Jacob Feala

PhD student, Fall 2003 - Early 2008

/Projects (private)


Research Interests

Using the fruit fly Drosophila melanogaster as a model organism, my work focuses on:

  • Engineering new high-throughput technology for cardiac phenotyping
  • Gathering high-throughput data using existing methods, for example NMR metabolomics
  • Reconstructing computer models of integrated regulatory, signaling, and metabolic networks in cardiac myocytes, and
  • Combining models and high-throughput data in a systems biology approach to understanding how these networks function in health and disease

Although I would ultimately be interested in applying this approach to any cardiac dysfunction and disease, hypoxia and aging are two phenomena that are especially amenable to this research, because

  • Both hypoxia and aging have broad, far-reaching effects within the cardiac myocyte, suggesting that genome-scale analysis might be useful, and
  • Both fields of research rely increasingly on Drosophila as a model organism

I have had several undergrad volunteers help me with rearing and crossing flies, preparing samples for NMR experiments, and taking high-throughput measurements. I am currently looking for more volunteers - please email me if you are interested.

Publications

Feala JD, Coquin L, Paternostro G, McCulloch AD (2007) Integrating metabolomics and phenomics with systems models of cardiac hypoxia. Prog Biophys Mol Biol in press

Broderick KE, Balasubramanian M, Chan A, Potluri P, Feala J, Belke DD, McCulloch A, Sharma VS, Pilz RB, Bigby TD, Boss GR (2007) The cobalamin precursor cobinamide detoxifies nitroprusside-generated cyanide. Exp Biol Med (Maywood) 232(6): 789-98

Feala JD, Coquin L, McCulloch AD, Paternostro G (2007) Flexibility in energy metabolism supports hypoxia tolerance in Drosophila flight muscle: metabolomic and computational systems analysis. Mol Syst Biol 3: 99

Broderick KE, Feala J, McCulloch A, Paternostro G, Sharma VS, Pilz RB, Boss GR (2006) The nitric oxide scavenger cobinamide profoundly improves survival in a Drosophila melanogaster model of bacterial sepsis. Faseb J 20: 1865-1873.

Ferrarini L, Bertelli L, Feala J, McCulloch AD, Paternostro G (2005) A more efficient search strategy for aging genes based on connectivity. Bioinformatics 21: 338-348.

Posters

Feala J, Paternostro G, Omens JH, McCulloch AD. Systems analysis of the hypoxia response in Drosophila heart. Jacobs School of Engineering Student Symposium, Univ. of California, San Diego. February, 2006.

Feala J, Omens JH, Paternostro G, McCulloch AD. High-throughput cardiac phenotyping in Drosophila. International Conference on Systems Biology, Boston, Mass. October, 2005

Costa S., Feala J, McCulloch AD, Paternostro G. Higher global connectivity in aging genes. Keystone Symposium on Systems Biology, Keystone, Colorado. April, 2005

Feala J, Omens JH, Paternostro G, McCulloch AD. High-throughput cardiac phenotyping in Drosophila. Bioengineering Student Symposium, Univ. of California, San Diego. March, 2004.

Oral Presentations

Feala JD, McCulloch AD, Paternostro G (2007) Systems analysis of cardiac hypoxia in Drosophila: phenotypes, metabolomics, and modeling. BMES Annual Meeting .ppt

Feala JD, Coquin L, McCulloch AD, Paternostro G (2006) Flexibility in energy metabolism supports hypoxia tolerance in Drosophila flight muscle: metabolomic and computational systems analysis. RECOMB Satellite Conf on Sys Bio and Comp Proteomics .ppt video

UCSD Extreme Oxygen Group seminar, March 2007 .ppt

Fairberg Conference (draft slides) .ppt

Software

This is a collection of Python and Matlab code that I've written for my personal research. Feel free to use it at your own risk, with the knowledge that much of it is untested. This section is under construction for now but I will be adding more attachments soon.

Python BioNet

Biopython-compatible scripts for working with molecular interaction networks. Includes parsers and writers for import/export of PSI-MI (Proteomics Standards Initiative - Molecular Interaction), Cytoscape, and flat file formats. The Network class wraps around the NetworkX module, which must be downloaded separately.

  • BioNet Documentation

    • BioNet.html HTML documentation for the BioNet scripts

    BioNet classes

    • InteractionRecord.py This is a generic storage object for biological interactions. Future work: mold to PSI-MI specifications Network.py Network objects wrap either the XGraph or XDiGraph class from NetworkX, and also holds an InteractionRecord for each edge.

    Network IO

    • GRID.py Parses GRID flat files into InteractionRecords PSI-MI.py Parses PSI-MI XML files into InteractionRecords Cytoscape.py Parses and writes Cytoscape-format files to/from InteractionRecords. SBML.py Parses SBML files into InteractionRecords

    Network SQL

    • BioNetSQL Scripts for storage/retrieval of InteractionRecords to/from a local SQL database

Python Automated Microscopy

I use Python to automate mounting and measurement of fly hearts on a microscope slide. Here are some scripts for interfacing with a microscope-mounted CCD camera, automated stage (via serial port), and ADR101 DAQ board. Also, I'm including higher-level scripts for detecting the hearts and recording M-mode images.

Matlab M-mode analysis

Here are some m-files for displaying M-mode images of a fly heart, detecting beats, measuring wall diameter, etc. Also I have some utility scripts for general use in generating certain types of graphs, insets, etc.

. Jacob Feala homepage