Bevilacqua Lab Group

Current Lab Members:
(Click for more info)

Shuichi Nakano (Konan University)

Amy Parente (Penn State, Altoona)

Xiaofeng Zheng (Peking University)

Principal Investigator:

Hometown: I grew up in North Collins, NY.
Education: (1987) B.S. in Chemistry & Physics John Carroll University ; (1993) Ph.D. in Chemistry, University of Rochester (Advisor: Professor Doug Turner).

Professional Experience: (1993-1997) Jane Coffin Childs Post-doctoral Fellow in Chemistry and Biochemistry, University of Colorado, Boulder , HHMI (Advisor: Professor Tom Cech); (1997) Assistant Professor of Chemistry, Penn State University; (2003) Associate Professor of Chemistry, Penn State University; (2007) Professor of Chemistry, Penn State University.

Awards: Alfred P. Sloan Foundation Fellow, 2001.
Camille Dreyfus Teacher-Scholar, 2001.
National Science Foundation Career Award, 2000.
Howard Hughes Postdoctoral Fellow 1996-1997.
Jane Coffin Childs Postdoctoral Fellow 1993-1996.

Area of research: All things RNA. I am particularly fascinated by RNA function, including RNA catalysis, small molecule interaction, and antiviral activity. Our goal is to understand at the molecular level how RNA-based systems operate by combining structural, kinetic, and thermodynamic approaches.

Hobbies: Fly fishing, Soccer, Japanese Maple Gardening
Recommended Links:
PSU: Schreyers Honors College Fly Fishing Club Kids to Work Day

Postdoctoral Fellows:

Hometown: I grew up on the western coast of India in Bombay.
Education: B.S. in Microbiology, University of Bombay; M.S. in Life Sciences, University of Bombay; Ph.D. in Life Sciences (Biochemistry), University of Bombay

Professional Experience: Lecturer of Microbiology at Garware Institute, University of Bombay Lecturer of Life Sciences at Jai Hind College, University of Bombay

Awards: National Merit Scholarship awarded by the University Grants Commission, New Delhi, India, for carrying out doctoral research

Area of research: RNA Structure-Function Studies. I'm drawn by the theories that purport the RNA World Hypothesis. It is a fascinating concept that could be instrumental in our understanding of cellular functions at a fundamental level. I'm involved in a project that uses ribozyme folding and catalysis to understand the participation of RNA in a wide variety of roles.

Hobbies: I love to read, solve crossword puzzles, and watch movies (the kind that are as far removed from reality as is possible). I also like to cook and someday hope to write the "Idiots Guide to Cooking".
Recommended Links: I personally like to surf news channels from around the world, but I know it's not everybody's cup of tea, so it's not a recommended link!.

Area of research: I work on the double stranded RNA binding Protein Kinase PKR. My research involves in identifying new class of RNA activators of the PKR and their mechanism of activation. I use the molecular cloning techniques to construct the plasmid DNA’s for expression and purification of proteins. I also use the techniques such as electrophoretic mobility shift assays (EMSA), filter binding, cross linking, and directed hydroxyl radical mapping studies in order to understand the binding of RNA to protein. I intend to use techniques like isothermal titration calorimetry, analytical ultracentrifugation, stopped flow and surface plasmon resonance for elucidating the mechanism of activation of PKR by RNA.

Hobbies: Watching movies, reading
Recommended Links:

Graduate Students:

Hometown: Punxsutawney, PA
Education: B.S. in Chemistry, Allegheny College

Area of research: I focus on the thermodynamics of nucleic acid folding. I have two current projects. In the first, I am attempting to determine the basis of stability for family of stable nucleic acid hairpins. In the second, I am trying to elucidate the link between secondary and functional tertiary structures in RNA folding using multiple model systems. Currently, I utilize
UV/VIS spectroscopies as well as circular dichrosim.

Hobbies: Sports (Especially Football), video games, watching concerts and stand-up comedy.
Recommended Links: www.sciencemag.org, www.nature.com, www.postgazette.com,
www.dictionary.com, http://fantasysports.yahoo.com, www.espn.com

Hometown: Woodbury , MN (Suburb of St. Paul, MN)
Education: B.S. in Biochemistry/Chemistry minor, University of Minnesota

Area of research: I work with the RNA activated protein kinase, PKR. I am currently trying to characterize the mechanism of PKR activation. This protein has classically been shown to be activated by double-stranded viral RNA. To understand the mechanism of activation, we have made a homogenous, perfectly double-stranded 79 bp RNA. PKR activation is monitored using a radioactivity assay and ³²P-ATP as a substrate. In the future, I will test the ability of various viral RNA’s (with imperfections) to activate PKR.

Hobbies: Enjoying the outdoors, camping, traveling, fishing
Recommended Links:

Hometown: Amesbury, MA
Education: B.S. in Chemistry, University of Massachusetts at Amherst

My CV can be found here.

Area of Research: The tryptophan biosynthesis pathway in Bacillus subtilis is comprised of seven enzymes, six of which are under the control of a single promoter in the trpEDCFBA operon. The main regulatory element of this operon is TRAP, or trp RNA-binding attenuation protein. When activated by tryptophan, TRAP induces an impressive 1300-fold down-regulation of the trp genes. The goal of my research is to understand particular protein-RNA interactions that contribute to the high specificity and large amplitude of this regulation.

