A model of the roles of essential kinases in the induction and expression of late long-term potentiation.

The induction of late long-term potentiation (L-LTP) involves complex interactions among second-messenger cascades. To gain insights into these interactions, a mathematical model was developed for L-LTP induction in the CA1 region of the hippocampus. The differential equation-based model represents actions of protein kinase A (PKA), MAP kinase (MAPK), and CaM kinase II (CAMKII) in the vicinity of the synapse, and activation of transcription by CaM kinase IV (CAMKIV) and MAPK. L-LTP is represented by increases in a synaptic weight. Simulations suggest that steep, supralinear stimulus-response relationships between stimuli (e.g., elevations in [Ca(2+)]) and kinase activation are essential for translating brief stimuli into long-lasting gene activation and synaptic weight increases. Convergence of multiple kinase activities to induce L-LTP helps to generate a threshold whereby the amount of L-LTP varies steeply with the number of brief (tetanic) electrical stimuli. The model simulates tetanic, -burst, pairing-induced, and chemical L-LTP, as well as L-LTP due to synaptic tagging. The model also simulates inhibition of L-LTP by inhibition of MAPK, CAMKII, PKA, or CAMKIV. The model predicts results of experiments to delineate mechanisms underlying L-LTP induction and expression. For example, the cAMP antagonist RpcAMPs, which inhibits L-LTP induction, is predicted to inhibit ERK activation. The model also appears useful to clarify similarities and differences between hippocampal L-LTP and long-term synaptic strengthening in other systems.

Use of a modified delphi process for establishing occupational exposure limits in support of health surveillance for space travelers

On-orbit exposures can come from numerous factors related to the space environment as evidenced by almost 50 years of environmental samples collected for water analysis, air analysis, radiation analysis, and physiologic parameters. For astronauts and spaceflight participants the occupational exposures can be very different from those experienced by workers performing similar tasks in workplaces on Earth, because the duration of the exposure could be continuous for very long orbital, and eventually interplanetary, missions. The establishment of long-term exposure standards is vital to controlling the quality of the spacecraft environment over long periods. NASA often needs to update and revise its prior exposure standards (Spacecrafts Maximum Allowable Concentrations (SMACs)). Traditional standards-setting processes are often lengthy, so a more rapid method to review and establish standards would be a substantial advancement in this area. This project investigates use of the Delphi method for this purpose. ^ In order to achieve the objectives of this study a modified Delphi methodology was tested in three trials executed by doctoral students and a panel of experts in disciplines related to occupational safety and health. During each test/trial modifications were made to the methodology. Prior to submission of the Delphi Questionnaire to the panel of experts a pilot study/trial was conducted using five doctoral students with the goals of testing and adjusting the Delphi questionnaire to improve comprehension, work out any procedural issues and evaluate the effectiveness of the questionnaire in drawing the desired responses. The remainder of the study consisted of two trials of the Modified Delphi process using 6 chemicals that currently have the potential of causing occupational exposures to NASA astronauts or spaceflight participants. To assist in setting Occupational Exposure Limits (OEL), the expert panel was established consisting of experts from academia, government and industry. Evidence was collected and used to create close-ended questionnaires which were submitted to the Delphi panel of experts for the establishment of OEL values for three chemicals from the list of six originally selected (trial 1). Once the first Delphi trial was completed, adjustments were made to the Delphi questionnaires and the process above was repeated with the remaining 3 chemicals (trial 2). ^ Results indicate that experience in occupational safety and health and with OEL methodologies can have a positive effect in minimizing the time experts take in completing this process. Based on the results of the questionnaires and comparison of the results with the SMAC already established by NASA, we conclude that use of the Delphi methodology is appropriate for use in the decision-making process for the selection of OELs.^

Integrating sequence information in microarray data analysis by free energy modeling

Microarray technology is a high-throughput method for genotyping and gene expression profiling. Limited sensitivity and specificity are one of the essential problems for this technology. Most of existing methods of microarray data analysis have an apparent limitation for they merely deal with the numerical part of microarray data and have made little use of gene sequence information. Because it's the gene sequences that precisely define the physical objects being measured by a microarray, it is natural to make the gene sequences an essential part of the data analysis. This dissertation focused on the development of free energy models to integrate sequence information in microarray data analysis. The models were used to characterize the mechanism of hybridization on microarrays and enhance sensitivity and specificity of microarray measurements. ^ Cross-hybridization is a major obstacle factor for the sensitivity and specificity of microarray measurements. In this dissertation, we evaluated the scope of cross-hybridization problem on short-oligo microarrays. The results showed that cross hybridization on arrays is mostly caused by oligo fragments with a run of 10 to 16 nucleotides complementary to the probes. Furthermore, a free-energy based model was proposed to quantify the amount of cross-hybridization signal on each probe. This model treats cross-hybridization as an integral effect of the interactions between a probe and various off-target oligo fragments. Using public spike-in datasets, the model showed high accuracy in predicting the cross-hybridization signals on those probes whose intended targets are absent in the sample. ^ Several prospective models were proposed to improve Positional Dependent Nearest-Neighbor (PDNN) model for better quantification of gene expression and cross-hybridization. ^ The problem addressed in this dissertation is fundamental to the microarray technology. We expect that this study will help us to understand the detailed mechanism that determines sensitivity and specificity on the microarrays. Consequently, this research will have a wide impact on how microarrays are designed and how the data are interpreted. ^