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Biomedical subjects

S C Ray

Publications and source records attributed to S C Ray.

At least 37 records · Page 2Linked to original sources
PubMed1998

Assessment of hepatitis C virus sequence complexity by electrophoretic mobilities of both single-and double-stranded DNAs.

To assess genetic variation in hepatitis C virus (HCV) sequences accurately, we optimized a method for identifying distinct viral clones without determining the nucleotide sequence of each clone. Twelve serum samples were obtained from seven individuals soon after they acquired HCV during a prospective study, and a 452-bp fragment from the E2 region was amplified by reverse transcriptase PCR and cloned. Thirty-three cloned cDNAs representing each specimen were assessed by a method that combined heteroduplex analysis (HDA) and a single-stranded conformational polymorphism (SSCP) method to determine the number of clonotypes (electrophoretically indistinguishable cloned cDNAs) as a measure of genetic complexity (this combined method is referred to herein as the HDA+SSCP method). We calculated Shannon entropy, incorporating the number and distribution of clonotypes into a single quantifier of complexity. These measures were evaluated for their correlation with nucleotide sequence diversity. Blinded analysis revealed that the sensitivity (ability to detect variants) and specificity (avoidance of false detection) of the HDA+SSCP method were very high. The genetic distance (mean +/- standard deviation) between indistinguishable cloned cDNAs (intraclonotype diversity) was 0.6% +/- 0.9%, and 98.7% of cDNAs differed by <2%, while the mean distance between cloned cDNAs with different patterns was 4.0% +/- 3.2%. The sensitivity of the HDA+SSCP method compared favorably with either HDA or the SSCP method alone, which resulted in intraclonotype diversities of 1.6% +/- 1.8% and 3.5% +/- 3.4%, respectively. The number of clonotypes correlated strongly with genetic diversity (R2, 0.93), but this correlation fell off sharply when fewer clones were assessed. This HDA+SSCP method accurately reflected nucleotide sequence diversity among a large number of viral cDNA clones, which should enhance analyses to determine the effects of viral diversity on HCV-associated disease. If sequence diversity becomes recognized as an important parameter for staging or monitoring of HCV infection, this method should be practical enough for use in laboratories that perform nucleic acid testing.

Cloning, Molecular↗
PubMed1997

Characterization of a polyclonal cytolytic T lymphocyte response to human immunodeficiency virus in persons without clinical progression.

A total of 82 human immunodeficiency virus (HIV)-1-specific cytolytic T lymphocyte (CTL) clones were isolated and characterized from 5 HIV-infected subjects, utilizing multiple HLA class I alleles. B62-restricted, HIV-1 gag-specific CTL clones isolated from a single blood sample from 1 subject used four different Vbeta gene rearrangements. Multiple CTL clones could be isolated from the same time point directed against HIV-1 gag, nef, and env from 1 subject. A prospective analysis resulted in the isolation of CTL clones from 1 subject directed against multiple HIV-1 antigens, including the same highly conserved nef peptide, over a 1-year period, in the absence of detectable circulating viral plasma RNA. These data suggest that in some persons without clinical progression and low levels of circulating HIV-1, the CTL response is polyclonal, is directed against multiple HIV-1 proteins, including highly conserved peptides within these proteins, and is maintained over time.

Antigens, Viral↗
PubMed1996

Predominance of defective proviral sequences in an HIV + long-term non-progressor.

We examined the accessory genes and envelope V3 region of provirus obtained over a 5 year period from an HIV+ long-term non-progressor with very low viral load and no in vitro recoverable virus during that same time span. LTR sequences supported normal Tat-mediated promoter activity. Multiple clones of nef sequences were highly conserved with < 10% containing frame shift or stop codon mutations. Functional analysis of the predominant nef sequence indicated wild type downregulation of surface CD4 and good function in a complementation infectivity assay. By contrast, inactivating mutations were found in 64% of amplicons containing vif, vpr, vpu, tat1, and rev1, and in 41% of amplicons containing env V3. Identical inactive sequences were obtained at an interval of 2 years, suggesting persistence of quiescent defective provirus in a long-lived clonal cell population. Furthermore, genetic distance versus time analysis revealed an absence of progressive evolution or arborization of quasispecies over time. This contrasts with data generated from other asymptomatic HIV+ individuals. The non-progressive pattern of env sequence diversity and low R2 for genetic divergence over time suggests that the defective provirus circulating in the periphery of this patient represents a randomly sampled 'fossil record' of earlier replication competent HIV-1 genomes.

Defective Viruses↗
PubMed1996

Oral antibiotic treatment of right-sided staphylococcal endocarditis in injection drug users: prospective randomized comparison with parenteral therapy.