Hobbies: fly fishing, painting, guitar, baseball, looking at stuff
Recommended Links:

Hometown: Green Township, NJ
Education: BA in Chemistry and Spanish, Colby College

Area of research: Riboswitches are parts of RNA that bind to small metabolites in order to regulate their gene expression without use of proteins. My project involves looking for riboswitches in different organisms.

Hobbies: traveling, reading, field hockey
Recommended Links:

Hometown: Northampton , PA
Education: B.S. in Chemistry, Moravian College

Area of research: I focus on the thermodynamics of nucleic acid folding; in particular I study the linkage between structural changes and corresponding changes in nucleobase properties such as pK_a shifts. The main techniques I use are nuclear magnetic resonance and UV/VIS and circular dichroism spectroscopies. I intend to utilize isothermal titration calorimetry, differential scanning calorimetry, and fluorescence as well.

Hobbies: Reading , weight training, old school video games
Recommended Links: Always good for a laugh,
Amaze your friends with useless knowledge,

Area of research:

Hobbies: Knitting, sewing, renaissance fairs
Recommended Links:
Online knit and crochet community
Pennsylvania Renaissance Fair

Hometown: Evans City , PA & East Stroudsburg , PA
Education: B.S. in Chemistry, University of Pittsburgh
Robot from the future
Area of research: Thermodynamics of ligand binding to aptamers. Metal ion-RNA interactions through ITC.

Hobbies: Reading , writing, Quiz Bowl, College Democrats
Recommended Links:
Biopolymer calculator
Track hurricanes, etc at NOAA
Everything you need to know about mathematics

Hometown: Doylestown , PA
Education: B.S. in Biochemistry/Business Administration minor, Muhlenberg College

Area of research: I am currently investigating the mechanism of the hepatitis delta virus (HDV) genomic ribozyme using a variety of approaches, including traditional biochemical techniques (mutagenesis, hand-mixing/rapid quench kinetics) and novel biophysical methods. The primary objectives of this research are to gain a better understanding of the catalytic repertoire of RNA and to determine the optimal way by which to assign functions to chemical moieties in RNA. I am also studying the ability of the hepatitis delta antigens (HDAgs) to act as RNA chaperones, with an emphasis on understanding the role that the HDAgs play in the folding pathway of the HDV genomic ribozyme. The primary objectives of this research are to understand the nucleic acid sequence and structure specificities of the HDAgs and to develop a thermodynamic framework for the RNA chaperone-dependent folding of RNA, and to gain insight into the biological functions of the HDAgs.

Hobbies: Instrumental music (oboe, English horn, saxophone), baking, exercising, outreach
Recommended Links:
The Science Club, a non-profit educational corporation
Fun Science Websites:
Slashdot. News for nerds. Stuff that matters.
How Stuff Works

Hometown: Douglassville , PA
Education: B.A. in Chemistry, Franklin and Marshall College

Area of research: My work focuses on RNA-protein interactions, specifically between non-cellular RNA and the anti-viral RNA-activated protein kinase, PKR. As part of the innate immune response in humans, PKR is activated by binding to viral RNA during infection which leads to the shut down of protein translation. I am currently investigating how novel molecular patterns in pathogenic RNA, specifically the 5'-triphosphate, are distinguished by PKR from cellular RNA. I am attempting to characterize the effects of secondary and tertiary structure of 5'-triphosphate-dependent RNA activators of PKR on PKR activation. The objective of this research is to examine the link between RNA folding and human disease using biochemical (hydroxyl radical and nuclease structure mapping, crosslinking, mutagenisis) and biophysical (fluorescence competition, stopped-flow) techniques.

Hobbies: reading, playing the cello, singing, skiing, cooking, going to PSU football games, napping, watching M*A*S*H and Friends re-runs,
Recommended Links:

Area of research:

Hobbies: Spending time with friends and family, watching movies, cooking and baking, and being crafty
Recommended Links:

Undergraduate Students:

Hometown: Girard, PA (near Erie)
Education: B.S. in Biochemistry and Molecular Biology, Penn State (2008)

Area of research: I am working with Josh to study the bonding interactions of the Malachite Green aptamer with small molecules: TMR and Malachite Green. In addition, I will soon be beginning a NAIM experiment to determine whether I can use conformationally restricted nucleotides (8-BrG and 8-BrA) in distinct locations in the aptamer to induce a tighter bind.

Hobbies: Spending time with friends and family, reading, playing piano, spending time outside, working out, PSU Football and watching movies and old seasons of Friends, Will and Grace, and Gilmore Girls.
Recommended Links: THON, Schreyer Honors College

Hometown: Scranton, PA
Education: B.S. in Chemistry, Penn State (2007)
Area of research: .

Hobbies: Golf, Caddyshack, Office Space, and the Office on NBC
Recommended Links: Red Sox,

http://www.redsox.com; http://sports.espn.go.com/espn/page2/simmons/index

Hometown: Kensington, MD
Education: B.S . in Chemistry, Penn State (2009)
Area of research:

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Recommended Links:

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Hometown: Bellwood, PA
Hobbies: oil painting, scrapbooking, exercising, spending time with my family, house improvements
Recommended Links: