Krasilnikov, Nekrutenko receive Young Investigator Awards

Andrey Krasilnikov and Anton Nekrutenko, both assistant professors of biochemistry and molecular biology at Penn State, have received Young Investigator Awards from the Arnold and Mabel Beckman Foundation. The award recognizes the most promising young faculty members in the chemical and life sciences.

Andrey Krasilnikov studies the spatial organization of highly structured RNA molecules and the complexes such molecules form with RNA-binding proteins. Krasilnikov uses X-ray crystallography to achieve an atomic-resolution level of detail. "Using a combination of crystallographic and biochemical studies we can answer a very broad variety of fundamental questions," explained Krasilnikov. "Questions range from the mechanisms of substrate recognition and catalysis to the structural and functional roles of individual parts of the molecule or complex."

Despite the fact that only four basic building blocks make up RNA molecules, RNA is a very flexible molecule that can form intricate networks having various intramolecular interactions, explained Krasilnikov. This flexibility allows RNA to fold into complicated, three-dimensional structures and to play advanced roles, including substrate recognition and catalysis. "RNA used to be considered a simple disposable copy of DNA serving as a template to make proteins," said Krasilnikov. "However, highly structured RNA molecules play a crucial role in regulation of gene expression and are capable of catalyzing chemical reactions, just like the proteins do."

Krasilnikov is particularly interested in several key RNA molecules and RNA-protein complexes including Ribonuclease MRP, a universal enzyme found in eukaryotic, or nucleus-containing, cells consisting of a large RNA component and several proteins. Ribonuclease MRP plays a role in DNA replication in mitochondria, maturation of ribosomal RNA, and regulation of the cell cycle in yeast. In humans, some mutations of Ribonuclease MRP can cause a form of short-limbed dwarfism causing abnormal skeletal growth and Cartilage-Hair Hypoplasia, also known as McKusick-type metaphyseal chondrodysplasia, a rare syndrome affecting the immune system.

Krasilnikov was awarded a National Research Service Award for his research from 2002 to 2004 by the National Institutes of Health. He is a reviewer for scientific journals such as Nucleic Acids Research, RNA, and Biochemistry. In 2004, he presented his study on crystal structures of bacterial Rribonuclease P at the Ninth Annual International Meeting of the RNA Society.

Before joining Penn State in 2005, Krasilnikov was a postdoctoral fellow in biochemistry, molecular biology and cell biology at Northwestern University from 2000 to 2005. He was a postdoctoral fellow in molecular genetics at the University of Illinois at Chicago from 1996 to 1999 and a scientist at the Institute of Molecular Genetics at the Russian Academy of Sciences from 1995 to 1996. He received a master's degree in physics, cum laude, from the Moscow Institute of Physics and Technology in 1991 and a doctoral degree from the Institute of Chemical Physics at the Russian Academy of Sciences in 1995.

Anton Nekrutenko's research blends bioinformatics -- the study of the inherent structure of biological information and biological systems -- with molecular evolution into the single field of evolutionary genomics. Also known as comparative genomics, evolutionary genomics draws on genomic information from different species in order to find common functional elements such as genes. "Comparative genomics is an intuitive and simple way to increase the process of identifying specific protein-encoding segments of the DNA molecule," said Nekrutenko. "The main problem with gene prediction is that genes occupy only a tiny proportion of our genome, like small islands in a sea of random -- or not so random -- noise." Because there are many genetic similarities between species, the comparison of human-DNA sequences to those of other mammals increases precision in identifying these genetic islands.

In addition to identifying the genes themselves, the technique is useful for identifying promoters, which are regions of the genome responsible for turning genes on and off. Identifying the structure and role of promoters is a key to understanding how organisms function.

Because the number of genes does not reflect the complexity of an organism -- that is, simple organisms can have almost as many genes as significantly more complex organisms -- the more complex organisms must possess more sophisticated ways of regulating genes. Tracking similarities and differences in these promoters across species provides insight into the evolution of more complex organisms. "Isolating these control mechanisms provides answers to many fundamental evolutionary and genetic questions," Nekrutenko said. "Our approach to this problem is to identify the grouping of regions conserved among multiple species and to study their combinations. This approach allows us to focus on the common promoters."

Before joining the Penn State faculty in April 2003, Nekrutenkowas a postdoctoral research associate and instructor in the Department of Ecology and Evolution at the University of Chicago from 1999 to 2003. He earned a master's degree in biochemistry and molecular biology at Kiev State University in the Ukraine in 1995 and a doctoral degree in biology at Texas Tech University in 1999.

The Arnold and Mabel Beckman Foundation Young Investigator Award recognizes young faculty members in the early stages of their academic careers. Since 1991, the Beckman Foundation has awarded more than 230 Young Investigator Awards to young scientists at prominent universities and research institutions across the United States in order to promote research in chemistry and the life sciences and to foster the invention of methods, instruments, and materials that will open up new avenues of research in science.