J Biomol Screen 2002 Aug;7(4):383-9
Development of a high throughput screening assay for mitochondrial membrane potential in living cells.
Huang SG.
Biology II, Tularik Inc., South San Francisco, CA.
The mitochondrion plays a pivotal role in energy metabolism in eukaryotic cells. The electrochemical potential across the mitochondrial inner membrane is regulated to cope with cellular energy needs and thus reflects the bioenergetic state of the cell. Traditional assays for mitochondrial membrane potential are not amenable to high-throughput drug screening. In this paper, I describe a high-throughput assay that measures the mitochondrial membrane potential of living cells in 96- or 384-well plates. Cells were first treated with test compounds and then with a fluorescent potentiometric probe, the cationic-lipophilic dye tetramethylrhodamine methyl ester (TMRM). The cells were then washed to remove free compounds and probe. The amount of TMRM retained in the mitochondria, which is proportional to the mitochondrial membrane potential, was measured on an LJL Analyst fluorescence reader. Under optimal conditions, the assay measured only the mitochondrial membrane potential. The chemical uncouplers carbonylcyanide m-chlorophenyl hydrazone and dinitrophenol decreased fluorescence intensity, with IC(50) values (concentration at 50% inhibition) similar to those reported in the literature. A Z' factor of greater than 0.5 suggests that this cell-based assay can be adapted for high-throughput screening of chemical libraries. This assay may be used in screens for drugs to treat metabolic disorders such as obesity and diabetes, as well as cancer and neurodegenerative diseases.
Genomics 2002 Aug;80(2):138
Comparative analysis of human genome assemblies reveals genome-level differences.
Li S, Liao J, Cutler G, Hoey T, Hogenesch J, Cooke M, Schultz P, Ling X.
Tularik, Inc. Two Corporate Drive, South San Francisco, California, 94080, USA
Previous comparative analysis has revealed a significant disparity between the predicted gene sets produced by the International Human Genome Sequencing Consortium (HGSC) and Celera Genomics. To determine whether the source of this discrepancy was due to underlying differences in the genomic sequences or different gene prediction methodologies, we analyzed both genome assemblies in parallel. Using the GENSCAN gene prediction algorithm, we generated predicted transcriptomes that could be directly compared. BLAST-based comparisons revealed a 20-30% difference between the transcriptomes. Further differences between the two genomes were revealed with protein domain PFAM analyses. These results suggest that fundamental differences between the two genome assemblies are likely responsible for a significant portion of the discrepancy between the transcript sets predicted by the two groups. |
