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Biomedical subjects

T F Smith

Publications and source records attributed to T F Smith.

At least 145 records · Page 8Linked to original sources
PubMed1991

Automatic evaluation of protein sequence functional patterns.

A procedure that automatically provides an evaluation of the diagnostic ability of a protein sequence functional pattern is described. The procedure relies on the identification of the closest definable set in terms of a (protein sequence) database functional annotation to the set of database instances containing a given pattern. Assuming annotation correctness and completeness in the protein sequence database, the degree of statistical association between these sets provides an appropriate measure of the diagnostic ability of the pattern. An experimental implementation of the procedure, using the NBRF/PIR protein database, has been applied to a diverse collection of published sequence patterns. Results obtained reveal that frequently it is not possible to define (in NBRF/PIR database terminology) the set of database instances containing a given pattern, suggesting either lack of pattern diagnostic ability or protein database annotation incompleteness and/or inconsistencies.

Algorithms↗
PubMed1991

Comparison of shell vials and conventional tubes seeded with rhabdomyosarcoma and MRC-5 cells for the rapid detection of herpes simplex virus.

Shell vials (SV) and conventional tubes (CT) were seeded with rhabdomyosarcoma (RD) and MRC-5 cells and inoculated with clinical specimens, and the systems were evaluated for the rapid diagnosis of herpes simplex virus (HSV) infections by detection of cytopathic effects (CPE) (for CT, for 7 days) and by using fluoresceinated monoclonal antibodies (for SV, 16 h postinoculation). Of 245 genital specimens (16 from males and 229 from females) 56 (23%) seeded with MRC-5 cells (14 type 1 and 42 type 2) and 55 (22%) seeded with RD cells were detected in CT; however, CPE were recognized in only 26 (46%) of the total HSV-positive cultures 1 day postinoculation. Forty-eight (86% sensitivity, MRC-5) and 46 (84% sensitivity, RD) HSV strains were detected immunologically in SV 16 h postinoculation. Early CPE in CT or fluorescent foci in SV were easier to detect in MRC-5 than in RD cell cultures. MRC-5 and RD cells were equally sensitive to infection with HSV. CT cell cultures were more sensitive than SV but less rapid for the detection of HSV infection (P less than 0.01). We recommend using SV for the rapid diagnosis of HSV infections, but in addition, CT must be inoculated with MRC-5 or RD to ensure maximum detection of this virus.

Animals↗
PubMed1991

Epstein-Barr virus and persistent graft dysfunction after liver transplantation.

Epstein-Barr virus infection has been associated with a broad spectrum of clinical manifestations, depending on the immune status of the host. In this report, we describe two liver transplant patients who received hepatic allografts from donors serologically positive for Epstein-Barr virus and who experienced primary infection with Epstein-Barr virus associated with prolonged liver graft dysfunction. In both patients, Epstein-Barr serologies converted within 3 mo of liver transplantation, and hepatic histological study revealed mononuclear infiltration of the sinusoids evolving to pronounced immunoblastic features suggestive of evolving lymphoma. In both cases, in situ hybridization studies confirmed the presence of Epstein-Barr virus genome in the liver. Furthermore, polymerase chain reaction analysis suggested that high levels of Epstein-Barr virus DNA were present in biopsy specimens obtained during the episode of acute hepatitis that followed Epstein-Barr virus seroconversion. The degree of Epstein-Barr virus DNA estimated by polymerase chain reaction appeared to increase in parallel with the progression of parenchymal lymphocytic infiltrates. In one patient, a biopsy sample from a cervical node also revealed high levels of Epstein-Barr virus DNA estimated using the polymerase chain reaction technique. Furthermore, in these patients, Epstein-Barr virus DNA levels appeared to decrease dramatically after discontinuing azathioprine administration and beginning treatment with acyclovir. These two cases illustrate the dynamics of Epstein-Barr virus immune regulation and confirm chronic hepatic allograft dysfunction related to Epstein-Barr viral infection.

Adult↗
PubMed1991

Subluxing peroneal tendons. An anatomic approach.

Chronic subluxing peroneal tendons represent an interesting presentation of pathoanatomy. An appreciation for the local anatomic considerations about the distal fibula as well as the pathologic relationships that occur during these painful syndromes is critical to understanding this condition. An anatomic approach to repair chronic subluxating peroneal tendons is presented. A literature review is included to reinforce the success of the procedure in multiple trials and in various clinical situations.

Fibula↗
PubMed1990

Early diagnosis of cytomegalovirus hepatitis in liver transplant recipients: role of immunostaining, DNA hybridization and culture of hepatic tissue.

Immunostaining techniques that use a monoclonal antibody against an early cytomegalovirus antigen or a polyclonal antibody, in situ DNA hybridization and inoculation of cell cultures for the detection of cytomegalovirus from liver biopsy specimens were studied in 20 liver transplant patients with cytomegalovirus hepatitis, as defined by histological criteria. A total of 108 liver biopsy specimens from 20 patients with a diagnosis of cytomegalovirus hepatitis (obtained per protocol at 7, 21, 90, and 180 days or whenever liver dysfunction occurred), which had previously been examined histologically and in cell culture, were again studied by recutting the liver tissue for histological examination, DNA hybridization and immunostaining with monoclonal or polyclonal antibodies to cytomegalovirus. In 5 of 20 patients, the diagnosis of cytomegalovirus hepatitis could have been made earlier (mean = 9.6 days) by immunostaining with a monoclonal antibody. Of 47 biopsy specimens with cytomegalovirus inclusion bodies, the sensitivity and specificity of the diagnostic procedures were immunostaining with monoclonal antibody (84% and 90%) and polyclonal antibody (72% and 97%), in situ DNA hybridization (72% and 100%) and cell culture detection (52% and 95%), respectively. Immunostaining with a monoclonal antibody against an early CMV antigen frequently detected cytomegalovirus infection in the liver allograft earlier than identification of typical histological inclusion bodies. DNA in situ hybridization was less sensitive than other techniques but highly specific; cytomegalovirus cell culture lacked sensitivity compared with the other procedures.

