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Biomedical subjects

R Sharan

Publications and source records attributed to R Sharan.

At least 19 recordsLinked to original sources
PubMed2004

Multiplexing schemes for generic SNP genotyping assays.

A generic genotyping assay utilizes a fixed set of reagents, which is independent of the actual target sample, to determine all present alleles. An example is the interrogation of several amplicons spanning polymorphic sites using an all k-mer array. Due to the high cost associated with a genotyping experiment, it is desirable to design a set of experiments, which maximizes the number of SNPs that can be genotyped in parallel per assay. In this study we investigate algorithmic approaches for optimally multiplexing SNP genotyping using generic assays. We devise a graph theoretic formulation of the problem and use it to derive an approximation algorithm for the problem, and several practical heuristics. We apply our methods to simulated and real data, for evaluating the multiplexing rates afforded by generic techniques. The results on real human data show the practicality of generic approaches for genotyping, allowing, e.g., the genotyping of 5000 SNPs using four all 7-mer arrays.

Algorithms↗
PubMed2004

Reconstructing chain functions in genetic networks.

Deciphering the mechanisms that control gene expression in the cell is a fundamental question in molecular biology. This task is complicated by the large number of possible regulation relations in the cell, and the relatively small amount of available experimental data. Recently, a new class of regulation functions called chain functions was suggested. Many signal transduction pathways can be accurately modeled by chain functions, and the restriction to chain functions greatly reduces the vast search space of regulation relations. In this paper we study the computational problem of reconstructing a chain function using a minimum number of experiments, in each of which only few genes are perturbed. We give optimal reconstruction schemes for several scenarios and show their application in reconstructing the regulation of galactose utilization in yeast.

Computational Biology↗
PubMed2003

Scoring clustering solutions by their biological relevance.

MOTIVATION: A central step in the analysis of gene expression data is the identification of groups of genes that exhibit similar expression patterns. Clustering gene expression data into homogeneous groups was shown to be instrumental in functional annotation, tissue classification, regulatory motif identification, and other applications. Although there is a rich literature on clustering algorithms for gene expression analysis, very few works addressed the systematic comparison and evaluation of clustering results. Typically, different clustering algorithms yield different clustering solutions on the same data, and there is no agreed upon guideline for choosing among them. RESULTS: We developed a novel statistically based method for assessing a clustering solution according to prior biological knowledge. Our method can be used to compare different clustering solutions or to optimize the parameters of a clustering algorithm. The method is based on projecting vectors of biological attributes of the clustered elements onto the real line, such that the ratio of between-groups and within-group variance estimators is maximized. The projected data are then scored using a non-parametric analysis of variance test, and the score's confidence is evaluated. We validate our approach using simulated data and show that our scoring method outperforms several extant methods, including the separation to homogeneity ratio and the silhouette measure. We apply our method to evaluate results of several clustering methods on yeast cell-cycle gene expression data. AVAILABILITY: The software is available from the authors upon request.

Algorithms↗
PubMed2001

On the complexity of positional sequencing by hybridization.

In sequencing by hybridization (SBH), one has to reconstruct a sequence from its l-long substrings. SBH was proposed as an alternative to gel-based DNA sequencing approaches, but in its original form the method is not competitive. Positional SBH (PSBH) is a recently proposed enhancement of SBH in which one has additional information about the possible positions of each substring along the target sequence. We give a linear time algorithm for solving PSBH when each substring has at most two possible positions. On the other hand, we prove that the problem is NP-complete if each substring has at most three possible positions. We also show that PSBH is NP-complete if the set of allowed positions for each substring is an interval of length k and provide a fast algorithm for the latter problem when k is bounded.

Algorithms↗
PubMed2000

CLICK: a clustering algorithm with applications to gene expression analysis.

