all Department of Systems Biology stories

Massachusetts Lt. Governor tours Harvard research facilities

404132862 — Fri, 26 Jun 2009 13:43:08 -0400

Massachusetts Lt. Governor Timothy Murray on Wednesday toured Harvard labs in both Cambridge and Boston.

"The Patrick Administration has been very supportive of the university research sector in Massachusetts and we welcomed the opportunity to show him the range of projects ongoing at Harvard, in both Cambridge and Longwood, that are cutting-edge, multidisciplinary and often involve collaboration with partners from other institutions, including the University of Massachusetts, and industry," Casey said.

John P. Holdren named President-elect Obama’s Science Advisor

404132862 — Fri, 19 Dec 2008 12:13:59 -0500

President-elect Barack Obama today announced that he has selected Harvard’s John P. Holdren to serve as Assistant to the President for Science and Technology in the new administration. The post, popularly known as “the President’s science advisor,” also includes directorship of the Office of Science and Technology Policy in the Executive Office of the President and requires Senate confirmation.

Scientists synthesize memory in yeast cells

404132862 — Sun, 16 Sep 2007 15:03:55 -0400

Harvard Medical School (HMS) researchers have successfully synthesized a DNA-based memory loop in yeast cells, an experiment that marks a significant step forward in the emerging field of synthetic biology.

After constructing genes from random bits of DNA, researchers in the lab of Pamela Silver, a faculty member in Harvard Medical School’s Department of Systems Biology, not only reconstructed the dynamics of memory, but also created a mathematical model that predicted how such a memory “device” might work.

Radhika Nagpal nets prestigious NSF award for up-and-coming researchers

50443248 — Tue, 02 Oct 2007 15:28:44 -0400

Radhika Nagpal, assistant professor of computer science in Harvard’s School of Engineering and Applied Sciences (SEAS), has won a Faculty Early Career Development Award from the National Science Foundation (NSF). The honor is considered one of the most prestigious for up-and-coming researchers in science and engineering.

Nagpal, whose work bridges computer science and biology, plans to use the $400,000 award (paid over five years) to further her research on self-organizing systems. In particular, she is interested in learning how to better engineer self-organizing, self-repairing distributing computing systems. She also wants to gain a fuller understanding of robust collective behavior in biological systems.

Proteasome recognized as nuclear player on gene-transcription team

70652986 — Mon, 26 Mar 2007 06:26:37 -0400

One of the most common agents in the cytoplasm of the cell, the proteasome, also plays a widespread and critical role in transcription from inside the cell nucleus.

Pam Silver, Kathryn Auld, and their colleagues report in the March 17, 2006 Molecular Cell that the proteasome binds and critically regulates the transcription of some of the most highly expressed and important genes in the yeast genome, including those involved in lipid metabolism, mating behavior, and the making of ribosomal proteins.

"We found the proteasome to be very important in so many roles in yeast transcription that I cannot imagine it is not important in other organisms," Auld said.

Dog genome unleashed

70652986 — Mon, 26 Mar 2007 06:23:31 -0400

An international research team led by scientists at the Broad Institute of MIT and Harvard has decoded the DNA of the domestic dog and pinpointed millions of genetic differences that distinguish dog breeds. The study also includes the first comparative analysis to encompass three distinct mammalian genomes, revealing important DNA elements common among them. Such shared genetic signatures offer crucial insights into genome organization and function, particularly in humans. Their efforts, described in the Dec. 8, 2005 issue of Nature, shed light on the genetic similarities between dogs and humans as well as the genetic differences between dog breeds, and may guide future discoveries that improve the health of both species.

"Of the more than 5,500 mammals living today, dogs are arguably the most remarkable," said senior author Eric Lander, director of the Broad Institute, professor of biology at MIT and of systems biology at Harvard Medical School, and a member of the Whitehead Institute for Biomedical Research. "The incredible physical and behavioral diversity of dogs - from chihuahuas to great danes - is encoded in their genomes. It can uniquely help us understand embryonic development, neurobiology, human disease and the basis of evolution."

More than two years ago, the Nature paper's authors embarked on a mission to assemble a complete map of the dog genome. In the first phase of the project they obtained high-quality DNA sequence from a female boxer named "Tasha," covering nearly 99 percent of the dog's genome. Because dogs sit at a key branch point in the evolutionary tree relative to humans, the dog genome sequence enabled researchers to make novel observations regarding the genetic similarities among mammals.

