2012 “Biology of Genomes” in 140 ch@r@cters

Posted on May 25, 2012 by Hema Bashyam

CSHL’s annual “The Biology of Genomes” meeting, held May 8-12 this year, has come to be known as the yearly shindig for researchers working in the vast and rapidly growing field of genomics. Named one of the top scientific conferences based on many criteria such as the quality of speakers, networking opportunities, etc., the meeting is over-subscribed every year and this year was no different.

Credits: Duffy@CSHL

Reflecting the democratic, (relatively) open nature of science, most of their speakers made their talks “tweetable.” So for those unable to attend, the next best alternative to being here on CSHL’s lovely campus was to follow the conversation on Twitter using the rather unfelicitous hashtag #bog12. The tweets are a great mix of research talking points, the “seen and heard” buzz during break times, and general observations about presentations.

Fair warning for those who want to catch up now: It might take a while to get through the tweets—all 2021 of them—in one go!

But if genomics in 140 characters won’t do, here are some links to news summaries of various talks: Continue reading →

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Spreading science through the community

Posted on April 25, 2012 by Hema Bashyam

Pollen is not the only thing spreading around the north shore of Long Island this spring. Science is too, courtesy of a trio of researchers from CSHL who infused scientific flavor into two community events this month.

CSHL geneticist Rob Martienssen and neuroscientist Anne Churchland were on hand at Huntington’s Cinema Arts Center recently to offer moviegoers some insights on the science of addiction before settling down for a screening of “Trainspotting,” the classic cult hit about a group of heroin addicts set in Edinburgh in the 1980s.

This science-and-cinema pairing was one of several similar events taking place at theaters around the country as part of a popular program, Science on Screen. (The next event on May 3 pairs a particle physicist from Brookhaven National Laboratory with the time travel movie “12 Monkeys.”) The program aims to provide the “perfect combination of entertainment and enlightenment” by inviting renowned experts from the scientific and medical world to use movies as anchor points to introduce the public to a scientific topic and the latest advances in related research.

Churchland, who studies the neural circuitry of decision-making, took moviegoers on a tour through the brain’s so-called “pleasure circuit,” the network of neurons that ensures that we repeat life-sustaining activities by associating those activities with pleasure and reward.

Most drugs, including heroin—the villain in “Trainspotting”—overstimulate the brain’s reward system by flooding the circuit with dopamine, a chemical neurotransmitter that facilitates communication between neurons. Churchland drew on the movie’s plot to highlight various aspects of drug addiction, such as the mechanistic basis of relapse and the tendency to co-abuse another stimulant, such as alcohol. Read Churchland’s take on the science of Trainspotting here.  Continue reading →

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Alea Mills explains mouse modeling at the Secret Science Club

Posted on April 3, 2012 by Hema Bashyam

A rapt audience of more than 450 New Yorkers gathered at the Secret Science Club in Brooklyn on one unseasonably balmy night in mid-March to listen to tales of gene hunting expeditions by CSHL Professor Alea Mills. She is an expert in chromosome engineering, a technique for developing mouse models of human disease that can help pinpoint key genes and mechanisms.

Dr. Alea Mills

Mills has successfully used this technique to uncover two powerful cancer-related genes: p63, which plays a role in development, aging and suppressing tumor formation; and CHD5, a long-elusive tumor suppressor that is now known to be mutated or deleted in multiple types of cancer.

Mills recently used chromosome engineering to develop a new mouse model of autism that provided the first functional evidence of autism’s genetic basis, showing that the deletion of a 27-gene cluster on chromosome 16 leads to the development of autism-like features in mice. The mice, whose behavior has been documented and analyzed using state-of-the-art video capture, will be invaluable for identifying new diagnostic methods for autism before it becomes a full-blown syndrome as well as for designing clinical interventions. Mills explains all these advances and more in the lecture titled, ”Where will the future of genetic engineering take us?”

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Double duty: How an anti-cancer protein guards neurons against death after stroke

Posted on February 28, 2012 by Hema Bashyam

Cancer biologists know the PTEN gene as a powerful tumor suppressor and one that is among the most commonly deleted genes in human cancer. For more than a decade, CSHL’s Dr. Lloyd Trotman has studied the role of PTEN in cancer, developing many of the animal models that have delivered key insights into how its loss triggers tumor growth.

