic never really registered. Then I started working in industry, at a startup, and suddenly you had to be careful about which journals you could subscribe to as a company. As I moved further and further away from hands on science, at the same time becoming even more interested in disparate fields, access to a variety of journals became more important, and more difficult.

That’s when it really dawned on me. Just like the availability of data sets has always been a big deal, the availability of published content and perhaps even more importantly the data contained within was critical for the practice and understanding of science. Anything other than that was not science. Everyone should have access to the same scientific information (what that information should be is the subject of another post). It’s not even about who pays for it. It is science, and as such belongs to everyone.

Perform your Civic Duty [Bayblab]

Posted: 13 Oct 2008 11:09 PM CDT

It's election day today in Canada but I'm not going to use this space to try to sell a particular party, just emphasize the importance of exercising your democratic right to vote.

First, take a look at some numbers [source]: In the past 4 general federal elections (1997-2006), the average voter turn-out was 63.4%. That means in the past decade, an average of 36.6% of registered voters stayed home. In the last federal election (January 2006), the Conservative Party formed a minority government with 36.3% of the vote - this is actually only 23.3% of registered voters. Who says your vote can't make a difference?

Many people, unfortunately, feel that way and our first-past-the-post system doesn't do much to discourage vote swapping, strategic voting and feelings of disenfranchisment. The Elections Canada website has a page explaining the importance of voting. It highlights the importance of democracy and the legitimacy of governments. Others will argue that if you don't vote you don't have a right to complain about the government. There are also more tangible reasons to vote. Political parties and individual candidates receive money depending on the vote. Any party that receives 2% or more of the national vote gets about $1.75 per vote from the federal government - this was a major breakthrough for the Green party last year. On top of that, candidates who earn more than 10% of the vote in their riding have 60% of their campaign expenses reimbursed. So even if your preferred candidate doesn't win, your vote is like a political donation for to help your candidate or party win a future campaign.

Another thing that tends to get forgotten is that the election doesn't just decide who will become prime minister - unless you live in particular ridings, you won't even see a leader's name on the ballot - but also for who is going to represent your local interests at the federal level. Harper, Dion et al. may have many people apathetic about federal politics, so you can instead focus on who will fight harder for money to come to your area for public transit or building projects, etc. (or who will fight against them if that happens to be your fancy).

Or, if you really feel like your vote doesn't count, opt for a party that will move on electoral reform. But a guaranteed way to ensure your vote doesn't count is to choose not to cast it.

Body’s anti-HIV drug explained [Think Gene]

Posted: 13 Oct 2008 10:42 PM CDT

Josh: I wrote about this same enzyme earlier in the year, but this is a new paper on it. The earlier study reported the NMR structure of the enzyme, but this study focused on the X-ray crystal structure. The authors note “In the X-ray structure, these APOBEC3G active-site loops [that are directly involved in substrate binding] form a continuous 'substrate groove' around the active centre. The orientation of this putative substrate groove differs markedly (by 90 degrees) from the groove predicted by the NMR structure”.

Humans have a built-in weapon against HIV, but until recently no one knew how to unlock its potential.

A study published online by the journal Nature reveals the atomic structure of this weapon – an enzyme known as APOBEC-3G – and suggests new directions for drug development.

APOBEC-3G is present in every human cell. It is capable of stopping HIV at the first step of replication, when the retrovirus transcribes its RNA into viral DNA.

The study’s authors, led by Xiaojiang Chen of the University of Southern California, were able to show the atomic structure of the active portion of APOBEC-3G.

The discovery suggests how and where the enzyme binds to the viral DNA, mutating and destroying it.

“We understand how this enzyme can interact with DNA,” said Chen, a professor of molecular and computational biology at USC. “This understanding provides a platform for designing anti-HIV drugs.”

If APOBEC-3G works so well, why do people get AIDS? Because the HIV virus has evolved to encode the protein Vif, known as a “virulence factor,” that blocks APOBEC-3G.

With APOBEC-3G out of the way, the RNA of the HIV virus can be successfully transcribed to viral DNA, an essential step for infection and for producing many more HIV viruses.

Chen said his group’s research offers important clues on where Vif binds to APOBEC-3G. The knowledge could be used to design drugs that would prevent Vif from binding and allow APOBEC-3G to do its job, Chen said.

That would unlock humans’ innate ability to fight HIV.

“We were born with it, and it’s there waiting,” Chen said.

In addition to fighting HIV, APOBEC-3G can inhibit the Hepatitis B virus. Other members of the APOBEC family serve important roles in antibody maturation, fat metabolism and heart development.

Mapping the structure of APOBEC-3G at the atomic level is a goal that “has been sought after worldwide because of its significance,” Chen said.

Source: University of Southern California

Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications. Lauren G. Holden, Courtney Prochnow, Y. Paul Chang, Ronda Bransteitter, Linda Chelico, Udayaditya Sen, Raymond C. Stevens, Myron F. Goodman & Xiaojiang S. Chen. Nature. Advance online publication. 12 October 2008

You Can Still Win a Nobel Prize Even When You Engage With The Public [adaptivecomplexity's column]

Posted: 13 Oct 2008 08:26 PM CDT

Whatever your political views, this is an example to follow:

Ezra Klein on Paul Krugman:


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