PURPOSE: To compare the efficacy and safety of inpatient oral antibiotic treatment (oral) versus standard parenteral antibiotic treatment (intravenous) for right-sided staphylococcal endocarditis in injection drug users. PATIENTS AND METHODS: In a prospective, randomized, non-blinded trial, febrile injection drug users were assigned to begin oral or intravenous (IV) treatment on admission, before blood culture results were available. Oral therapy consisted of ciprofloxacin and rifampin. Parenteral therapy was oxacillin or vancomycin, plus gentamicin for the first 5 days. Antibiotic dosing was adjusted for renal dysfunction. Administration of other antibacterial drugs was not permitted during the treatment or follow-up periods. Bacteremic subjects having right-sided staphylococcal endocarditis received 28 days of inpatient therapy with the assigned antibiotics. Test-of-cure blood cultures were obtained during inpatient observation 6 and 7 days after the completion of antibiotic therapy, and again at outpatient follow-up 1 month later. Criteria for treatment failure and for drug toxicity were prospectively defined. RESULTS: Of 573 injection drug users who were hospitalized because of a febrile illness and suspected right-sided staphylococcal endocarditis, 93 subjects (16.2%) had two or more sets of blood cultures positive for staphylococci; 85 of these bacteremic subjects (14.8%) satisfied diagnostic criteria for at least possible right-sided staphylococcal endocarditis (no other source of bacteremia was apparent) and entered the trial. Forty-four (oral, 19; IV, 25) of these 85 subjects completed inpatient treatment and evaluation including test-of-cure blood cultures. There were four treatment failures (oral, 1 [5.2%]; IV, 3 [12.0%]; not significant, Fisher's exact test). Drug toxicity was significantly more common in the parenterally treated group (oral, 3%; IV, 62%; P < 0.0001), consisting largely of oxacillin-associated increases in liver enzymes. CONCLUSIONS: For selected patients with right-sided staphylococcal endocarditis, oral ciprofloxacin plus rifampin is effective and is associated with less drug toxicity than is intravenous therapy.

Administration, Oral↗
PubMed1995

Human immunodeficiency virus type 1 env and p17gag sequence variation in polymerase chain reaction-positive, seronegative injection drug users.

Variation in gene sequences from human immunodeficiency virus type 1 (HIV-1) p17gag and the third hypervariable region (V3 loop) of env was examined in a cross-sectional study of single specimens from 4 HIV-1 polymerase chain reaction-positive, seronegative injection drug users. As observed in sexually transmitted disease, clones of HIV-1 genes isolated from an individual were remarkably homogeneous, with amino acid variation in the envelope region of 0.3%-0.9% and in p17gag of 0.0%-0.7%. Intersubject variation was much greater (at the amino acid level, 15% for the envelope and 4.3% for p17gag), with conservation in the envelope only of regions at the base of the V3 loop. Since at least some subjects likely acquired infection intravenously, the ability of virus to survive in seminal fluid or on mucosal surfaces cannot explain the observed homogeneity, which may depend on direct interactions between the virus and the infected cell.

Amino Acid Sequence↗
PubMed1995

Convergent evolution within the V3 loop domain of human immunodeficiency virus type 1 in association with disease progression.

Phylogenetic analysis was used to study in vivo genetic variation of the V3 region of human immunodeficiency virus type 1 in relation to disease progression in six infants with vertically acquired human immunodeficiency virus type 1 infection. Nucleotide sequences from each infant formed a monophyletic group with similar average branch lengths separating the sets of sequences. In contrast to the star-shaped phylogeny characteristic of interinfant viral evolution, the shape of the phylogeny formed by sequences from the infants who developed AIDS tended to be linear. A computer program, DISTRATE, was written to analyze changes in DNA distance values over time. For the six infants, the rate of divergence from the initial variant was inversely correlated with CD4 cell counts averaged over the first 11 to 15 months of life (r = -0.87, P = 0.024). To uncover evolutionary relationships that might be dictated by protein structure and function, tree-building methods were applied to inferred amino acid sequences. Trees constructed from the full-length protein fragment (92 amino acids) showed that viruses from each infant formed a monophyletic group. Unexpectedly, V3 loop protein sequences (35 amino acids) that were found at later time points from the two infants who developed AIDS clustered together. Furthermore, these sequences uniquely shared amino acids that have been shown to confer a T-cell line tropic phenotype. The evolutionary pattern suggests that viruses from these infants with AIDS acquired similar and possibly more virulent phenotypes.

Acquired Immunodeficiency Syndrome↗
PubMed1991

Eukaryotic start and stop translation sites.

Sequences flanking translational initiation and termination sites have been compiled and statistically analyzed for various eukaryotic taxonomic groups. A few key similarities between taxonomic groups support conserved mechanisms of initiation and termination. However, a high degree of sequence variation at these sites within and between various eukaryotic groups suggest that translation may be modulated for many mRNAs. Multipositional analysis of di-, tri-, and quadrinucleotide sequences flanking start/stop sites indicate significant biases. In particular, strong tri-nucleotide biases are observed at the -3, -2, and -1 positions upstream of the start codon. These biases and the interspecific variation in nucleotide preferences at these three positions have lead us to propose a revised model of the interaction of the 18S ribosomal RNA with the mRNA at the site of translation initiation. Unusually strong biases against the CG dinucleotide immediately downstream of termination codons suggest that they may lead to faulty termination and/or failure of the ribosome to disassociate from the mRNA.