Novel DNA microarray technologies enable the monitoring of expression levels of thousands of genes simultaneously. This allows a global view on the transcription levels of many (or all) genes when the cell undergoes specific conditions or processes. Analyzing gene expression data requires the clustering of genes into groups with similar expression patterns. We have developed a novel clustering algorithm, called CLICK, which is applicable to gene expression analysis as well as to other biological applications. No prior assumptions are made on the structure or the number of the clusters. The algorithm utilizes graph-theoretic and statistical techniques to identify tight groups of highly similar elements (kernels), which are likely to belong to the same true cluster. Several heuristic procedures are then used to expand the kernels into the full clustering. CLICK has been implemented and tested on a variety of biological datasets, ranging from gene expression, cDNA oligo-fingerprinting to protein sequence similarity. In all those applications it outperformed extant algorithms according to several common figures of merit. CLICK is also very fast, allowing clustering of thousands of elements in minutes, and over 100,000 elements in a couple of hours on a regular workstation.

Algorithms↗
PubMed1998

Sp1 as a target site for metal-induced perturbations of transcriptional regulation of developmental brain gene expression.

Differential gene expression is partially regulated by zinc finger proteins (ZFP) such as Sp1, which may be potential targets for perturbations by environmental metals. In this paper, we discuss the selective effects of lead (Pb) and other heavy metals on the in vitro and in vivo DNA-binding of Sp1, and the developmental expression of its target genes. We have found that the presence of Pb, Zn and Cd in a DNA-binding assay differentially modulated the binding of Sp1 to its specific DNA sequence, while Ca, Mg and Ba, did not. In PC12 cells, cultured in the presence of low concentrations of Pb, a premature enhancement of Sp1 DNA-binding was observed. Similarly, Sp1 DNA-binding in the cerebellum of Pb-exposed animals was shifted to the first week after birth, while the developmental profile of a non-ZFP, NFkB, was not. Furthermore, selective premature peaks of myelin basic protein and proteolipid protein mRNA expression were observed to occur in a manner relative to the changes in Sp1 DNA-binding. Since these genes are high targets for Sp1, these data suggest that exposure to heavy metals may alter developmental gene expression and brain development through selective modulation of the transcriptional activity of Sp1.

Animals↗
PubMed1998

Immunomodulating activity of analogs of noninflammatory fragment 163-171 of human interleukin-1beta.

The synthetic nonapeptide Val-Gln-Gly-Glu-Glu-Ser-Asn-Asp-Lys corresponding to the amino acid sequence 163-171 of human interleukin-1beta (IL-1beta) has been reported to retain considerable immunostimulatory activity of the native protein without the induction of the inflammatory or pyrogenic responses. Two lipophilic derivatives of this nonapeptide, one having a lauroyl residue (1) and the other having a palmitoyl residue (2) at the N-terminus of the peptide, and a more stable analog carrying D-Val residue at position 1 of the peptide (3) were synthesized with a view to find out if these structural modifications had a favorable effect on in vitro mouse thymocyte proliferation and IL-1 dependent inhibition of A375 cells. We have found that analogs (1) and (2) are active in both the tests like the parent nonapeptide. The lipophilic analog (2) is in fact, effective at a lower dose as compared to the parent nonapeptide in mouse thymocyte proliferation assay. Although the analog (3) has the ability to inhibit A375 cells, it does not stimulate mouse thymocyte proliferation in vitro. The IL-1beta fragment (163-171) and the analog (2) were further compared for their effects on pyrogenicity, blood glucose level, acute phase response and radioprotection. Unlike IL-1beta, its fragment (163-171) and the analog (2) do not induce pyrogenicity and any of the acute phase related changes such as the increase in C-reactive protein and hypoglycemia following their administration in Balb/c mice. We have found that 40% of animals treated with analog (2) survive more than 21 days after lethal irradiation as compared to 20% survivors in groups treated with recombinant IL-1beta or its nonapeptide fragment (163-171), under conditions when all the control animals died within 10 days. This study may help in designing small peptides which may be more effective and stable.

