ncRNA portal

Science Magazine is hosting a webinar on non-coding RNAs (ncRNA) on Wednesday, October 22. Here’s the invitation:

Noncoding RNAs WEBINAR

You are invited to join our panel of experts on Wednesday, 22 October 2008, for a live, online educational seminar, “Noncoding RNAs: A New Paradigm for Gene Regulation.”

Submit your questions LIVE to the experts during the webinar!

Date: Wednesday, October 22, 2008
Time: 12:00 noon ET; 9:00 a.m. PT; 4:00 p.m. GMT
Duration: 1 hour

Register now! For more information and complimentary registration visit:

www.sciencemag.org/webinar

Noncoding RNAs (ncRNAs) are a large group of RNAs that are transcribed, but not translated into protein. They include well-characterized transfer RNAs and ribosomal RNAs, as well as newer and more elusive miRNAs which have been shown to play a crucial role in gene regulation. ncRNAs produce functional RNA molecules rather than encoding proteins and have been found to have roles in a plethora of cellular processes including transcriptional regulation, RNA processing and modification, mRNA stability, and even protein degradation. Even though a large number of genomes have been sequenced, the number and diversity of ncRNA-encoding genes is largely unknown.

Many more ncRNAs have been discovered than were predicted, with recent transcriptomic and microarray studies suggesting that, for the mouse genome alone, there exist more than 30,000 long ncRNAs. The challenge now facing researchers is to determine the size of the full complement of ncRNAs, as well as elucidate their function, particularly in disease. This online discussion will center on the different forms of ncRNAs, and the roles they may play in the biology and pathology of human disease.

During this webinar, the expert panel will:
• Provide a general introduction to the different types of ncRNAs
• Discuss how technologies for detecting and characterizing ncRNAs can be applied in disease research
• Share data on recent ncRNA studies
• Answer your questions live!

Participants:

George Calin, M.D./Ph.D.
Department of Experimental Therapeutics
The University of Texas M. D. Anderson Cancer Center
Houston, TX

Joshua Mendell, M.D./Ph.D.
Institute of Genetic Medicine
Johns Hopkins University
Baltimore, MD

REGISTER NOW AT: www.sciencemag.org/webinar

Nature offers a technology feature on Metabolomics this week.

Metabolomics is the “systematic study of the unique chemical fingerprints that specific cellular processes leave behind” - specifically, the study of their small-molecule metabolite profiles. The metabolome represents the collection of all metabolites in a biological organism, which are the end products of its gene expression. Thus, while mRNA gene expression data and proteomic analyses do not tell the whole story of what might be happening in a cell, metabolic profiling can give an instantaneous snapshot of the physiology of that cell. One of the challenges of systems biology is to integrate proteomic, transcriptomic, and metabolomic information to give a more complete picture of living organisms. (Thanks, Wikipedia!)

Metabolomics: Biochemistry’s new look p697

Until now, metabolomics researchers have had to adapt technology developed mainly for proteomics. But there are now solutions designed with them in mind. Nathan Blow reports.

Nathan Blow - doi:10.1038/455697a
Full Text | PDF (638K)
See also: Editor’s summary

Metabolomics: Dark matter p698

doi:10.1038/455698a
Full Text | PDF (149K)

Metabolomics: Wine-omics p699

doi:10.1038/455699a
Full Text | PDF (210K)

Metabolomics: Table of suppliers p701

doi:10.1038/455701a
Full Text | PDF (53K)

Further reading:

• B. Daviss, “Growing pains for metabolomics,” The Scientist, 19[8]:25-28, April 25, 2005
• Metabolomics
• The Human Metabolomics Project website
• The Metabolomics Society website

Piled Higher and Deeper (PhD) is usually right on the money (pun intended) and yesterday’s comic was no different:

Creator of the NIH Roadmap for Medical Research and the Clinical and Translational Science Awards will leave the NIH at the end of October

Departure Memo:

From: Zerhouni, Elias (NIH) [E]
Sent: Wednesday, September 24, 2008 10:33 AM

Dear Friends and Colleagues:

For over six years, I have had the privilege of leading one of the greatest institutions in the world, the National Institutes of Health, the “Nation’s Medical Research Agency.” I have decided, however, that it is time for me to turn my attention to new opportunities, including several writing projects.