Animals↗
PubMed1990

The individual over time: time series applications in health care research.

This paper presents a summary and a brief theoretical introduction to time series ARIMA modeling of single subject data. Time series, a statistical technique that may be appropriate when data are measured repeatedly and at nearly equal intervals of time, has potential research applications in the study of chronic diseases such as diabetes, hypertension, and herpes simplex. Both intervention models and multivariate models are covered, with examples illustrating the utility of time series techniques in chronic disease research. Time series modeling of a subject with diabetes before and after being placed on a regimen of chlorpropamide is used to demonstrate the potential of intervention analysis. Multivariate time series techniques are illustrated by modeling the relationship between exercise and blood glucose, and by modelling the relationship between psychosocial distress and lymphocyte subsets of the cellular immune system.

Blood Glucose↗
PubMed1979

Open heart surgery in first year of life using profound hypothermia (core cooling) and circulatory arrest. Experience with 134 consecutive cases.

Between April 1970 and December 1977, 134 infants aged 2 days to 12 months underwent open heart surgery using profound hypothermia and total circulatory arrest. The technique of bypass (core) cooling is described. Results are reviewed for 4 principal diagnoses: 'simple' transposition of the great vessels, total anomalous pulmonary venous connection, ventricular septal defect, and Fallot's tetralogy. A mortality of 44 per cent in 32 cases during the first 3-year period has been reduced to 22 per cent in 102 cases during the subsequent 5 years. The overall mortality for the entire period was 28 per cent. The policy for the management of each diagnostic group is outlined.

Cardiac Surgical Procedures↗
PubMed1978

Variations in the structure of thyroglobulins from normal and goitrous human thyroids.

Thyroglobulin samples were prepared individually be gel chromatography from the thyroids of five persons without thyroid disease and four with goiters. Gel electrophoresis at different pHs and gel concentrations showed a single major band corresponding to 19S thyroglobulin in rabbits, with occasional faint bands corresponding to 12S and 27S species. The thyroglobulins of the normals differed from each other in electrophoretic pattern on sodium dodecyl sulfate (SDS)-urea gels and in composition of iodine, monosaccharides, and amino acids. Nine amino acids showed significant variation among the five thyroglobulins at the P less than 0.01 level, and only two (lysine and alanine) did not vary. The content of both sialic acid and fucose varied widely, but their sum was similar among the five samples. Thyroglobulin samples from the goiters differed from the normals and from each other in composition and in pattern on SDS-urea gels. The variability itself was more impressive than were differences in any particular component. Relative to the normals, these thyroglobulins showed increases in content of sialic acid (P less than 0.01) and lysine (P less than 0.10), and increases in the faster bands on gel electrophoresis in SDS-urea. Two goiters were from patients with the multiple hamartoma syndrome, and the only metabolic abnormality found was a low content of iodothyronine in thyroglobulin. The other two goiters also showed inadequate coupling of iodotyrosyls. In addition, one contained a soluble iodoprotein of very high molecular weight, which was immunologically identical to 19S thyroglobulin but differed in chemical composition. We conclude from the compositional data that there is not a single structure for "normal" thyroglobulin, but that multiple molecular configurations occur naturally and are compatible with adequate hormone synthesis. Extensive variations in thyroglobulin structure are frequently found with goiter, and we suggest that these may be involved in its pathogenesis.

Adult↗
PubMed1975

Changes in the structure of thyroglobulin following the administration of thyroid-stimulating hormone.

In each of three separate experiments, female guinea pigs in groups of 20 were given 4 units of thyroid-stimulating hormone (TSH) each day for 3 days, while controls were given saline. Na125I was injected on the 3rd day, and the animals were killed 22 hours later. The pooled throids of each group were homogenized, and thyroglobulin was purified by one of the following methods: gel filtration on Sephadex G-200 followed by density gradient ultracentrifugation, two sequential filtrations on 4 percent agarose, or filtration on 4 percent agarose followed by Sephadex G-200. TSH administration was associated with the folling changes in thyroglobulin: (1) an increase in the ratio of tri-iodothyronine to thyroxine; (2) a decrease in dissociation of the 19 S to the 12 S form; (3) an alteration in its pattern on gel electrophoresis in sodium dodecyl sulfate-urea; and (4) changes in its amino acid composition, with significant increases in the content of lysine (by 15 percent), isoleucine (by 15 percent), and methionine (by 7 percent) relative to leucine. Over-all, there were no significant changes in the content of iodine, fucose, hexosamine, or sialic acid. These data show that TSH can alter the composition of thyroglobulin independently of its effects on iodine content. We suggest that these changes may stem from alterations in the subunit composition of thyroglobulin. There were also small but significant variations in amino acid composition among the three preparations of thyroglobulin from saline-treated animals and among the three from the TSH-treated. This finding shows that thyroglobulin can be heterogeneous in its protein portion as well as in its iodine content.

Amino Acids↗