Acute-Phase Proteins↗
PubMed1997

Stimulation of IL-2 production and CD2R expression by splenopentin analogs.

Splenopentin (SP-5), is a pentapeptide corresponding to the amino acid sequence 32-36 (Arg-Lys-Glu-Val-Tyr) of the splenic hormone splenin. Its synthetic analogs: Lys-Lys-Glu-Val-Tyr(1) and D-Lys-Lys-Glu-Val-Tyr (2) have been evaluated for active T-cell rosette (CD2R), total T-cell rosette (CD2), interleukin-2 (IL-2) stimulation and effect on antibody production. SP-5 as well as both the analogs stimulated CD2R. Analogs (1) and (2) were also found to stimulate IL-2 production. These observations suggest that in vitro human NK cell augmentation with analogs (1) and (2) reported earlier may be due to enhanced IL-2 production.

Adjuvants, Immunologic↗
PubMed1993

Cerebral palsy.

In a prospective study it was found that cerebral palsy constituted 0.29% of total paediatric outdoor cases during the study period of 1988-1990. Seventy-five children suffering from cerebral palsy were studied at SN Children Hospital, Allahabad. Male to female ratio was 1:2. There were 42.8% cases who belonged to the age between one and 2 years. Hypertonic cases were predominant over hypotonic cases (3:1). Hemiplegia was commonest (68%) while triplegia was least common (2.7%). There were 24.5% cases who were mentally retarded. Hypertonic cases improved more frequently than hypotonic cases. An early management by paediatric physiotherapy may play an important role in the treatment of cerebral palsy.

Cerebral Palsy↗
PubMed1992

Surgical manifestations of ascariasis in childhood.

Amongst 50 patients with surgical complications of Ascaris lumbricoides 35 patients (70%) were treated conservatively and 15 patients (30%) required surgical intervention which included squeezing of worms to distal colon, resection and anastomosis of ileum, appendicectomy and peritoneal lavage. Intestinal perforation was observed in 3 cases. Two patients (4%) died because of postoperative complications. Those presenting with subacute intestinal obstruction had no mortality or morbidity. Although a large number of roundworms were seen in the jejunum, the obstruction was generally observed in the distal ileum.

Anthelmintics↗
PubMed1991

Effect of chronic microwave radiation on T cell-mediated immunity in the rabbit.

Experiments were conducted to elucidate the effects of chronic low power-level microwave radiation on the immunological systems of rabbits. Fourteen male Belgian white rabbits were exposed to microwave radiation at 5 mW/cm2, 2.1 GHz, 3 h daily, 6 days/week for 3 months in two batches of 7 each in specially designed miniature anechoic chambers. Seven rabbits were subjected to sham exposure for identical duration. The microwave energy was provided through S band standard gain horns connected to a 4K3SJ2 Klystron power amplifier. The first batch of animals were assessed for T lymphocyte-mediated cellular immune response mechanisms and the second batch of animals for B lymphocyte-mediated humoral immune response mechanisms. The peripheral blood samples collected monthly during microwave/sham exposure and during follow-up (5/14 days after termination of exposures, in the second batch animals only) were analysed for T lymphocyte numbers and their mitogen responsiveness to ConA and PHA. Significant suppression of T lymphocyte numbers was noted in the microwave group at 2 months (P less than 0.01, delta % 21.5%) and during follow-up (P less than 0.01, delta % 30.2%). The first batch animals were initially sensitised with BCG and challenged with tuberculin (0.03 ml) at the termination of microwave irradiation/sham exposure and the increase in foot pad thickness (delta mm), which is a measure of T cell-mediated immunity (delayed type hypersensitivity response, DTH) was noted in both the groups. The microwave group revealed a better response than the control group (delta % +12.4 vs. +7.54). The animals were sacrificed and the tissue T lymphocyte counts (spleen and lymph node) were analysed.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