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Thomas Mitchell

Publications and source records attributed to Thomas Mitchell.

10 recordsLinked to original sources
PubMed2006

MGOS: A resource for studying Magnaporthe grisea and Oryza sativa interactions.

The MGOS (Magnaporthe grisea Oryza sativa) web-based database contains data from Oryza sativa and Magnaporthe grisea interaction experiments in which M. grisea is the fungal pathogen that causes the rice blast disease. In order to study the interactions, a consortium of fungal and rice geneticists was formed to construct a comprehensive set of experiments that would elucidate information about the gene expression of both rice and M. grisea during the infection cycle. These experiments included constructing and sequencing cDNA and robust long-serial analysis gene expression libraries from both host and pathogen during different stages of infection in both resistant and susceptible interactions, generating >50,000 M. grisea mutants and applying them to susceptible rice strains to test for pathogenicity, and constructing a dual O. sativa-M. grisea microarray. MGOS was developed as a central web-based repository for all the experimental data along with the rice and M. grisea genomic sequence. Community-based annotation is available for the M. grisea genes to aid in the study of the interactions.

Computational Biology↗
PubMed2005

'PACLIMS': a component LIM system for high-throughput functional genomic analysis.

BACKGROUND: Recent advances in sequencing techniques leading to cost reduction have resulted in the generation of a growing number of sequenced eukaryotic genomes. Computational tools greatly assist in defining open reading frames and assigning tentative annotations. However, gene functions cannot be asserted without biological support through, among other things, mutational analysis. In taking a genome-wide approach to functionally annotate an entire organism, in this application the approximately 11,000 predicted genes in the rice blast fungus (Magnaporthe grisea), an effective platform for tracking and storing both the biological materials created and the data produced across several participating institutions was required. RESULTS: The platform designed, named PACLIMS, was built to support our high throughput pipeline for generating 50,000 random insertion mutants of Magnaporthe grisea. To be a useful tool for materials and data tracking and storage, PACLIMS was designed to be simple to use, modifiable to accommodate refinement of research protocols, and cost-efficient. Data entry into PACLIMS was simplified through the use of barcodes and scanners, thus reducing the potential human error, time constraints, and labor. This platform was designed in concert with our experimental protocol so that it leads the researchers through each step of the process from mutant generation through phenotypic assays, thus ensuring that every mutant produced is handled in an identical manner and all necessary data is captured. CONCLUSION: Many sequenced eukaryotes have reached the point where computational analyses are no longer sufficient and require biological support for their predicted genes. Consequently, there is an increasing need for platforms that support high throughput genome-wide mutational analyses. While PACLIMS was designed specifically for this project, the source and ideas present in its implementation can be used as a model for other high throughput mutational endeavors.

Algorithms↗
PubMed2004

Intradermal ballistic delivery of micro-particles into excised human skin for pharmaceutical applications.

A unique form of needle-free drug and vaccine delivery is under investigation. The principle of the concept is to accelerate pharmaceuticals in particle form to a momentum sufficient to penetrate the outer layer of the human skin for a pharmacological effect. The relationship between the key particle impact parameters and particle penetration depth in excised human skin has been experimentally determined. Research devices have been used to deliver particles of a range of radii (0.89-53 microm), and density (1.08-18.2 g/cm3) at controlled and incremental impact velocities between 160 and 640 m/s. Analysis of the particle impact data reveals particle penetration depth as a function of particle density, radius and impact velocity. The experimental relationship provides a criterion for the optimal selection of particle parameters and velocity to target specific layers within the skin. Furthermore, some sources of variability in penetration depth have also been established. The experimental data have also been compared with a mechanistic Unified Penetration Model with good agreement.

Administration, Cutaneous↗
PubMed2004

Effects of relative humidity and ambient temperature on the ballistic delivery of micro-particles to excised porcine skin.

The effectiveness of ballistic particle delivery to the skin is often dependent upon breaching the stratum corneum (SC) and targeting cells within defined layers of the viable epidermis. This paper experimentally determines the influence of relative humidity (RH) and temperature on the ballistic delivery of particles to the skin. Gold particles of radius 0.9+/-0.6 microm were accelerated by a hand-held supersonic device to impact freshly excised porcine skin at 410-665 m per s. Increasing the RH from 15% to 95% (temperature at 25 degrees C) led to a particle penetration increase by a factor of 1.8. Temperature increases from 20 degrees C to 40 degrees C (RH at 15%) enhanced particle penetration 2-fold. In both cases, these increases were sufficient to move the target layer from the SC to the viable epidermis. Relative trends in particle penetration compared well with predictions from a theoretical model well. Calculated absolute penetration depths are 6-fold greater than the measurements. The inversely calculated dynamic yield stress of the SC is up to a factor of 10 higher than reported quasi-static measurements, due to changes in tissue failure modes over a strain-rate range spanning 10 orders of magnitude. If targeted particle delivery is required, it is recommended that the environmental RH and temperature be monitored.

