Responding to Epidemic Threats Using Modern Bioinformatics Tools

Contact

Bud Mishra
Courant Institute of Mathematical Sciences
T: 212.998.3464    F: 212.995.4121    mishra@cs.nyu.edu


Project Synopsis

Our goal for this project is to answer the urgent questions of how to deal with a “new” epidemic like SARS or Avian Flu: Are we equipped to rapidly identify and study new pathogens? Do we have the requisite analytical tools to classify the pathology of previously unknown biological agents? Do we have the detection technologies necessary to monitor our environments for biological threats and more importantly, how do we know if our tools are up to the task at hand?

Research groups in universities and governmental institutions have already developed many technologies for analyzing and classifying the behavior of pathogens. What is lacking, however, are the following:

Key activities:


Recent Accomplishments

We have enhanced the capabilities of Simpathica to simulate nanotechnology-based simulation. We have published several journal and conference articles describing how the enhanced Simpathica-Valis toolset can accomplish rapid tool development and how they can be applied in practice.

We have completed a detailed analysis of host-pathogen interaction by analyzing the response of human kidney cells to staphylococcus enterotoxin B (SEB) with data collected by Walter-Reed Army Institute of Research. A paper summarizing this analysis is under preparation. We have recently designed a database schema to keep track of the results of these analyses for different strains of pathogen and use these data to understand the best responses to different strains.

The other main activities have been in designing a novel nano-biosensor and in setting up the experimental infrastructures to validate it. During the summer, with the help of a summer student, we plan to revise the code and the model completely in order to improve the accuracy of the prediction and revise our original design. In collaboration with the bench scientists at UCLA and NYU, we are conducting some simple tests and validation. We are also augmenting the proteomic assay with single molecule genomic assay in order to determine minute amount of pathogenic DNA. We have initiated several simple experiments involving viral materials (e.g., adeno and lambda) to determine if they can be detected in minute amounts using LNA and PNA probes.

References

Patents Filed