Super Yang-Mills Theory as a Random Matrix Model

We generalize the Gervais-Neveu gauge to four-dimensional N=1 superspace. The model describes an N=2 super Yang-Mills theory. All chiral superfields (N=2 matter and ghost multiplets) exactly cancel to all loops. The remaining hermitian scalar superfield (matrix) has a renormalizable massive propagator and simplified vertices. These properties are associated with N=1 supergraphs describing a superstring theory on a random lattice world-sheet. We also consider all possible finite matrix models, and find they have a universal large-color limit. These could describe gravitational strings if the matrix-model coupling is fixed to unity, for exact electric-magnetic self-duality.Comment: 15 pg., uuencoded compressed postscript file (.ps.Z.uu), other formats (.dvi, .ps, .ps.Z, 8-bit .tex) available at http://insti.physics.sunysb.edu/~siegel/preprints/ or at ftp://max.physics.sunysb.edu/preprints/siege

Assessment by 1H NMR spectroscopy of the structural behaviour of human parathyroid-hormone-related protein(1-34) and its close relationship with the N-terminal fragments of human parathyroid hormone in solution

Human parathyroid-hormone-related protein (hPTHrP) is a hormone that is over-expressed by a large number of tumors and is produced by a variety of normal cells. Its main biological functions are shown by the N-terminal fragment (1-34) and are similar to those of parathyroid hormone with which it shares a common G-protein-coupled receptor. Hence to gain insight into the structure-function relationship of these hormones we have investigated the solution structure of hPTHrP(1-34) in pure water alone and have monitored the effect of adding TFE. CD spectra in pure water showed that it only possesses a small content of alpha-helical secondary structure, which from the NMR data, consists of a short unstable helix between Gln-16 and Leu-24 with the rest of the peptide in an essentially unstructured state. On adding 50% TFE (v/v) there was a considerable increase in stable secondary structure, without any evidence of stable tertiary structure. The subsequent structure calculations showed the presence of two well defined helices, from Ser-3 to Gly-12 and from Asp-17 to Thr-33, connected by a flexible linker. The similarity in behaviour of hPTHrP(1-34) and the N-terminal fragments of PTH under various solution conditions is shown from the 1H NMR data presented here and an extensive review of the literature data

Pathway Correlation Profile of Gene-Gene Co-Expression for Identifying Pathway Perturbation

<div><p>Identifying perturbed or dysregulated pathways is critical to understanding the biological processes that change within an experiment. Previous methods identified important pathways that are significantly enriched among differentially expressed genes; however, these methods cannot account for small, coordinated changes in gene expression that amass across a whole pathway. In order to overcome this limitation, we use microarray gene expression data to identify pathway perturbation based on pathway correlation profiles. By identifying the distribution of gene-gene pair correlations within a pathway, we can rank the pathways based on the level of perturbation and dysregulation. We have shown this successfully for differences between two experimental conditions in <em>Escherichia coli</em> and changes within time series data in <em>Saccharomyces cerevisiae</em>, as well as two estrogen receptor response classes of breast cancer. Overall, our method made significant predictions as to the pathway perturbations that are involved in the experimental conditions.</p> </div

Pathway correlation profiles for Ribosome Pathway (sce03010) in <i>S. cerevisiae</i>.

<p>(<b>a</b>) Gene expression level plots of the Ribosome Pathway (<b>b</b>) Pathway correlation profile kernel density smoothed graphs before fisher transformation of the Ribosome Pathway. (<b>c</b>) Pathway correlation profile kernel density smoothed graphs after fisher transformation of the Ribosome Pathway. (Control: black, 0 minutes: red, 15 minutes: blue, 45 minutes: green, 90 minutes: yellow, and 360 minutes: magenta).</p

The structure of human parathyroid hormone from a study of fragments in solution using 1H NMR spectroscopy and its biological implications

In order to gain insight into the structure of human parathyroid hormone (hPTH), four fragments [hPTH(1-34), hPTH(18-48), hPTH(28-48), and hPTH(53-84)], which cover all regions of the intact hormone, have been investigated by CD and NMR spectroscopy in combination with distance geometry, and restrained molecular dynamics and energy minimization calculations, under a variety of solution conditions. Significantly, all fragments showed little propensity to form stable structures in aqueous solution alone, and it was only on the addition of trifluoroethanol (TFE) that defined structural features were observed. In an extension of earlier work [Klaus et al. (1991) Biochemistry 30, 6936-6942], hPTH(1-34) in 70% trifluoroethanol (TFE) showed two helices that were longer than in 10% TFE, but essentially showed the same characteristics. Although overlap in the 1H NMR spectra prevented the determination of quantitative NOE data for residues 26-30, the combination of the alpha-proton chemical shift data and quantitative NOE data indicated the helices extend from residues 3 to 13 and 15 to 29. No evidence was found for interaction of the two helical regions. The nature and extent of this second helix in the intact hormone were better defined from the data for hPTH(18-48). Under limiting solution conditions, where the fragment assumed its maximum helical content, a well-defined helix was observed between residues 21 and 38 with a possible discontinuity between Leu-28 and Gln-29. There was little evidence of any form of secondary structure between Gly-38 and the terminus of this fragment, Ser-48. In keeping with this result, the shorter fragment, hPTH(28-48), showed little evidence of stable secondary structure on addition of TFE. From the alpha-proton chemical shifts residues 23-27 appeared to sustain helical structure more readily than the rest of molecule under all solution regimes in both hPTH(1-34) and hPTH(18-48). In contrast to the other two longer fragments hPTH(53-84) showed little propensity for helical secondary structure even at the highest TFE concentrations. However, there was evidence that the molecule did adopt a defined three-dimensional structure. Various long-range NOE's were observed in 10% TFE that allowed the calculation of an open tertiary structure consisting of an initial series of turns surrounded by a loop structure of several loose turn

Flowchart describing pathway correlation perturbation method for analyzing gene expression data on a pathway level.

<p>Initially, gene expression data is processed and normalized. Expression profiles are then created for the set of genes involved in each pathway. Using these expression profiles, pathway correlation profiles are created in each condition for each pathway. These results are then combined to determine the pathway’s mean difference in gene-gene pair correlations, and then ranked based on their significance of perturbation.</p

Comparison between DAVID Gene Set Enrichment analysis and Pathway Correlation Profile analysis of the human breast cancer data set.

<p>Pathway rankings based on adjusted p-values. Those pathways with positive mean differences show that the gene-gene pairs on average have a higher correlation in ER-positive patient samples and a lower correlation in ER-negative patient samples for that pathway. (Full pathway ranking in Supplemental Data). *: Benjamini correction.</p