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Algorithm Predicts Interactions Between Unsolved Protein Structures

Researchers in New York have developed an algorithm that can predict interactions between proteins whose structures are unsolved. The computational tool takes protein interaction prediction to a new level because it works on proteins on which little structural information exists, providing three-dimensional models of the protein-protein complex and identifying the amino acid residues that interact. Said the team’s lead researcher: “The overall goal is to develop personalized medicine, which is based on understanding how a drug affects you versus how it affects me.”

Using Computers, Scientists Successfully Predict Evolution of E. Coli

For more than a decade, researchers have been trying to create accurate computer models of Escherichia coli (E. coli), a bacterium that makes headlines for its varied roles in food poisoning, drug manufacture and biological research. By combining laboratory data with recently completed genetic databases, researchers can craft digital colonies of organisms that mimic, and even predict, some behaviors of living cells to an accuracy of about 75 percent. Now, NSF-supported researchers at the University of California at San Diego have created a computer model that accurately predicts how E. coli metabolic systems adapt and evolve when the bacteria are placed under environmental constraints.

Researchers catch stem cells in the act of morphing

Researchers at Stanford University have tracked the path of bone marrow stem cells as they transform into an adult tissue. This work, published in the Nov. 15 issue of the journal Cell, marks the first time scientists have seen the individual steps of the progress. In previous work, researchers have seen injected bone marrow cells integrate into the muscles, livers and brains of mice. But until now, they have not witnessed the sequence of events that leads to this transformation. In their Cell paper, the researchers describe how they saw transplanted bone marrow cells first locate to the muscle as a muscle-specific stem cell called a satellite cell. These former bone marrow cells lurked in the muscle until exercise-induced muscle damage signaled them to help repair the injury by fusing with existing muscle cells.

Defeating ‘clingy’ bacteria could help treat urinary tract infections

Clingy bacteria often spell trouble. Scientists have discovered how bacteria manufacture hair-like fibers used to cling to the lining of the kidney and bladder where they cause urinary tract infections (UTIs). The results are published in the Nov. 15 issue of the journal Cell. “Our findings should lead to new drugs to treat UTIs by blocking the formation of these protein fibers,” says study leader Scott J. Hultgren, Ph.D., the Helen Lehbrink Stoever Professor of Molecular Microbiology. “They also should improve our general understanding of how disease-causing bacteria build, fold and secrete proteins that enable them to cause disease.”

Heads to roll as gov’t fights fire ants with decapitating flies

Heads will roll as a U.S. Department of Agriculture plan to control imported fire ants is put into practice this month in Florida. The plan introduces tiny South American phorid flies to the United States to control the pesky ants, whose spread has been unaffected by poisons and other measures. Phorid flies use the decapitated heads of imported fire ants to reproduce. “This is the only way we’re ever going to see a reduction in the number of fire ants in North America,” said one official associated with the plan.

Scientists show how Kaposi’s sarcoma virus causes cancer cells to grow

Scientists have shown for the first time how the virus that causes Kaposi’s sarcoma inhibits the body’s immune response and causes cancer cells to grow through a technique called immune evasion. Kaposi’s sarcoma-associated herpesvirus, or KSHV,causes Kaposi’s sarcoma, a cancer of the blood vessel cells that often occurs in tissues under the skin or mucous membranes, and is the most common malignancy occurring among AIDS patients. KSHV belongs to the family of herpesviruses that includes the causes of genital herpes, cold sores and chickenpox. The same researchers who previously discovered KSHV examined the expression of a virus-derived cytokine (a hormone-like substance that regulates cells during an immune response) in KSHV and found it not only inhibits immune function, but also causes cancerous cells to grow

Infant stroke severely under-recognized, researcher says

A neurologist at the University of California at San Francisco says stroke in neonates and children is severely under-recognized, with about 1 case per 4,000 live births. About 6 percent of those children will die, 20 to 35 percent will go on to have another stroke, and more than two-thirds of survivors will have neurological deficits or seizures.