NIH is one of the true “wonders of the world,” and its strength comes from you, our scientists, administrators, staff, contractors, and trainees. As NIH Director, I have had the unparalleled privilege of working with the most extraordinary staff in the world, each one of you dedicated to a great, single mission: improving the nation’s health. Every one of you has played an integral part in our ability as an agency to build upon an outstanding record of achievement while creating new inroads that will continue to pay off for years to come. I want to express my sincere thanks for your support and your spirit of commitment, cooperation, and resourcefulness during my term as NIH director. It has made all the difference during my time here.

I admire your unparalleled dedication to advancing innovative research, fostering scientific collaboration, and enhancing basic and clinical research for the benefit of people everywhere. I feel a special debt to the people I have worked with most closely-the Institute and Center Directors and my staff in the Office of the Director.

To everyone at NIH, thank you for your support. Together, we are experiencing a true revolution in the biomedical sciences, one that continues to have broad and profound implications for human health. I am extremely fortunate to have led the agency that has been at the center of this revolution, and an agency that met every challenge put to it as a result of that revolution.

I will be leaving NIH by the end of October, and Secretary Leavitt and I are working together to ensure an orderly transition in the weeks ahead. We will keep you informed of plans as they develop.

Elias A. Zerhouni, M.D.

Further reading:

• NY Times article: Federal Health Official to Step Down
• Scientific American: NIH director Zerhouni resigns

Good morning!

As you likely know, Washington University will host the Vice-Presidential debate on October 2. Senator Biden and Governor Palin will debate each other beginning at 8 p.m. (CDT) Oct. 2 in the Washington University in St. Louis Athletic Complex.

Last week, the Washington University newspaper, The Record, announced the following debate-related item:

Have an opinion about politics? Enter this contest

By Neil Schoenherr

Students are invited to show their creativity in this election season by entering the Make it Clear multimedia competition, a collaboration between the St. Louis Post-Dispatch and the Vice Presidential Debate Programming Committee.The Make It Clear competition is one of several activities planned as part of the I Vote event series, designed to engage the University community in the electoral process.

To enter, students should address the following prompt: “You have five minutes one-on-one with the next would-be president of the United States. Write, describe, express or otherwise show what you would say or what would transpire.”

Submissions are due by noon Oct. 1 and can be e-mailed to the Gephardt Institute for Public Service at gephardtinstitute@wustl.edu.

The competition is open to the community at large, too, and a number of finalists will be posted on the St. Louis Post-Dispatch Web site. The public then will be able to vote for their favorite entries.

Winners will be announced Oct. 12. The Vice Presidential Debate Program Planning Committee will award $100 each to the top two WUSTL students. Community members will receive recognition from the St. Louis Post-Dispatch.

The competition rules are:

• Refrain from using anything obscene or offensive;
• Do not exceed 500 words or five minutes of video. If a submission is a work of art or other visual piece, it must be reproduced or shown in a format that can be posted on the Internet;
• If utilizing music, images, etc., please note rules governing the use of copyrighted work.

For more information, e-mail Robin Hattori, program director of the Gephardt Institute for Public Service, at rhattori@wustl.edu.

In a previous post, I linked to Senator Obama’s answers to the 14 top science questions facing America. Earlier this week, John McCain released his responses, too. Check out Science Debate2008 website for a side-by-side comparison of each candidate’s answers to these critical issues facing our country.

