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S Ramachandran

Publications and source records attributed to S Ramachandran.

At least 91 records · Page 5Linked to original sources
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↗
PubMed1997

Molecular differences between several species of Strongyloides and comparison of selected isolates of S. stercoralis using a polymerase chain reaction-linked restriction fragment length polymorphism approach.

The relationships between the parasitic nematodes of medical importance belonging to the genus Strongyloides was studied using a polymerase chain reaction (PCR)-linked restriction fragment length polymorphism approach. We used several human and dog isolates of S. stercoralis, a monkey isolate of S. fulleborni, and S. ratti, a rodent parasite. The molecular analysis was based on amplification of the internal transcribed spacer and the 5' portion of the 23S-like rRNA gene followed by restriction enzyme digests. The length of the PCR product was specific to each species and varied around 1.5 kilobase pairs. Using nine restriction enzymes, we were able to analyze both interspecific and intraspecific variations. With four restriction enzymes (Taq I, Dde I, Dra I, and Mwo I), human isolates of S. stercoralis from different parts of the world showed identical patterns and could be differentiated from the dog isolate of S. stercoralis. Interspecific differences were readily observed with these and other enzymes. In addition to providing new information on the genomic characteristics of Strongyloides parasites, the results suggest that this technique could be useful for diagnostic and epidemiologic investigations.

Animals↗
PubMed1997

Detection of Chlamydia trachomatis in urine samples by polymerase chain reaction and enzyme immunoassay.

First-void urine samples collected from sexually transmitted diseases (STD) clinic patients were examined by a nested polymerase chain reaction (PCR) and a commercial enzyme immunoassay (IDEIA Chlamydia) for the diagnosis of Chlamydia trachomatis urethritis or cervicitis. The primers for the PCR amplified a target in the major outer membrane protein (MOMP) gene in C trachomatis while the IDEIA detected genus-specific chlamydial lipopolysaccharide. Discrepant results were resolved by retesting urine specimens with a second (plasmid-based) PCR and taking urethral or endocervical swab results into consideration. For 231 men (chlamydial prevalence 20.4%), the sensitivity, specificity, positive and negative predictive values were 59.6%, 99.5%, 96.6% and 90.6% for urine IDEIA, 68.1%, 99.5%, 97% and 92.4% for urethral swab IDEIA and 97.9%, 99.5%, 97.9% and 99.5% for urine PCR. The corresponding rates for 66 women (chlamydial prevalence 54.6%) were 19.4%, 100%, 100% and 50.8% for urine IDEIA, 86.1%, 96.7%, 96.9% and 85.3% for endocervical swab IDEIA and 91.7%, 93.3%, 94.3% and 90.3% for urine PCR. Hence, in a high prevalence population, the urine IDEIA was a suitable alternative to the male urethral swab IDEIA but significantly less sensitive than the endocervical swab IDEIA. The urine PCR was, however, much more sensitive than the urine IDEIA for both men and women and could replace the endocervical swab IDEIA for the diagnosis of chlamydial cervicitis.

Adolescent↗
PubMed1997

Contact dermatitis with cervical lymphadenopathy following exposure to the hide beetle, Dermestes peruvianus.

Contact with beetles of the family Dermestidae can produce a variety of disorders including skin, gastrointestinal and respiratory tract disease. Dermatological disorders include dermatitis, vesicular, pustular and vasculitic lesions. In addition, there may be pruritus, desquamation and urticaria. We report a patient who developed dermatitis, a vasculitic eruption, cervical lymphadenopathy and pulmonary nodular interstitial infiltration as a result of contact with the 'hide beetle' Dermestes peruvianus.

Adult↗
PubMed1997

Assessment of iodine deficiency in selected blocks of east and west Champaran districts of Bihar.

