Bernhard Palsson, Ph.D.

A new study has demonstrated that “foreign” DNA — DNA transferred horizontally into a species from a source other than a parent — can become functional over time and can impact an organism’s evolution and fitness, according to a paper published August 10 in Nature Ecology and Evolution.

Horizontal gene transfer is the lateral exchange of foreign DNA between unrelated species. Horizontal gene transfer can contribute to the spread of antimicrobial resistance but can also facilitate the engineering of “designer organisms” with desired phenotypes.

Therefore, understanding how these genes from foreign DNA assimilate into a new genome is of interest. The mechanisms of basic gene transfer have been established, but studies on the functionality of gene replacement are insufficient to show how organisms adapt to foreign DNA that initially provides no benefit to the fitness of the organism, but that later becomes functional… Continue reading.

International researchers have developed a computer tool capable of proving a 3D view of genes, proteins and metabolites for improved insight into drug reactions. Findings were published in Nature Biotechnology.

Led by Bernhard Palsson, a professor of bioengineering at the University of California, San Diego (UCSD), a team of researchers developed the 3D tool to improve the understanding of disease causing mutations and develop new drug theories for diseases like cancer. In this study, the production and findings of the Recon3D tool were outlined.

Currently, analyzing the human metabolic network involved methods the sequence data of DNA in a linear fashion. However, because DNA is structured with coils, twists and folds, comprehensive research has not been completed. The Recon3D is able to integrate 3,288 open reading frames, which are stretches of DNA and RNA that contain protein-producing genes; 13,542 metabolic reactions; and the 3D structures of 4,140 metabolites and 12,890 proteins, making it the most comprehensive network reconstruction… Continue reading.

Building on earlier pioneering work by researchers at the University of California, San Diego, an international consortium of university researchers has produced the most comprehensive virtual reconstruction of human metabolism to date. Scientists could use the model, known as Recon 2, to identify causes of and new treatments for diseases like cancer, diabetes and even psychiatric and neurodegenerative disorders. Each person’s metabolism, which represents the conversion of food sources into energy and the assembly of molecules, is determined by genetics, environment and nutrition.

The researchers presented Recon 2 in a paper published online March 3 in the journal Nature Biotechnology.

Doctors have long recognized the importance of metabolic imbalances as an underlying cause of disease, but scientists have been ramping up their research on the connection as a result of compelling evidence enabled by the Human Genome Project and advances in systems biology, which leverages the power of high-powered computing to build vast interactive databases of biological information.

“Recon 2 allows biomedical researchers to study the human metabolic network with more precision than was ever previously possible. This is essential to understanding where and how specific metabolic pathways go off track to create disease,” said Bernhard Palsson, Galletti Professor of Bioengineering at UC San Diego Jacobs School of Engineering.

“It’s like having the coordinates of all the cars in town, but no street map. Without this tool, we don’t know why people are moving the way they are,” said Palsson.

Open an undergraduate biochemistry textbook and you will learn that enzymes are highly efficient and specific in catalyzing chemical reactions in living organisms, and that they evolved to this state from their “sloppy” and “promiscuous” ancestors to allow cells to grow more efficiently. This fundamental paradigm is being challenged in a new study by bioengineers at the University of California, San Diego, who reported in the journal Science what a few enzymologists have suspected for years: many enzymes are still pretty sloppy and promiscuous, catalyzing multiple chemical reactions in living cells, for reasons that were previously not well understood.

In this study, the research team, led by Bernhard Palsson, Galetti Professor of Bioengineering at the UC San Diego Jacobs School of Engineering, brought together decades of work on the behavior of individual enzymes to produce a genome-scale model of E. coli metabolism and report that at least 37 percent of its enzymes catalyze multiple metabolic reactions that occur in an actively growing cell.

“We’ve been able to stitch all of the enzymes together into one giant model, giving us a holistic view of what has been driving the evolution of enzymes and found that it isn’t quite what we’ve thought it to be,” said Palsson.

Eight professors at the University of California, San Diego have been named new Fellows of the American Association for the Advancement of Science (AAAS), the world’s largest general scientific society.

Philip E. Bourne, Xiang-Dong Fu, Kun-Liang Guan, Yishi Jin, Peter J. Novick, Bernhard Palsson and Kang Zhang were among 503 AAAS members selected by colleagues in their disciplines to be honored this year for “efforts toward advancing science applications that are deemed scientifically or socially distinguished.”

The new Fellows will be presented with an official certificate and a gold and blue (representing science and engineering, respectively) rosette pin at a special ceremony Feb. 19 at the AAAS Fellows Forum during the 2011 AAAS annual meeting in Washington, D.C. Their names will also be published in the Jan. 28 issue of the journal Science, published by the AAAS.