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Biomedical subjects

R Ramaswamy

Publications and source records attributed to R Ramaswamy.

At least 19 recordsLinked to original sources
PubMed2000

Identification of parasitic genes by computational methods.

A number of parasite genome projects are under way, and large amounts of nucleotide sequence data are becoming available for analysis. There is an urgent need for development of theoretical tools to analyze the genome data, including identification of protein-coding sequences. The majority of the methods developed to date require prior information about the genome before accurate predictions can be made. Because such information is not available for many parasites, these methods cannot be directly applied. In this article, Alok Bhattacharya and colleagues describe some of the gene-prediction methods commonly in use, and a new method, GeneScan, that they have developed for the analysis of parasite genomes.

Animals↗
PubMed1998

Effects of cyclic AMP on expression of myelin genes in the N20.1 oligodendroglial cell line.

The N20.1 immortalized cell line has several characteristics of differentiating oligodendrocytes (OLs), including expression of the glycolipids galactocerebroside (GalC) and sulfatide, and the myelin proteins CNPase and myelin basic protein (MBP) (1,2). Addition of 1-100 microM forskolin to elevate cyclic AMP (cAMP) levels changed cell morphology from irregular and flattened to a more rounded birefringent cell with multiple branched processes. GalC and sulfatide were detected immunocytochemically after permeabilization in the untreated cells and levels appeared to increase slightly following exposure to forskolin. Further analysis showed that most of the glycolipid was internal, with virtually no detectable levels on the cell surface in untreated cells and a very slight change following treatment with forskolin. Synthesis of the two lipids as measured by [H3]galactose incorporation doubled within 24 hours of treatment with forskolin. Levels of message for UDP-galactose: ceramide galactosyl transferase (CGT), a key enzyme in the synthesis of GalC and sulfatide, were compared with those of MBP and proteolipid protein (PLP), before and after elevation of cAMP. No changes were observed in levels of mRNA for CGT and PLP after 24 hours, with a possible increase by 48 hours. In contrast, levels of MBP message dropped precipitously by 24 hours; this was accompanied by an increase in levels of message for suppressed cAMP-inducible POU (SCIP). Thus CGT transcription is regulated independently of MBP and SCIP in N20.1 cells. Analysis of MBP levels by immunocytochemistry and Western blot showed little or no change in protein levels at 24 and 48 hours, in contrast to the sharp decrease in message levels by 24 hours, indicating a relatively long half life for MBP in this cell line. Thus, the N20.1 cells are an informative model for examining regulation of expression of myelinotypic proteins and GalC, as well as the transport of this lipid to the plasma membrane.

Animals↗
PubMed1997

Application of rank analysis of covariance methods to analysis of multiple anatomical regions with treatment for seborrheic dermatitis.

This paper presents the advantages of rank analysis of covariance in contrast to the Mantel-Haenszel procedure in the presence of a covariate. In this paper, data from a clinical trial with an indication for seborrheic dermatitis, which afflicts multiple anatomical regions, is presented. This paper presents analysis performed using both the Mantel-Haenszel procedure and rank analysis of covariance for separate anatomical regions, as well as for the combined anatomical regions. The analysis for the combined anatomical regions involves weighted sums over different strata.

Dermatitis, Seborrheic↗
PubMed1997

Prediction of probable genes by Fourier analysis of genomic sequences.

MOTIVATION: The major signal in coding regions of genomic sequences is a three-base periodicity. Our aim is to use Fourier techniques to analyse this periodicity, and thereby to develop a tool to recognize coding regions in genomic DNA. RESULT: The three-base periodicity in the nucleotide arrangement is evidenced as a sharp peak at frequency f = 1/3 in the Fourier (or power) spectrum. From extensive spectral analysis of DNA sequences of total length over 5.5 million base pairs from a wide variety or organisms (including the human genome), and by separately examining coding and non-coding sequences, we find that the relative-height of the peak at f = 1/3 in the Fourier spectrum is a good discriminator of coding potential. This feature is utilized by us to detect probable coding regions in DNA sequences, by examining the local signal-to-noise ratio of the peak within a sliding window. While the overall accuracy is comparable to that of other techniques currently in use, the measure that is presently proposed is independent of training sets or existing database information, and can thus find general application. AVAILABILITY: A computer program GeneScan which locates coding open reading frames and exonic regions in genomic sequences has been developed, and is available on request.

Algorithms↗
PubMed1996

Prognostic criteria in Clostridium difficile colitis.