Animals↗
PubMed2003

Control of Bcl-2 expression by reactive oxygen species.

Reactive oxygen species (ROS) mediate apoptosis in many different cell types. We have previously shown that the antioxidant Mn(III) tetrakis(5,10,15,20-benzoic acid)porphyrin (MnTBAP) decreased intracellular ROS and prevented the apoptosis of activated T cells in vitro. To determine the mechanism(s) by which MnTBAP afforded such protection, we used Affymetrix (Santa Clara, CA) gene arrays to compare gene expression in T cells activated with staphylococcal enterotoxin B in vivo then cultured with or without MnTBAP. This analysis showed that the antioxidant increased the expression of Bcl-2, an antiapoptotic molecule whose levels are normally decreased by T cell activation. Culture with MnTBAP revealed a tight inverse correlation between the levels of Bcl-2 and ROS within T cells. In vivo, production of ROS in activated T cells occurred before Bcl-2 down-regulation. Furthermore, MnTBAP's ability to prevent death required the expression of Bcl-2 in most T cells. Finally, neither ROS production nor the effects on Bcl-2 expression required Bim, the Bcl-2 antagonist that mediates the death of activated T cells in vivo. Taken together, our results suggest that ROS sensitize T cells to apoptosis by decreasing expression of Bcl-2.

Animals↗
PubMed2003

Transcriptional regulation of biomass-degrading enzymes in the filamentous fungus Trichoderma reesei.

The filamentous fungus Trichoderma reesei produces and secretes profuse quantities of enzymes that act synergistically to degrade cellulase and related biomass components. We partially sequenced over 5100 random T. reesei cDNA clones. Among the sequences whose predicted gene products had significant similarity to known proteins, 12 were identified that encode previously unknown enzymes that likely function in biomass degradation. Microarrays were used to query the expression levels of each of the sequences under different conditions known to induce cellulolytic enzyme synthesis. Most of the genes encoding known and putative biomass-degrading enzymes were transcriptionally co-regulated. Moreover, despite the fact that several of these enzymes are not thought to degrade cellulase directly, they were coordinately overexpressed in a cellulase overproducing strain. A variety of additional sequences whose function could not be ascribed using the limited sequence available displayed analogous behavior and may also play a role in biomass degradation or in the synthesis of biomass-degrading enzymes. Sequences exhibiting additional regulatory patterns were observed that might reflect roles in regulation of cellulase biosynthesis. However, genes whose products are involved in protein processing and secretion were not highly regulated during cellulase induction.

Biomass↗
PubMed2002

The Niemann-Pick C1 protein in feline fibroblasts.

Niemann-Pick type C (NPC) disease is a rare inherited metabolic disorder characterized by hepatosplenomegaly, progressive neurodegeneration, and storage of lipids such as cholesterol and glycosphingolipids in most tissues. The current study was conducted to characterize the Niemann-Pick C1 (NPC1) protein in feline fibroblasts. This was accomplished by generating rabbit polyclonal antibodies against a peptide corresponding to amino acids 1256-1275 of the feline NPC1 protein. The results obtained using immunoblot analysis identified two major proteins that migrated at approximately 140 and 180 kDa. These two proteins were absent when immunoblots were incubated in the presence of feline NPC1 antibody and immunizing peptide, or preimmune serum. Fluorescence microscopy of feline fibroblasts incubated with the feline NPC1 antibody revealed granular staining within the perinuclear region of the cell. This granular staining was diminished when feline fibroblasts were incubated in the presence of feline NPC1 antibody and immunizing peptide, or was completely absent when feline fibroblasts were incubated in the presence of preimmune serum. Additional studies using double-labeled fluorescence microscopy indicated that feline NPC1 partially colocalized with markers for late endosomes/lysosomes, endoplasmic reticulum, and microtubules, but not the trans-Golgi network. In summary, the results presented in this report demonstrate that the NPC1 protein in feline fibroblasts has a similar distribution as that previously described for human and murine fibroblasts.

Animals↗