Biomedical subjects

A Dhiman

Publications and source records attributed to A Dhiman.

4 recordsLinked to original sources

PubMed2004

Data-driven computer simulation of human cancer cell.

Using the Diagrammatic Cell Language trade mark, Gene Network Sciences (GNS) has created a network model of interconnected signal transduction pathways and gene expression networks that control human cell proliferation and apoptosis. It includes receptor activation and mitogenic signaling, initiation of cell cycle, and passage of checkpoints and apoptosis. Time-course experiments measuring mRNA abundance and protein activity are conducted on Caco-2 and HCT 116 colon cell lines. These data were used to constrain unknown regulatory interactions and kinetic parameters via sensitivity analysis and parameter optimization methods contained in the DigitalCell computer simulation platform. FACS, RNA knockdown, cell growth, and apoptosis data are also used to constrain the model and to identify unknown pathways, and cross talk between known pathways will also be discussed. Using the cell simulation, GNS tested the efficacy of various drug targets and performed validation experiments to test computer simulation predictions. The simulation is a powerful tool that can in principle incorporate patient-specific data on the DNA, RNA, and protein levels for assessing efficacy of therapeutics in specific patient populations and can greatly impact success of a given therapeutic strategy.

Apoptosis↗

PubMed2001

Identification of oligomerizing peptides.

The AraC DNA binding domain is inactive in a monomeric form but can activate transcription from the arabinose operon promoters upon its dimerization. We used this property to identify plasmids encoding peptide additions to the AraC DNA binding domain that could dimerize the domain. We generated a high diversity library of plasmids by inserting 90-base oligonucleotides of random sequence ahead of DNA coding for the AraC DNA binding domain in an expression vector, transforming, and selecting colonies containing functional oligomeric peptide-AraC DNA binding domain chimeric proteins by their growth on minimal arabinose medium. Six of seven Ara(+) candidates were partially characterized, and one was purified. Equilibrium analytical centrifugation experiments showed that it dimerizes with a dissociation constant of approximately 2 micrometer.

Amino Acid Sequence↗

PubMed2000

Recognition of overlapping nucleotides by AraC and the sigma subunit of RNA polymerase.

The Escherichia coli promoter p(BAD), under the control of the AraC protein, drives the expression of mRNA encoding the AraB, AraA, and AraD gene products of the arabinose operon. The binding site of AraC at p(BAD) overlaps the RNA polymerase -35 recognition region by 4 bases, leaving 2 bases of the region not contacted by AraC. This overlap raises the question of whether AraC substitutes for the sigma subunit of RNA polymerase in recognition of the -35 region or whether both AraC and sigma make important contacts with the DNA in the -35 region. If sigma does not contact DNA near the -35 region, p(BAD) activity should be independent of the identity of the bases in the hexamer region that are not contacted by AraC. We have examined this issue in the p(BAD) promoter and in a second promoter where the AraC binding site overlaps the -35 region by only 2 bases. In both cases promoter activity is sensitive to changes in bases not contacted by AraC, showing that despite the overlap, sigma does read DNA in the -35 region. Since sigma and AraC are thus closely positioned at p(BAD), it is possible that AraC and sigma contact one another during transcription initiation. DNA migration retardation assays, however, showed that there exists only a slight degree of DNA binding cooperativity between AraC and sigma, thus suggesting either that the normal interactions between AraC and sigma are weak or that the presence of the entire RNA polymerase is necessary for significant interaction.

AraC Transcription Factor↗

PubMed1988

Cytocortical organization during natural and prolonged mitosis of mouse 8-cell blastomeres.

Late 8-cell blastomeres were harvested within the first 45 min after entering mitosis. Some mitotic cells were analysed within the ensuing 2 h for the organization of their surface in relation to their progress through mitosis. Whereas in most late interphase cells microvilli were restricted to a discrete polar region, in mitotic cells at all stages from early metaphase to immediately postcytokinesis microvilli were found to be present over more of the cell surface. Other mitotic cells were placed in nocodazole to arrest them in M-phase for up to 10 h. They were found to show an even more extensive distribution of microvilli over the whole surface, the longer periods of incubation yielding more extended coverage such that many cells no longer appeared to have any residual surface polarity. Removal from nocodazole at all time points from 1 to 10 h resulted in most cells completing mitosis to yield pairs of cells which, in most cases, resembled pairs derived from nonarrested blastomeres and in which a defined polar area of microvilli was restored. However, the percentage of differentiative divisions decreased after 6 h arrest. If, instead of removing cells from nocodazole, they were placed in both nocodazole and cytochalasin D (CCD) for periods of up to 3 h, most microvilli retracted to reveal a tight polar zone of CCD-resistant microvilli. This result suggests that a heterogeneity of cytocortical organization may still exist within the arrested mitotic cell. We propose a model to explain the origin of this heterogeneity of organization and its relationship to the generation of cell diversity.

Animals↗