OBJECTIVE: A survey conducted in 1964 reported a goitre prevalence of 40.3% in East and West Champaran districts of Bihar. No recent survey has been documented on the prevalence of iodine deficiency in these districts. The present study was therefore undertaken (i) to assess the prevalence of IDD in these districts, and (ii) to estimate the iodine content of salt consumed by population. METHODOLOGY: In each district, one block was selected. In each block more than 630 children in the age group of 6-12 years were included in the study and were clinically examined. Urine samples were collected from 261 children and were analyzed using standard laboratory procedures. A total of 456 salt samples were collected from children and 35 from traders from the two districts and analyzed using the standard iodometric titration method. RESULTS: The total goiter prevalence was 11.6%. The percentage of children with < 2, 2.0-4.9, 5.0-9.9 and > or = 10 mcg/dl of urinary iodine excretion level were 12.3, 13.4, 23.4 and 51.0, respectively. The median urinary iodine excretion of the children was 10.0 mcg/dl. None of the families were consuming salt with a nil iodine content and about 29.3%, were consuming salt with less than 15 ppm of iodine. Of the 35 salt samples collected from traders, all had iodine and about 17% had less than 15 ppm of iodine. CONCLUSION: The study stresses the need for strengthening the existing system of monitoring of quality of salt being provided in the East and West Champaran districts by Government of Bihar.

Child↗
PubMed1996

Stabilization of barstar by chemical modification of the buried cysteines.

The internal packing of residues in the small monomeric protein barstar was severely perturbed by chemical modification of the two buried cysteine residues with the thiol reagent 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) after prior unfolding of the protein using guanidine hydrochloride (GdnHCl). The modification produces mixed disulfides between 5-thio(2-nitrobenzoic acid) and the two Cys residues. To understand the effects of the modification of the individual cysteine residues, Cys40 and Cys82, the modification was also carried out on the two single Cys --> Ala mutant forms of barstar, C40A and C82A, whose structures, activities, and stabilities were first shown to be similar to those of wt barstar. Equilibrium GdnHCl-induced denaturation studies on wt barstar show that the modification causes the midpoint of the denaturation curve to increase by 0.6 M and the stability to increase by 1.3 kcal mol-1. Both C40A and C82A also denature at higher concentrations of GdnHCl after modification. Modification of Cys40 has approximately the same stabilizing contribution as does modification of Cys82. The structures of the modified and unmodified proteins have been compared using circular dichroism (CD) spectroscopy, UV difference absorption spectroscopy, and fluorescence spectroscopy. It is shown that the 5-thio(2-nitrobenzoic acid) groups introduced by reaction with DTNB are buried in hydrophobic environments in the modified C40A and C82A mutant proteins, as well as in modified wt barstar. The far-UV CD spectra of the modified and unmodified proteins are similar, but the mean residue ellipticity at 220 nm of wt barstar is reduced by 30% upon modification. Such a decrease is not seen for either C40A or C82A. The barnase-inhibiting activities of the three modified proteins are shown to be similar to those of the corresponding unmodified proteins. Thus, the severe perturbations of the internal packing, which result in a significant increase in stability, do not appear to affect the overall fold of barstar.

Bacterial Proteins↗
PubMed1996

Arabidopsis profilins are functionally similar to yeast profilins: identification of a vascular bundle-specific profilin and a pollen-specific profilin.

Four members of the Arabidopsis profilin (pfn) multigene family have been cloned, sequenced and analyzed. By RNA gel blot analysis it has been shown that these four genes fall into two groups: one group (pfn1 and pfn2) is expressed in all organs of the plant and the other group (pfn3 and pfn4) in floral tissues only. Based on amino acid sequence alignment Arabidopsis profilins can be divided into the same two groups: PFN1 and PFN2 are 89% identical and PFN3 and PFN4 are 91% identical. Between these two groups they are 71-75% identical. The Arabidopsis profilins bind poly-L-proline and can complement both the Saccharomyces cerevisiae profilin deletion mutant and the Schizosaccharomyces pombe cdc3-124/profilin mutation, showing that the plant profilins are functionally similar to yeast profilins despite the low amino acid sequence homology. Analysis of pfn promoter-GUS fusion genes in transgenic Arabidopsis shows that pfn2 is specifically expressed in the vascular bundles of roots, hypocotyls, cotyledons, leaves, sepals, petals, stamen filaments and stalks of developing seeds, whereas expression of pfn4 is restricted to mature and germinating pollen grains.

Amino Acid Sequence↗
PubMed1996

Identification of plant cytoskeletal, cell cycle-related and polarity-related proteins using Schizosaccharomyces pombe.