OBJECTIVE: To determine the prognostic factors in Clostridium difficile (CD) colitis. METHODS: We conducted a retrospective study of proven cases of CD colitis in l8 months. Seventy six patients (from a 605-bed community hospital in the Bronx, NY) with proven CD colitis were studied. Mortality in patients with CD colitis was also examined. RESULTS: Seventy six patients with proven CD colitis were admitted between January 1993 and June 1994. Eighteen patients died during the same admission. Upon admission, serum albumin was less than 25 g/L in 12 (20.6%) of the survivors and in eight (44%) of the deceased patients (p <0.05). A fall in serum albumin levels was noted with the onset of symptoms of CD colitis in those who survived as well as in those who died, with a greater fall of 11.2 g/L (range 10-20 g/L) in patients who died compared with a fall of 6 g/L (range 5-10 g/L)in those who survived (p <0.05). Use of more than three antibiotics was noted in 13 (72%) of those who died and in 18 (31%) of those who survived (p <0.05). Persistence of CD cytotoxin 7 or more days after initiation of treatment was present in 14 (77%) of those who died and in eight (13%) of the survivors (p <0.01). Duration of hospitalization correlated with the development of CD colitis (35.89 vs 11.7 days) with no significant difference between survivors and deceased patients with CD colitis. Factors such as age, sex, residence, past medical history score, mean score of presenting complaints of CD colitis, history of prior episodes CD colitis, and mean number of recurrent episodes showed no difference in mortality. CONCLUSION: Factors predictive of an increased mortality in patients with CD colitis include a serum albumin of less than 25 g/L on admission, a fall in serum albumin level of greater than 11 g/L at the onset of symptoms of CD colitis, use of three or more antibiotics, and persistence of positive CD cytotoxin in the stool after completion of 7 or more days of treatment.

Adult↗
PubMed1995

Age-adjusted survival curves with application in the Framingham Study.

Kaplan-Meier curves provide descriptors of survival information for different subgroups within a data set. Investigators frequently use these figures for descriptive comparison of the effect of a particular measure upon survival. When subjects enter a study at different ages and age is associated with survival, it is often desirable to adjust survival information for age differences in the subgroups. This report discusses several methods for age-adjustment of survival curves, including direct age-adjustment and proportional hazard modelling with age as a covariate.

Adult↗
PubMed1994

Syncytial mutations in the herpes simplex virus type 1 gK (UL53) gene occur in two distinct domains.

Syncytial (syn) mutants of herpes simplex virus cause cell fusion. Many syn mutations map to the syn1 locus, which has been identified with the gK (UL53) gene. In this work, the gK genes of eight syn mutants derived from the KOS strain were sequenced to identify residues and, possibly, domains important for the fusion activity of mutant gK. DNA sequencing showed that six mutants (syn30, syn31, syn32, syn102, syn103, and syn105) had single missense mutations in the gK gene. Two of these, syn31 and syn32, had identical mutations that caused the introduction of a potential site for N-linked glycosylation. syn31 gK was analyzed by in vitro translation and found to utilize the novel glycosylation site. Two other mutants, syn8 and syn33, had three mutations each, resulting in three amino acid substitutions in syn8 and two substitutions in syn33. Of the 10 gK syn mutant sequences known, 8 have mutations in the N-terminal domain of gK, suggesting that this domain, which is likely to be an ectodomain, is important for the function of the protein. The other two mutants, syn30 and syn103, have mutations near the C terminus of gK.

Amino Acid Sequence↗
PubMed1992

In vitro characterization of the HSV-1 UL53 gene product.

The UL53 gene is the locus altered in many syncytial mutants of herpes simplex virus type 1 (HSV-1). However, the protein encoded by this gene has not been characterized. In this study, the UL53 protein was produced by in vitro translation of in vitro-transcribed UL53 RNA. Post-translational processing of the protein was studied by translation in the presence of pancreatic microsomal membranes. These microsomes carry out the processing steps that normally occur in the rough endoplasmic reticulum. The unprocessed protein had an apparent molecular weight of 27K, whereas the microsomally processed form had an apparent molecular weight of 36K. Two types of post-translational modification were detected: Addition of N-linked oligosaccharides and cleavage of an N-terminal signal sequence. N-linked glycosylation occurred in the first 112 residues of the protein, consistent with the presence of N-linked glycosylation signals at residues 48 and 58. Signal sequence cleavage occurred after residue 30. A membrane-binding, possibly transmembrane, domain was found between residues 113 and 170, probably consisting of the hydrophobic sequence 125-139. These results establish that the N-terminal domain of the UL53 protein, which is the site of those syncytial mutations that have been sequenced, is on the interior side of the microsomal membranes, which is topologically equivalent to the lumen of the rough endoplasmic reticulum and to the extracellular side of the plasma membrane. Additional hydrophobic, possibly transmembrane, domains exist nearer the C-terminus of the protein. It also was found that the in vitro-translated UL53 protein aggregated when heated, even in the presence of SDS. This property was mapped to the C-terminal one-third of the protein.

Amino Acid Sequence↗