J. Patrick Fitch

Proteomic Characterization of Yersinia pestis Virulence

The Yersinia pestis proteome was studied as a function of temperature and calcium by two-dimensional differential gel electrophoresis. Over 4,100 individual protein spots were detected, of which hundreds were differentially expressed. A total of 43 differentially expressed protein spots, representing 24 unique proteins, were identified by mass spectrometry. Differences in expression were observed for several virulence-associated factors, including catalase-peroxidase (KatY), murine toxin (Ymt), plasminogen activator (Pla), and F1 capsule antigen (Caf1), as well as several putative virulence factors and membrane-bound and metabolic proteins. Differentially expressed proteins not previously reported to contribute to virulence are candidates for more detailed mechanistic studies, representing potential new virulence determinants.

Serum Protein Profile Alterations in Hemodialysis Patients

Background: Serum protein profiling patterns can reflect the pathological state of a patient and therefore may be useful for clinical diagnostics. Here, we present results from a pilot study of proteomic expression patterns in hemodialysis patients designed to evaluate the range of serum proteomic alterations in this population. Methods: Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) was used to analyze serum obtained from patients on periodic hemodialysis treatment and healthy controls. Serum samples from patients and controls were first fractionated into six eluants on a strong anion exchange column, followed by application to four array chemistries representing cation exchange, anion exchange, metal affinity and hydrophobic surfaces. A total of 144 SELDI-TOF-MS spectra were obtained from each serum sample. Results: The overall profiles of the patient and control samples were consistent and reproducible. However, 30 well-defined protein differences were observed; 15 proteins were elevated and 15 were decreased in patients compared to controls. Serum from 1 patient exhibited novel protein peaks suggesting possible additional changes due to a secondary disease process. Conclusion: SELDI-TOF-MS demonstrated consistent serum protein profile differences between patients and controls. Similarity in protein profiles among dialysis patients suggests that patient physiological responses to end-stage renal disease and/or dialysis therapy have a major effect on serum protein profiles.

Extended-image reconstruction through horizontal path turbulence using bispectral speckle interferometry

Results are presented from a horizontal path imaging experiment in which a 0.5-m telescope was focused on targets located at a range of 1 .2 km. The targets varied in complexity from simple binary letters to extended representations of satellites with gray scale and size variations. Imaging at a center wavelength of 0.7 μm, we found an atmospheric degradation factor of D / r 0 = 17, on average. We used a slow read-rate bare CCD detector and thus had to deal effectively with additive noise in the speckle measurements. Our image reconstruction algorithms are based on the use of the complex bispectrum, and we have demonstrated diffraction-limited imaging down to light levels approaching a few photons per speckle per resolution area. We have paid careful attention to the effects of additive noise on the reconstruction process and have shown that they can be adequately overcome. These results support the feasibility of high-resolution speckle imaging of high-earth-orbit satellites using CCDs.

Interpreting microarray data to build models of microbial genetic regulation networks

Microarrays and DNA chips are an efficient, high-throughput technology for measuring temporal changes in the expression of message RNA (mRNA) from thousands of genes (often the entire genome of an organism) in a single experiment. A crucial drawback of microarray experiments is that results are inherently qualitative: data are generally neither quantitatively repeatable, nor may microarray spot intensities be calibrated to in vivo mRNA concentrations. Nevertheless, microarrays represent by the far the cheapest and fastest way to obtain information about a cells global genetic regulatory networks. Besides poor signal characteristics, the massive number of data produced by microarray experiments pose challenges for visualization, interpretation and model building. Towards initial model development, we have developed a Java tool for visualizing the spatial organization of gene expression in bacteria. We are also developing an approach to inferring and testing qualitative fuzzy logic models of gene regulation using microarray data. Because we are developing and testing qualitative hypotheses that do not require quantitative precision, our statistical evaluation of experimental data is limited to checking for validity and consistency. Our goals are to maximize the impact of inexpensive microarray technology, bearing in mind that biological models and hypotheses are typically qualitative.

Bispectral-based optimization algorithms for speckle imaging

Abstract not available.

Experimental validation of extended image reconstruction using bispectral speckle interferometry

Results will be presented from a horizontal path imaging experiment in which we used a 0.5 meter telescope focused on a target located at a range of 1 .2 km. The targets included various extended objects from simple binary letters to extended representations of satellites with grey scale and size variations. Imaging at a center wavelength of 0.7 microns, we found an atmospheric degradation factor of Dir0 = 17, on average. We used a slow read-rate bare CCD detector and thus had to effectively deal with additive noise in the speckle measurements. Our image reconstruction algorithms are based on the use of the complex bispectrum and we have demonstrated diffraction-limited imaging down to light levels approaching a few photons per speckle per resolution area. We have paid careful attention to the effects of additive noise on the reconstruction process and shown that they can be adequately overcome.

Simulating speckle interferometry

This paper describes a simulator we have developed to model speckle imaging and resconstruction of astronomical objects. The simulator was designed as a tool in the development of new signal and image processing techniques for our high resolution imaging research. It has been found to accurately replicate the speckle imaging process, and can be used to predict experimental results under various environmental conditions. The simulator is described in detail, including the modeling of atmospheric turbulence effects, the generation of speckle images, and the simulation of the telescope and image detection processes.

Testing a potential national strategy for cost-effective medical technology

The Center for Healthcare Technologies at Lawrence Livermore National Laboratory is a partnership among government, industry, and universities that focuses on improving healthcare through development of cost-effective technology. With the guidance of healthcare providers, medical institutions, and medical instrument manufacturers, technology can be harnessed to reduce healthcare costs. The partnership is a miniature test case for a potential national strategy for development and adoption of technology specifically to reduce costs.