The fission yeast Schizosaccharomyces pombe has been used to identify Arabidopsis thaliana proteins that may play a role in cell shape maintenance or cell cycle regulation. An Arabidopsis thaliana cDNA library was constructed in pREP5N vector under the control of the inducible nmt1 promoter and transformed into S. pombe. Expression of the A. thaliana sequences was induced and clones showing severe morphological changes were identified and analysed. Comparison of the sequences of the inserts with the sequence data bases revealed that several cDNAs encode proteins known to play a role in function of the cytoskeleton, the cell cycle and establishment of cell polarity. These include alpha-1, alpha-2, alpha-6 and beta-6 tubulins, myosin heavy chain-like protein, ubiquitin conjugating enzymes UBC9 (E2), 26S protease subunits, Ranbinding protein, myb protein, PRL1 gene product and rho protein. Approximately 30% of the clones encode novel sequences. The results suggest that S. pombe phenotypic screening can be used to identify plant proteins involved in cell shape maintenance and regulation during cell cycle and development.

Actin Depolymerizing Factors↗
PubMed1996

Insect Control and Dosage Effects in Transgenic Canola Containing a Synthetic Bacillus thuringiensis cryIAc Gene.

Zygotic hypocotyls of canola (Brassica napus L.) cv Oscar, cv Westar, and the breeding line UGA188-20B were transformed with a truncated synthetic Bacillus thuringiensis insecticidal crystal protein gene (Bt cryIAc) under the control of the cauliflower mosaic virus 35S promoter using Agrobacterium tumefaciens-mediated transformation. Fifty-seven independently transformed lines were produced, containing 1 to 12 copies of the transgenes. A range of cry expressors was produced from 0 to 0.4% Cry as a percentage of total extractable protein. The Brassica specialists, the diamondback month (Plutella xylostella L.) and the cabbage looper (Trichoplusia ni Hubner), were completely controlled by low-, medium-, and high-expressing lines. Whereas control of the generalist lepidopteran, the corn earworm (Helicoverpa zea Boddie), was nearly complete, the other generalist caterpillar tested, the beet armyworm (Spodoptera exigua Hubner), showed a dose response that had a negative association between defoliation and cry expression. These plants were produced as models for an ecological research assessment of the risk involved in the field release of naturalized transgenic plants harboring a gene (Bt) that confers higher relative fitness under herbivore-feeding pressure.

Journal Article↗
PubMed1996

The one-stop coronary cholesterol clinic: a multidisciplinary approach to implementing evidence-based treatment.

We describe a 'one-stop' cholesterol clinic implementing a regime based on the Scandinavian Simvastatin Survival Study (4S) in patients with established coronary heart disease in a district general hospital. The clinic has been established in collaboration with the cardiac rehabilitation centre. It was commissioned as an audit project by the purchasing authority, Walsall Health, a need having been shown in a previous audit. In the new clinic, audit is inbuilt, rather than being carried out as a separate retrospective exercise, and undertaken prospectively for all patients. Central to this is a database, used for routine correspondence and administration, as well as monitoring outcome. This application of information technology has improved clinical practice. Attendance at the clinic has been excellent. Half the consultations have resulted in therapeutic interventions, many of which may otherwise have been missed. Over 50% of patients were eligible for lipid-lowering medication under the protocol. Cholesterol targets based on 4S were achieved but with much lower drug doses, which may have major cost implications. Cholesterol levels measured within 24 hours of admission for myocardial infarction were poor predictors of results obtained after convalescence. After the clinic visit, most patients were taking aspirin plus one or two other secondary prevention treatments. Guidelines have been issued to primary care. Future plans for audit links with general practitioners, integration of the metabolic and cardiological assessment of survivors of myocardial infarction, and for long-term monitoring of clinical events in treated patients are discussed.

Aged↗
PubMed1996

Quenching the thirst in dialysis patients.

In a double-blind cross-over trial, 22 stable end-stage renal failure patients on maintenance haemodialysis were subjected to conventional dialysis with dialysate containing 137 mEq/l sodium and constant ultrafiltration (UF) and to a different dialysis therapy, in which, by linear sodium modelling, the dialysate sodium was reduced from 137 to 128 mEq/l. A computerized UF program was used to gradually reduce the UF to a minimum towards the end of the session. Severity of thirst, interdialytic weight gain and intradialytic complications were less with low sodium dialysate. It allowed adequate UF with absolute hemodynamic stability. The reduced incidence of complication with low sodium dialysate therapy was probably because they required less UF.

Adult↗