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C Stoeckert

Publications and source records attributed to C Stoeckert.

8 recordsLinked to original sources
PubMed2001

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation has been the lack of standards for presenting and exchanging such data. Here we present a proposal, the Minimum Information About a Microarray Experiment (MIAME), that describes the minimum information required to ensure that microarray data can be easily interpreted and that results derived from its analysis can be independently verified. The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools. With respect to MIAME, we concentrate on defining the content and structure of the necessary information rather than the technical format for capturing it.

Computational Biology↗
PubMed2001

A relational schema for both array-based and SAGE gene expression experiments.

MOTIVATION AND RESULTS: A relational schema is described for capturing highly parallel gene expression experiments using different technologies. This schema grew out of efforts to build a database for collaborators working on different biological systems and using different types of platforms in their gene expression experiments as well as different types of image quantification software. The tables are conceptually organized into three categories of information: Platform, Experiment (which includes image scanning and quantification), and Data. The strengths of the schema are: (i) integrating information on array elements using a gene index; (ii) describing samples using ontologies; (iii) reducing an experiment to a single RNA source for precise descriptions yet not losing the relationships between experiments done at the same time or for the same project; and (iv) maintaining both raw and processed (e.g. cleansed and normalized) data and recording how the data is processed. The result is a novel schema, which can hold both array and non-array data, is extensible for detailed experimental descriptions that are precise and consistent, and allows for meaningful comparisons of genes between experiments.

Databases, Factual↗
PubMed1996

The myosin filament XV assembly: contributions of 195 residue segments of the myosin rod and the eight C-terminal residues.

A mixture of two peptides of approximately M(r) 13000 has been isolated from a papain digest of LC2 deficient myosin. The peptides assemble into highly ordered aggregates which in one view are made up of strands of pairs of dots with an average side to side spacing of 13.0 nm and an average axial repeat of 9.0 nm. In another view there are strands of single dots with a side-to-side spacing of 7.8 nm and an axial repeat of 9.1 nm. From N-terminal peptide sequencing, the two peptides have been shown to come from regions of the myosin rod displaced by 195 residues. We have shown that either peptide alone can assemble to form the same aggregates. The 195 residue displacement of the M(r) 13000 peptides corresponds closely to the 196 residue repeat of charges along the myosin rod. This finding permits us to designate 195 residue segments of the myosin rod and to relate assembly characteristics directly to the similar 195 residue segments and 196 residue charge repeat. The most C-terminal 195 residue segment carries information for assembly into helical strands. The contiguous 195 residue segment, in major part, carries information for the unipolar assembly, characteristic of the assembly in each half of the myosin filament. The next contiguous 195 residue segment, in major part, carries information for bipolar assembly which is characteristic of the bare zone region of the filament; and for the transition from the bipolar bare zone to unipolar assembly. The effect of the eight C-terminal residues of the myosin rod on the assembly of the contiguous 195 residues has also been studied. The entire fragment of 195 + eight C-terminal residues assembled to form helical strands with an axial repeat of 30 nm. Successive deletion of charged residues changed the axial repeat of the helical strands suggesting that the charged residues at the C-terminus are involved in determining the pitch in the helical assembly of the contiguous 195 residues.

Amino Acid Sequence↗
PubMed1995

Immunomodulation of pancreatic islet allografts in mice with CTLA4Ig secreting muscle cells.

In an effort to create a model of in vivo production of immunosuppressants, we have transfected C2C12 muscle cells (H-2k) with the cDNA for CTLA4Ig, a fusion protein that prevents the activation of T cells by blocking the costimulatory signal transduced by the T cell receptors CD28 and CTLA4. CTLA4Ig-secreting clones were cotransplanted with islets as composite grafts in the renal subcapsular space of diabetic mice. When the myoblasts were syngeneic to C3H/HeJ hosts (H-2k), there was a significant prolongation of survival of allogeneic C57Bl/6J (H-2b) islets from a mean 11.0 days to 31.7 days. When the graft was completely allogeneic (H-2k myoblasts and islets into H-2b recipients), there was no benefit in survival. A transient blockade of LFA-1 with the mAb M17 was synergistic in this combination: 8 out of 12 C57Bl/6J recipients achieved long-term acceptance. Systemic CTLA4Ig levels were detected up to 60 days after transplantation. In conclusion, we have shown that C2C12 muscle cells can be genetically engineered to secrete functional CTLA4Ig and that they can be used as a gene reservoir for the continuous in vivo production of CTLA4Ig to modulate the survival of islet cell allografts.

Abatacept↗
PubMed1988

Globin gene expression in hereditary persistence of fetal haemoglobin and (delta beta) (0)-thalassaemia.

Recent advances in molecular and cell biology have led to major insights into understanding the regulation of globin gene expression in erythroid cells. Studies on HPFH and related syndromes have contributed much to this knowledge. Although no single explanation has emerged concerning the mechanism by which the deletional HPFH and (delta beta)(0)-thalassaemia affect HbF expression, they have led to new testable hypotheses to explain how different deletions result in similar phenotypes. The non-deletional HPFH and related syndromes have been the subject of recent intense interest, and a number of these disorders are now known to be associated with single-base changes in the promoter regions of one or the other fetal globin genes. If these base changes are causally related to the observed phenotypes, the molecular basis by which they increase HbF and simultaneously decrease HbA production remains to be determined. In addition, it has been recognized that other single-base changes 5' to the fetal-globin genes are associated with and may affect the phenotypic expression of certain forms of sickle-cell disease and beta-thalassaemia. Increased HbF production and high G gamma: A gamma ratios result in these individuals only under conditions of erythropoietic stress. The relationship between these point mutations and the cell biology of erythroid development clearly needs to be better delineated. Studies on HbF expression in humans will no doubt lead to elucidation of the mechanisms controlling the regulated expression of globin gene switching in normal and disease states, and hopefully, result in the design of molecular strategies for the amelioration of many of the human haemoglobinopathies.

Animals↗