His relationship with PTEN took an entirely new direction recently, when his team at CSHL and collaborators led by Dr. Seong-Seng Tan at the Florey Neuroscience Institutes in Australia discovered a new role for the PTEN protein in the brain, one that could potentially be exploited in designing a therapy for stroke.

Staining of coronal brain slices from mice that have suffered stroke shows an injured area in the top right corner (white area).

When a stroke cuts off blood supply to a brain region, the neurons in that region are in danger of perishing due to the resulting drop in the levels of oxygen and essential nutrients. Trotman and the other researchers have discovered how modulation of PTEN function, via a change in the protein’s cellular location within neurons, aids their survival in this situation.

Trotman’s collaborators were interested in understanding the genetics of stroke and finding genes that are important in repairing damage and boosting neuronal survival. While investigating genetic activity within the affected brain areas of mice that had undergone stroke, the team found two genes that seem to be regulated by ischemia – the loss in blood supply that causes stroke. Continue reading →

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Splicing studies detail a protein’s role in creating cancer’s mixed messages

Posted on February 13, 2012 by Hema Bashyam

Cancer cells are a hotbed of mixed or incorrect molecular “messages” – a result of defects in a cellular mechanism called RNA splicing. When a cell’s DNA is copied into an intermediary molecule called RNA, splicing is the editing step that removes unwanted bits of the RNA message while pasting the rest, called exons, together. The edited message, or messenger RNA, is then translated into protein.

Much of the time though, some of the exons get left out or spliced back together in alternative ways. The resulting message, called a splice variant, produces a different protein. CSHL Professor and splicing expert Adrian Krainer explains this editing variation, called alternative splicing, and its consequences in the short video below.

Credit: www.Learnaboutsma.org

Continue reading →

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To celebrate 40th anniversary, the Protein Data Bank returns to its birthplace

Posted on November 10, 2011 by Hema Bashyam

Databases can have birthdays and anniversaries too. The Protein Data Bank (PDB)—a gigantic repository that allows anyone with an internet connection to view the atomic structures of more than 77,000 biological molecules in all their three dimensional glory—just celebrated its 40th anniversary.

At the PDB40 anniversary, scientists presented and discussed their vision for PDB80

The occasion was marked by a special symposium at the end of October at Cold Spring Harbor Laboratory, where a meeting held 40 years ago sparked the discussions that gave birth to the PDB.

By 1971, the structures of about a dozen proteins had been “solved.” Because a protein’s function depends on its ability to coil into a specific three-dimensional shape, structural biologists had begun to chart the precise architectural coordinates of every atom within a protein (or a nucleic acid) to learn how these molecules work and how alterations in their structure can affect their function.

As recounted in this historical perspective on the PDB, scientists at the time were keeping track of structural coordinates using a system that seems unimaginably complicated and labor-intensive when viewed from the fast-moving front of the cloud computing, internet era. In this system, each atom in a protein was represented by a punched card. So if one lab wanted to send structural information about a protein such as hemoglobin to another lab, this could mean a transfer of more than 1000 cards. Continue reading →

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High School Science Clubs: The kids are all right

Posted on October 17, 2011 by Dagnia Zeidlickis

I recently had the chance to ask twenty 9th and 10th graders at Flushing International High School why they participate in an after-school science club. “Is it because you want to be scientists when you grow up?” I asked. The collective answer was “No.” Surprised? I was. And what surprised me was how sophisticated their motivation for learning about science was:

To be able to help solve the world’s problems.

To be able to solve any problem using scientific thinking.

To understand the way things work.

To understand their own health issues and the way their own bodies work.

The only anticipated response that I got was: To help me get into college. Continue reading →

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CSHL research takes center stage at the Secret Science Club

Posted on September 21, 2011 by Hema Bashyam

Like most scientists, HHMI-GBMF Investigator and CSHL Professor Rob Martienssen is used to giving lectures in darkened, cavernous auditoriums with plush seating where the audience holds its applause until after his talk. So it was quite the surprise when he strode out on to the podium during his latest lecture at a venue in Brooklyn, NY and was greeted like a rock star by a lively, enthusiastic audience.

Dr. Rob Martienssen

Of the 300-something people packed into the room, the lucky majority sat atop foldable chairs. The rest camped out on the floor or stood three deep around the room. Some even perched on the open bar that nestled against one wall and served, among other things, a cocktail called “Planter’s punch” in honor of Dr. Martienssen’s talk on plant genetics. Welcome to the Secret Science Club!

Billed as “a science lecture, arts, and performance series,” the Club is based at the Bell House, a Brooklyn bar that is as renowned for its mixology as it is for its performance calendar, which regularly features up-and-coming indie bands or the hottest one-person shows. The Secret Science series, which just celebrated its fifth anniversary, features a science-related event once or so a month at 8pm on a Wednesday. “There’s no cover charge. Just bring your smart self,” say the Club’s organizers, and the audience does, packing the space to the rafters and lingering late into the night to discuss and debate. Continue reading →

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Better science through volleyball

Posted on September 12, 2011 by Jessica Giordano

Volleyball is serious business at Cold Spring Harbor Laboratory. The campus league is currently holding playoffs for its 21st season and is more popular than ever with close to 200 scientists and staff members taking part.

volleyballMichael Cressy, who recently completed his Ph.D. dissertation in Dr. Josh Dubnau’s laboratory, joined the league his first summer here. He cites the on-court interactions between senior faculty, grad students and other staff as a major plus for those who play, and helps foster scientific collaboration. CSHL Professor Adrian Krainer agrees, saying “People get to know each other across buildings and laboratories who otherwise might not even meet.” Dr. Krainer’s own laboratory includes members of multiple teams in the league, so volleyball chatter is a frequent occurrence in the summers.

Tiernan cup

The Tiernan Cup - the volleyball league's championship trophy

With 19 teams, there is a volleyball home for everyone who wants to play. The league includes more casual teams just looking to get a game in and have fun. But it also has a few all-star sides who are rumored to recruit, hold practice outside of scheduled games, and battle to win the league’s championship trophy and the year’s worth of bragging rights that go with it.

No matter the competitive focus, all agree that the league is a big part of campus life each summer. Recognizing its importance, the Laboratory’s leadership built official sand courts in 1997. Volleyball also plays a central role in the culmination of the laboratory’s Undergraduate Research Program – CSHL’s summer program for college students from around the world who live on campus and work with senior Laboratory staff members on independent research projects.

The URP vs. faculty game was even featured in this recent segment on MyLITV.com.

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CSHL scientist takes the plunge in support of cancer research

Posted on August 29, 2011 by Hema Bashyam

The non-profit organization, Swim Across America (SAA), raises funds for cancer research by conducting pool and open water swims across the country. A Long Island-based activity that has gained immense popularity over the last few years is the “Sound to Cove” swim, a ½ mile, 1 mile, 5K, or 10K swim in Long Island Sound finishing on the beach at beautiful Morgan Park in the City of Glen Cove. To date, the 2011 Sound to the Cove event has raised over $320,000 for cancer research, prevention and treatment.

Dr. Raffaella Sordella prepares for her "Sound to the Cove" swim on August 13, 2011.

Since 2009, the laboratory of CSHL Assistant Professor Raffaella Sordella has been one of the beneficiaries of the funds raised by SAA. She has put her share to good use — to find therapies that will improve the treatment outcomes of patients with lung cancer. On a gorgeous Saturday morning in mid-August, Dr. Sordella took a break from lab work, donned her swim cap and goggles, and dived into Long Island Sound along with 200 other swimmers to complete a 1 mile swim. She wanted to do her part in helping raise the funds that she and her colleagues benefit from.

“The support that my lab has received from SAA has been critical in helping us pursue novel ideas and make important discoveries about how non-small cell lung cancer becomes resistant to current therapies,” Dr. Sordella commented after her swim. “I thought joining the community of supporters in their efforts would be a nice way of thanking them for their drive and commitment.”

Continue reading →

Posted in Cancer, Disease research, Faculty & Friends | Tagged , | 1 Comment