For more information, please check out the following:

• AAAS - Science and Technology in the 2008 Presidential Election
• …and this handy-dandy comparison chart from AAAS

From a press release from the Lasker Foundation:

NEW YORK, Saturday, September 13, 2008 – The 2008 Albert Lasker Medical ResearchAwards were announced today. First presented in 1946, the Lasker Awards are the nation’s most distinguished honor for outstanding basic and clinical medical research discoveries and for lifetime contributions to medical science.

The Lasker Award for Basic Medical Research honors Victor R. Ambros, 54, of the University of Massachusetts Medical School, Worcester, David C. Baulcombe, 56, of the University of Cambridge, and Gary B. Ruvkun, 56, of Massachusetts General Hospital, Boston and Harvard Medical School, who discovered tiny RNAs that regulate gene function. These RNAs, some of which are known as microRNAs, govern a multitude of activities in animals and plants, and they have been implicated in a wide range of diseases.

The Lasker~DeBakey Award for Clinical Medical Research honors Akira Endo, 74, of Biopharm Research Laboratories, Inc., Tokyo, who discovered the first statin. Statins significantly lower LDL-cholesterol quantities in the blood, thus dramatically reducing the risk of coronary heart disease, a leading cause of death worldwide and the number one killer in the U.S. Statins are now the most widely prescribed medications in the United States, and benefit an estimated 30 million people worldwide.

The Lasker~Koshland Award for Special Achievement in Medical Science, awarded biennially, honors Stanley Falkow, 74, of the Stanford University School of Medicine, for his many contributions to our knowledge of disease-causing microbes. Falkow’s discoveries have shed light on how bacteria transmit antibiotic resistance and other traits to one another and revealed the means by which they infect animal hosts and elicit illness. He pioneered the field of molecular pathogenesis of infectious disease and trained an impressive number of leading investigators in this discipline.

The Awards will be presented at a luncheon ceremony on Friday, September 26th at the Pierre Hotel in New York City. The Honorable Michael Bloomberg, Mayor of the City of New York, will be the keynote speaker.

Dr. Joseph L. Goldstein, recipient of the 1985 Lasker Award for Basic Medical Research and the Nobel Prize in Medicine in 1985, chairs the 24-member international scientific jury that selects recipients of the Lasker Awards. He said that “the 2008 Lasker Awards honor investigators whose open-minded thinking and experimentation challenged conventional wisdom. Their work launched new fields of scientific research that have fostered significant advances in the medical arena.” The discovery of small regulatory ribonucleic acids (RNAs) by Victor Ambros, David Baulcombe, and Gary Ruvkun broke open an entire new field. Until that time, proteins, not RNAs, were thought to govern gene activity in animal cells. “No one imagined that such tiny RNAs could perform useful tasks. In fact, the notion that small RNAs could control gene expression was unheard of,” Goldstein said. “Now, laboratories all over the world study hundreds of these RNAs.” The tiny molecules control a vast number of genes in plants as well as animals, and play roles in human health and disease, including cancer, viral infections, and congestive heart failure.

Until Akira Endo, treatment for high LDL-cholesterol levels—the bad cholesterol—left much to be desired, a situation that resulted in an unacceptably high incidence of coronary heart disease and premature death. Dietary interventions and the few available drugs worked poorly and the medications came with unwanted side effects. Many scientists also worried that reducing cholesterol might be dangerous because the molecule carries out essential jobs in the cell. “Endo believed in the potential benefits of cholesterol-lowering drugs and toiled day and night for two years to find a compound, the first statin, with that effect,” Goldstein said. “Statins have prolonged countless lives and revolutionized the prevention and treatment of coronary heart disease.” Today, millions of people worldwide take statins to lower their LDL-cholesterol levels safely and markedly reduce their risk of heart attacks.

Early in his career, Falkow discerned that bacteria pass antibiotic resistance among one another on circular pieces of DNA—a finding that paved the way toward recombinant DNA technology. He then pioneered that new method to probe the molecular mechanisms by which bacteria invade their hosts, elude the immune system, and trigger disease. “Stanley Falkow has spent the last five decades delving into the workings of disease-causing microbes,” Goldstein said. “A legend in his own time, Falkow is regarded as one of the greatest microbe hunters ever and has trained more than 100 students, many of whom are making their own extraordinary contributions to the field of bacterial pathogenesis.”

This year marks the first presentation of the newly renamed Lasker~DeBakey and Lasker~Koshland Awards, honoring the late Michael DeBakey and Daniel Koshland, Jr. “We are proud to link the Lasker name with the names of these outstanding scientists and humanitarians, who dedicated their lives to medical science and human health and were lifelong supporters of the Lasker Foundation and the Lasker Awards,” said Dr. Maria C. Freire, President of the Albert and Mary Lasker Foundation.

The Lasker Awards are given by the Albert & Mary Lasker Foundation. Dr. Freire said that she and the Board of Directors are delighted at the recommendations of the Lasker Jury, and congratulates the winners of this year’s Awards. “They follow the tradition of prior laureates in their innovative scientific and medical research for the betterment of people worldwide.” The Albert and Mary Lasker Foundation

The Lasker Foundation fosters the prevention and treatment of disease and disabilities by honoring excellence in basic and clinical science, educating the public, and advocating for support of medical research. This year the Lasker Awards carry an honorarium of $300,000 for each Award category. The laureates will receive a citation highlighting their achievements and an inscribed statuette of the Winged Victory of Samothrace, the Lasker Foundation’s traditional symbol representing humanity’s victory over disease, disability, and death.

Lasker Awards often presage future recognition by the Nobel committee, so they have become popularly known as “America’s Nobels.” Seventy-five Lasker laureates have received the Nobel Prize, including 27 in the last two decades.

For more information, please read:

• Nature Medicine special focus issue on the awards
• the complete Press Release: 2008 Lasker Awards

Great news: we haven’t been swallowed up by a black hole today!

The Large Hadron Collider (LHC) is a giant particle accelerator built by the European Organization for Nuclear Research (CERN). The purpose of the LHC is to gain a better understanding of the relationship among fundamental forces (electromagnetism, the strong nuclear force, the weak nuclear force, and gravity). We may even even gain insight about the very origins of the universe itself. The first proton bean was circulated today and the first collision is scheduled for October 21, 2008.

Kate McAlpine’s rap about the LHC:

Excellent series of articles from Geoff Brumfiel in Nature:

• Voices from the collider: Nature talks to physicists about their hopes for the Large Hadron Collider.
• LHC switches on: Giant accelerator sees first beam circulate successfully.
• Physicists flock to Geneva: The start up of the world’s biggest particle collider lures researchers from around the world.
• LHC by the numbers: The largest particle accelerator in the world, which will feel its first full proton beams tomorrow, just oozes numerical hyperbole.

In-depth report on the LHC from Scientific American: Large Hadron Collider: Countdown and more recently: Large Hadron Collider (LHC) is live — and so are we

CERN resources:

• The safety of the LHC
• Facts and Figures
• Why the LHC?
• How the LHC works

PhD comics: Tales from the Road series at CERN:

• Tales from the Road - CERN, pt 1
• Tales from the Road - CERN, pt 2
• Tales from the Road - CERN, pt 3

Jonathan Eisen, professor at UC Davis and Academic Editor in Chief of PLoS, wrote an interesting entry in his blog: “Tracing the evolutionary history of Sarah Palin: links to a parasitic nematode and the pathogenic fungus Botryotinia fuckeliana“.

It is always fun to see unique application of sequence databases and tools. Dr. Eisen also mentioned looking for ELVIS in the protein sequence databases - an example I came across in some of my lectures when I was in grad school. Here’s another fun example, highlighted in NCBI educational materials.

It is interesting to see what one can do with these tools and databases! Does anyone have any other examples they’d like to share? Please let me know and I’ll be sure to share them on the blog.