Chimp genome effort shines light on human evolution

70652986 — Mon, 26 Mar 2007 06:21:59 -0400

A research effort, led by scientists at the Broad Institute of MIT and Harvard, the Washington University School of Medicine in St. Louis, and the University of Washington, Seattle, focused on the chimpanzee in hopes that genetic comparisons with humanity's closest relative will lead to answers to both practical questions - such as the causes of human disease - and to more fundamental questions on human biology.

In addition to their obvious physical differences, humans and chimpanzees have different responses to Alzheimer's disease, malaria, and HIV/AIDS, for example.

"We're focusing on the differences as a way to shed light on ourselves," said Eric Lander, Broad Institute director and professor of systems biology at Harvard Medical School, who led the project along with Richard Wilson of the Washington University School of Medicine in St. Louis and Robert Waterston of the University of Washington, Seattle. "This is a case where evolutionary analysis is a direct handmaiden to biomedicine."

Among the 3 billion base pairs in the DNA of both humans and chimpanzees, researchers found differences in 40 million sites. It is in those sites where the differences between the two species lie.

Functional protein changes caught and quantified

70652986 — Mon, 26 Mar 2007 06:17:58 -0400

Just knowing that a protein is expressed in a cell does not reveal what it is up to; increasingly, the chemical modifications it undergoes are the key to understanding its function at any given time. A study from the laboratory of Steven Gygi, Harvard Medical School assistant professor of cell biology, uses one of the most powerful tools of proteomics, mass spectrometry, to pinpoint the dynamics of a common alteration in cells: protein phosphorylation, or the addition of phosphate groups. In order to track the changes, Gygi's team bathed cells in a brew that contained two amino acids made from the stable isotope carbon-13 instead of standard carbon-12. Proteins in these cells were slightly heavier, so they could be distinguished from normal proteins in a mass spectrometer.

Method automates capture of cell image data

70652986 — Mon, 26 Mar 2007 05:36:38 -0400

A new type of drug profiling will be useful in identifying the biological targets of experimental compounds and predicting drug toxicity. "This work brings microscopy into the 'omics' era," said Timothy Mitchison, the Hasib Sabbagh professor of systems biology, codirector of the Harvard Medical School Institute of Chemistry and Cell Biology (ICCB) and co-author on the work, which was reported in the Nov. 12, 2004 Science. In the study, the researchers treated human cancer cells with widely varying concentrations of 100 different chemical compounds known to affect cell growth and metabolism. To measure changes in the cells' behavior, they used fluorescent stains for DNA and 10 different proteins.

Study yields insights into precancerous condition

70652986 — Mon, 26 Mar 2007 07:10:18 -0400

Caused by a mutation that inactivates the tumor suppressor gene LKB1, PJS causes gastrointestinal polyps that have a 30 to 50 percent chance of becoming cancerous, says senior author Lewis Cantley, PhD, chief of the Division of Signal Transduction at Beth Israel Deaconess Medical Center (BIDMC) and a member of the Department of Systems Biology at Harvard Medical School.

Research conducted by Cantley's laboratory on two other genetic conditions with symptoms similar to PJS had found that the diseases involved defects in the regulation of a protein called mTOR, so the researchers decided to look for a link between LKB1 and mTOR.

As predicted, they found that mouse cells lacking LKB1 and cells from PJS mouse polyps showed the activation of molecules known to be downstream of the mTOR protein.

"We knew that the drug rapamycin [commonly used to prevent newly transplanted organs from being rejected] could block mTOR," says Cantley. "These new results suggest that the use of mTOR inhibitors, including rapamycin analogs currently being tested in clinical trials for the treatment of cancers and tuberous sclerosis, may be useful for the treatment of polyps arising in PJS patients, and possibly in other tumors that result from the sporadic loss of LKB1."

Climate, asthma connected, according to research

70652986 — Mon, 26 Mar 2007 05:30:54 -0400

Christine Rogers, a research associate at the Harvard School of Public Health, measures particulates - pollen grains and fungal spores - in outdoor air and correlates levels with asthma events. She also examines how those particulate levels might change over time because of global warming. "One of the most predictable effects of global warming is that CO2 is going to increase," she says. "But also, seasonality is going to change. Springs will come earlier, lengthening our growing seasons. Both of these trends affect plants' biomass, making them larger at maturity and, logically, able to produce more pollen." To measure the effects of global warming on pollen production, Rogers and her colleagues forced ragweed plants to germinate two and four weeks earlier than they normally would, simulating the early springs that are likely to become more frequent. Half of each plant group was exposed to the normal, ambient CO2 level of 350 parts per million, and the other half to double that amount. Rogers found that total pollen production under ambient CO2 was higher in the plants grown in early spring than in those grown later. At high CO2 levels, however, plants grown later had higher total pollen production than those at ambient CO2.