Center for Molecular Science: Site Pages

jkw_nucleic-acids

Victor Jaffett — Fri, 22 Feb 2013 17:46:46 GMT

Riboswitches and Nucleic Acids Biochemistry

Our laboratory conducts experiments on naturally occurring and synthetic nucleic acids sequences. Our interest is in the mechanism of action as these biomolecules perform binding and catalysis events. We use standard molecular biology techniques and incorporate advanced optical methods to analyze the kinetics and thermodynamics of the interactions.

Ribonucleic acid (RNA) was, until recently, thought of as being relegated to the role of genetic middleman between DNA, the genome, and proteins, the workhorse of biology. However, the known roles of RNA in biology have been expanded dramatically with the discovery that RNA itself can impact DNA replication, transcription elongation, RNA processing, and translation initiation among other processes.

Riboswitches are untranslated RNA segments functioning as genetic control elements by binding a target metabolite and controlling the expression of genes associated with the biosynthesis or import of the target metabolite or a closely related molecule. Simply, a riboswitch is a naturally occurring aptamer appended to a gene express ion platform. Riboswitches are found in all three kingdoms of life and represent a fundamental and energetically conservative form of genetic control, yet this RNA-based genetic control mechanism was discovered only several years ago.

Further, both single-stranded RNA (ssRNA) and ssDNA sequences can be evolved in the test tube to perform binding and catalysis events. In vitro selection has proven to be a powerful method of developing biosensors to target molecules of interest to health care professionals and military analysts.

Our collaborators in this field include labs at Yale University, the University of Maryland-College Park, Carnegie Mellon University, the National Institute of Health, and the Walter Reed Army Institute of Research. We’ve been funded by DARPA, ARL, and the DMRDP through MRMC.

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jkw_clinical-experiments

Victor Jaffett — Fri, 22 Feb 2013 18:27:19 GMT

Assessment of Biomarker Levels in Clinical Experiments

Our laboratory is collaborating with clinicians at Keller Army Community Hospital (KACH) and scientists from the Department of Behavioral Sciences and Leadership (BS&L) and the Photonics Research Center (PRC) in several clinical trials. Our role is to process the biological samples, extracting the cells or molecules of interest for subsequent analysis by qPCR, microarray, ELISA, and other means.

We are working on a project to assess the relationship between the depression biomarker protein, p11, and Seasonal Affective Disorder (SAD) in cadets at West Point during the spring academic semester. We are collaborating with Dr. Per Svenningsson (Karolinska Institute, Sweden) and Dr. Paul Greengard (Rockefeller University) who was awarded the Nobel Prize for his advancements in neuroscience.

Further, we are collaborating with KACH physicians and researchers to investigate blood biomarkers that may be used to predict the outcome of ACL reconstruction in cadets at West Point. Given the prevalence of sports-related injury at West Point and in the Army, the medical leadership is interested in developing tools that may guide physicians in the future.

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jkw_gene-expression

Victor Jaffett — Fri, 22 Feb 2013 18:15:16 GMT

Gene Expression Analysis

Our group is working to elucidate the genetic and metabolomic circuits perturbed by the exposure of trace amounts of therapeutics and chemical contaminants such as military explosives. In order to analyze the dynamic relationships between the vast number of biological reactants that may respond to the presence of an external molecular stimulant, powerful techniques must be used. The United States Army is committed to understanding phenomena ranging from the off-target effects of therapeutics to the biological impact of high explosive ordinance contamination on military ranges. The tools for analyzing these complicated and dynamic networks are evolving but are currently restricted to the known relationships of the measured values of the gene products and metabolites. New algorithms designed to elucidate heretofore unknown relationships between these measured quantities. We are turning to Network Science techniques to analyze these enormous and complicated data sets.

We are interested in the expression level of specific genes and small molecule metabolites in response to an environmental exposure to trace amounts of a contaminant or drug. We are using the power of microarray technology to assess the up- and down-regulation of genes at the mRNA level in several different experiments. The information gained from this analysis helps identify “hot spots” of activity in response to a stimulus. The data from a typical experiment consists of a list of genes and metabolites and the corresponding relative expression (up- or down-regulated compared to a control). The significant conclusions are drawn from identifying the relationships between the nodes of these network maps. We are using the bacterium, E coli as a model organism to observe the effect of environmental insults such as RDX and HMX and we’re using human cell lines to study the off-target effects of different pools of siRNA-based therapies to address Heterotopic Ossification. Standard gene expression microarray for the monitoring of gene expression and advanced GCxGC-MS techniques for the assessment of metabolite levels will give us unsurpassed resolution and enable us to document the biological circuits impacted by the contaminant.

At its most fundamental level, Biology is the control and interplay between a vast number coupled chemical reactions. These chemical reactions control the basic processes of life as well as providing rapid response mechanisms to counter a plethora of environmental changes. Network Science involves the study of the relatedness of seemingly disparate phenomena.

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