Switches are a part of daily life, from snoozing your alarm, turning on the coffee maker, firing up your car engine, and so on until we turn off the lights at night. Researchers have now cataloged even more templates of possible switches within a living cell than we use throughout our day.Naren Ramakrishnan, associate professor of computer science at Virginia Tech, USA, and Upinder S. Bhalla, at the National Centre for Biological Sciences (NCBS), part of the Tata Institute of Fundamental Research in India, found that cells can make use of thousands of switches to support important biological functions.

Cells use switches for determining what kind of cell to become – skin or blood, for instance, in responding to stress, and in communication with other cells. “A switch is like a memory unit,” said Bhalla. “The state of the switch — whether it is on or off, is like a computer memory that can store a bit of 0 or 1. Although real biological switches are quite complex and regulated in many ways, we have shown the simplest possible ways in which switches could work”, Bhalla said.

The researchers report their work in the June 20 issue of the Public Library of Science (PLoS) Computational Biology, in the article “Memory Switches in Chemical Reaction Space.” Their collaboration began during a sabbatical visit by Ramakrishnan to NCBS in Bangalore, India. Ramakrishnan is a computer scientist whose expertise is in numerical simulation and data mining. Bhalla is a computational neuroscientist with broad interests in biochemical network modeling and simulation. They decided to use Virginia Tech’s System X supercomputer to search for the many ways in which cells can implement switches.

“Our exploration using System X is rather like how a tinkerer or a kid puts together things to see if they do something useful. We took a lot of ’spare parts’, each spare part being one chemical reaction, connected them together every which way, and we found that a surprising number of these artificially constructed networks actually were switches,” said Ramakrishnan.

“Popular opinion used to be that there are a small number of ways in which switches can be realized by biology, but we found thousands of switches in our search,” Ramakrishnan said.

The researchers report in PLoS Computational Biology, “We find nearly 4,500 reaction topologies, or about 10 percent of our tested configurations, that demonstrate switching behavior.”

Their research also led to a comprehensive “map” of biochemical switches. The map further revealed that most of the switches form a “family” – that is, the switches are all related to one another. “This has important implications since it suggests how evolution might stumble upon a switch rather easily.” Ramakrishnan said.

“Of course, there is more to cells than switches,” Bhalla said. “But switching and memory are the most basic behaviors possible. Armed with our catalog of switches, we can now proceed to investigate more interesting behaviors like complex information processing.”

As tumors progress they develop ways to escape recognition and attack by cells of the immune system. However, the mechanisms by which tumors modify the immune system have not been clearly determined. New insight into the way in which chronic lymphocytic leukemia (CLL) cells limit immune cell attack has now been provided by John Gribben and colleagues, at Barts and The London School of Medicine, United Kingdom.

For immune cells known as CD4+ and CD8+ T cells to become activated they must contact other cells known as APCs. The area of contact is known as the immunological synapse and it is highly organized. In the study, CD4+ and CD8+ T cells from patients with CLL were found to exhibit defective immunological synapse formation with APCs. Further, if CD4+ and CD8+ T cells from healthy individuals were cultured with CLL APCs, they also showed defective immunological synapse formation. As treatment with an immune system–modifying drug improved immunological synapse formation, the authors suggest that approaches to overcoming immunological synapse defects might improve the efficacy of new ways to treat cancer that are currently being developed and that are based on enhancing the antitumor activity of CD4+ and CD8+ T cells.

Researchers have uncovered details about how dietary restriction slows down aging. A team of University of Washington scientists have uncovered details about the mechanisms through which dietary restriction slows the aging process.  Working in yeast cells, the researchers have linked ribosomes, the protein-making factories in living cells, and Gcn4, a specialized protein that aids in the expression of genetic information, to the pathways related to dietary response and aging.  The study, which was led by UW faculty members Brian Kennedy and Matt Kaeberlein, appears in the April 18 issue of the journal Cell.

Previous research has shown that the lifespan-extending properties of dietary restriction are mediated in part by reduced signaling through TOR, an enzyme involved in many vital operations in a cell.  When an organism has less TOR signaling in response to dietary restriction, one side effect is that the organism also decreases the rate at which it makes new proteins, a process called translation.

In this project, the UW researchers studied many different strains of yeast cells that had lower protein production.  They found that mutations to the ribosome, the cell’s protein factory, sometimes led to increased life span.  Ribosomes are made up of two parts -the large and small subunits -and the researchers tried to isolate the life-span-related mutation to one of those parts.

“What we noticed right away was that the long-lived strains always had mutations in the large ribosomal subunit and never in the small subunit,” said the study’s lead author, Kristan Steffen, a graduate student in the UW Department of Biochemistry.

The researchers also tested a drug called diazaborine, which specifically interferes with synthesis of the ribosomes’ large subunits, but not small subunits, and found that treating cells with the drug made them live about 50 percent longer than untreated cells.  Using a series of genetic tests, the scientists then showed that depletion of the ribosomes’ large subunits was likely to be increasing life span by a mechanism related to dietary restriction -the TOR signaling pathway.

“We knew that dietary restriction decreased TOR signaling, and that decreased TOR signaling reduced translation or protein production, but this was the first direct evidence that all three were acting in the same genetic pathway,” said Kennedy, an associate professor of biochemistry.

“The big question then became what’s happening in these translation-deficient cells to slow aging,” added Kaeberlein, an assistant professor of pathology.  “That’s when Vivian MacKay, a co-author on the study, had the idea to look at Gcn4.”

Gcn4 is a specialized protein called a transcription factor, which helps transfer genetic information during cell growth.  The protein is activated when a cell is starving for amino acids.  What made Gcn4 interesting to the UW team was its unique mode of regulation.

“When ribosomes aren’t working at 100 percent capacity, most proteins are made less efficiently, but Gcn4 is different,” explained Dr. MacKay, a research professor of biochemistry.  “Sometimes, you actually get more Gcn4 produced even when everything else is going down.  That’s precisely what we found in the longer-lived yeast strains with mutations in the large subunit of the ribosome.”

To make the link between Gcn4 and longevity, the scientists then asked whether preventing the increase of Gcn4 would block life span extension.  In every case, cells lacking Gcn4 did not respond as strongly as Gcn4-positive cells.

“The increased production of Gcn4 in long-lived yeast strains, combined with the requirement of Gcn4 for full life-span extension, makes a compelling case for Gcn4 as an important downstream factor in this longevity pathway,” Kaeberlein said.

Although scientists don’t yet know whether Gcn4 plays a similar role in organisms other than yeast, Kennedy points out that worms, flies, mice and humans all have Gcn4-like proteins that appear to be regulated in a similar way.

“The role of TOR and translation in aging is known to be conserved across many different species, so it’s plausible that this function of Gcn4 is conserved as well,” Kennedy said.  Future research will be aimed at testing this hypothesis.

“Clearly TOR signaling is one component, and perhaps the major component, of the beneficial health effects associated with dietary restriction,” said Kaeberlein.  “The difficulty with TOR as a therapeutic target, however, is the potential for negative side effects.  As we learn more of the mechanistic details behind how TOR regulates aging, we will hopefully be able to identify even better targets for treating age-associated diseases in people.”

A team of researchers at Yale School of Medicine have identified, characterized and cloned ovarian cancer stem cells and have shown that these stem cells may be the source of ovarian cancer’s recurrence and its resistance to chemotherapy.

“These results bring us closer to more effective and targeted treatment for epithelial ovarian cancer, one of the most lethal forms of cancer,” said Gil Mor, M.D., associate professor in the Department of Obstetrics, Gynecology & Reproductive Sciences at Yale School of Medicine.

Mor presented his findings recently at the annual meeting of the American Association for Cancer Research (AACR) Meeting in San Diego, California.

Cancerous tumors are made up of cells that are both cancerous and non-cancerous.  Within cancerous cells, there is a further subclass referred to as cancer stem cells, which can replicate indefinitely.

“Present chemotherapy modalities eliminate the bulk of the tumor cells, but cannot eliminate a core of these cancer stem cells that have a high capacity for renewal,” said Mor, who is also a member of the Yale Cancer Center.  “Identification of these cells, as we have done here, is the first step in the development of therapeutic modalities.”

Mor and colleagues isolated cells from 80 human samples of either peritoneal fluid or solid tumors.  The cancer stem cells that were identified were positive for traditional cancer stem cell markers including CD44 and MyD88.  These cells also showed a high capacity for repair and self-renewal.

The isolated cells formed tumors 100 percent of the time.  Within those tumors, 10 percent of the cells were positive for cancer stem cell marker CD44, while 90 percent were CD44 negative.

Mor and his team were able to isolate and clone the ovarian cancer stem cells.  They found that these cells were highly resistant to conventional chemotherapy while the non-cancer stem cells responded to treatment.  “Isolating and cloning these cells will lead to development of new treatments to target and eliminate the cancer stem cells and hopefully prevent recurrence,” said Mor.