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S Bekiranov

Publications and source records attributed to S Bekiranov.

6 recordsLinked to original sources
PubMed2001

Reprogramming of the macrophage transcriptome in response to interferon-gamma and Mycobacterium tuberculosis: signaling roles of nitric oxide synthase-2 and phagocyte oxidase.

Macrophage activation determines the outcome of infection by Mycobacterium tuberculosis (Mtb). Interferon-gamma (IFN-gamma) activates macrophages by driving Janus tyrosine kinase (JAK)/signal transducer and activator of transcription-dependent induction of transcription and PKR-dependent suppression of translation. Microarray-based experiments reported here enlarge this picture. Exposure to IFN-gamma and/or Mtb led to altered expression of 25% of the monitored genome in macrophages. The number of genes suppressed by IFN-gamma exceeded the number of genes induced, and much of the suppression was transcriptional. Five times as many genes related to immunity and inflammation were induced than suppressed. Mtb mimicked or synergized with IFN-gamma more than antagonized its actions. Phagocytosis of nonviable Mtb or polystyrene beads affected many genes, but the transcriptional signature of macrophages infected with viable Mtb was distinct. Studies involving macrophages deficient in inducible nitric oxide synthase and/or phagocyte oxidase revealed that these two antimicrobial enzymes help orchestrate the profound transcriptional remodeling that underlies macrophage activation.

Animals↗
PubMed2001

Microarray-based analysis of early development in Xenopus laevis.

In order to examine transcriptional regulation globally, during early vertebrate embryonic development, we have prepared Xenopus laevis cDNA microarrays. These prototype embryonic arrays contain 864 sequenced gastrula cDNA. In order to analyze and store array data, a microarray analysis pipeline was developed and integrated with sequence analysis and annotation tools. In three independent experimental settings, we demonstrate the power of these global approaches and provide optimized protocols for their application to molecular embryology. In the first set, by comparing maternal versus zygotic transcription, we document groups of genes that are temporally regulated. This analytical approach resulted in the discovery of novel temporally regulated genes. In the second, we examine changes in gene expression spatially during development by comparing dorsal and ventral mesoderm dissected from early gastrula embryos. We have discovered novel genes with spatial enrichment from these experiments. Finally, we use the prototype microarray to examine transcriptional responses from embryonic explants treated with activin. We selected genes (two of which are novel) regulated by activin for further characterization. All results obtained by the arrays were independently tested by RT-PCR or by in situ hybridization to provide a direct assessment of the accuracy and reproducibility of these approaches in the context of molecular embryology.

Animals↗
PubMed2001

Asymmetric primitive-model electrolytes: Debye-Hückel theory, criticality, and energy bounds.

Debye-Hückel (DH) theory is extended to treat two-component size- and charge-asymmetric primitive models, focusing primarily on the 1:1 additive hard-sphere electrolyte with, say, negative ion diameters a(--) larger than the positive ion diameters a(++). The treatment highlights the crucial importance of the charge-unbalanced "border zones" around each ion into which other ions of only one species may penetrate. Extensions of the DH approach that describe the border zones in a physically reasonable way are exact at high T and low density rho and, furthermore, are also in substantial agreement with recent simulation predictions for trends in the critical parameters, T(c) and rho(c), with increasing size asymmetry. Conversely, the simplest linear asymmetric DH description, which fails to account for physically expected behavior in the border zones at low T, can violate a new lower bound on the energy (which applies generally to models asymmetric in both charge and size). Other theories, including those based on the mean spherical approximation, predict trends in the critical parameters quite opposite to those established by the simulations.

Biophysics↗
PubMed2001

Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome.

The approach to annotating a genome critically affects the number and accuracy of genes identified in the genome sequence. Genome annotation based on stringent gene identification is prone to underestimate the complement of genes encoded in a genome. In contrast, over-prediction of putative genes followed by exhaustive computational sequence, motif and structural homology search will find rarely expressed, possibly unique, new genes at the risk of including non-functional genes. We developed a two-stage approach that combines the merits of stringent genome annotation with the benefits of over-prediction. First we identify plausible genes regardless of matches with EST, cDNA or protein sequences from the organism (stage 1). In the second stage, proteins predicted from the plausible genes are compared at the protein level with EST, cDNA and protein sequences, and protein structures from other organisms (stage 2). Remote but biologically meaningful protein sequence or structure homologies provide supporting evidence for genuine genes. The method, applied to the Drosophila melanogaster genome, validated 1,042 novel candidate genes after filtering 19,410 plausible genes, of which 12,124 matched the original 13,601 annotated genes. This annotation strategy is applicable to genomes of all organisms, including human.

Animals↗
PubMed2000

Diffusion in inhomogeneous media: theory and simulations applied to whole cell photobleach recovery.

A continuum description for diffusion in a simple model for an inhomogeneous but isotropic media is derived and implemented numerically. The locally averaged density of diffusible marker is input from experiment to define the sample. Then a single additional parameter, the effective diffusion constant, permits the quantitative simulation of diffusive relaxation from any initial condition. Using this simulation, it is possible to model the recovery of a fluorescently tagged protein in the endoplasmic reticulum (ER) after photobleaching a substantial region of a live cell, and fit an effective diffusion constant which is a property both of the geometry of the ER and the marker. Such quantitative measurements permit inferences about the topology and internal organization of this organelle.

Algorithms↗