Adult↗
PubMed1990

Acid helix-turn activator motif.

A common sequence/structural motif pattern has been identified within the steroid/thyroid hormone receptors and other transcriptional activators using a new massively parallel symbolic learning assistant computer system. The pattern appears nearly diagnostic of transcription activation, including relative activation strength, among nuclear and DNA-binding prokaryotic proteins. In cases where mutation/deletion/chimeric studies have identified the activation domain, the pattern matches within that domain. These facts and the nature of the pattern itself strongly support the idea that the patterned domain is directly involved in a protein-protein transcription activation interaction.

Amino Acid Sequence↗
PubMed1990

Automatic generation of primary sequence patterns from sets of related protein sequences.

We have developed a computer algorithm that can extract the pattern of conserved primary sequence elements common to all members of a homologous protein family. The method involves clustering the pairwise similarity scores among a set of related sequences to generate a binary dendrogram (tree). The tree is then reduced in a stepwise manner by progressively replacing the node connecting the two most similar termini by one common pattern until only a single common "root" pattern remains. A pattern is generated at a node by (i) performing a local optimal alignment on the sequence/pattern pair connected by the node with the use of an extended dynamic programming algorithm and then (ii) constructing a single common pattern from this alignment with a nested hierarchy of amino acid classes to identify the minimal inclusive amino acid class covering each paired set of elements in the alignment. Gaps within an alignment are created and/or extended using a "pay once" gap penalty rule, and gapped positions are converted into gap characters that function as 0 or 1 amino acid of any type during subsequent alignment. This method has been used to generate a library of covering patterns for homologous families in the National Biomedical Research Foundation/Protein Identification Resource protein sequence data base. We show that a covering pattern can be more diagnostic for sequence family membership than any of the individual sequences used to construct the pattern.

Amino Acid Sequence↗
PubMed1990

Detection of JC virus DNA by polymerase chain reaction in patients with progressive multifocal leukoencephalopathy.

Polymerase chain reaction (PCR) was used in the detection of JC virus (JCV) DNA in formalin-fixed, paraffin-embedded brain tissue sections from 24 patients with progressive multifocal leukoencephalopathy. Brain sections from normal autopsies (n = 17) and other neurologic conditions (n = 4) were used as controls. Specific amplified products were detected in 20 (83%) of 24 patients with progressive multifocal leukoencephalopathy. PCR did not amplify JCV or human beta-globin gene sequences in four patients with characteristic demyelinating lesions of progressive multifocal leukoencephalopathy that were positive for JCV by in situ hybridization or immunocytochemistry. PCR from biopsy sections resulted in more intense amplification signals than PCR from autopsy tissue. Normal brain sections from 17 autopsies were negative by PCR. Low-grade amplification of JCV was observed in one patient with herpes simplex virus encephalitis. PCR served as a more rapid test for confirmation of progressive multifocal leukoencephalopathy than in situ hybridization. However, PCR performance was altered by prolonged formalin fixation of tissue and undetermined inhibitors of the amplification reaction. Laboratories and clinicians should be aware of the difficulties encountered when using paraffin-embedded tissue for PCR.

Base Sequence↗
PubMed1990

Ribosomal RNA gene sequences and hominoid phylogeny.

Sequences totaling 3,500 bases from the 28S rRNA gene and from one of the ribosomal internal transcribed spacers (ITS1) have been determined for human, chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and orangutan (Pongo pygmaeus). Analyses of the rRNA alignments show (1) a clustering of substitutions in the "variable regions" of the 28S gene, (2) a 1.5-3-fold increase in divergence in the transcribed spacer over that in the exon, and (3) that human and chimpanzee are the most closely related pair, in agreement with the results of Miyamoto et al., Sibley and Ahlquist, and Caccone and Powell.

Animals↗
PubMed1990

Alignment of protein sequences using secondary structure: a modified dynamic programming method.

A method for comparison of protein sequences based on their primary and secondary structure is described. Protein sequences are annotated with predicted secondary structures (using a modified Chou and Fasman method). Two lettered code sequences are generated (Xx, where X is the amino acid and x is its annotated secondary structure). Sequences are compared with a dynamic programming method (STRALIGN) that includes a similarity matrix for both the amino acids and secondary structures. The similarity value for each paired two-lettered code is a linear combination of similarity values for the paired amino acids and their annotated secondary structures. The method has been applied to eight globin proteins (28 pairs) for which the X-ray structure is known. For protein pairs with high primary sequence similarity (greater than 45%), STRALIGN alignment is identical to that obtained by a dynamic programming method using only primary sequence information. However, alignment of protein pairs with lower primary sequence similarity improves significantly with the addition of secondary structure annotation. Alignment of the pair with the least primary sequence similarity of 16% was improved from 0 to 37% 'correct' alignment using this method. In addition, STRALIGN was successfully applied to seven pairs of distantly related cytochrome c proteins, and three pairs of distantly related picornavirus proteins.

Amino Acid Sequence↗
PubMed1990

Relationship between serum IgG2 concentrations and antibody responses to pneumococcal polysaccharides in children with chronic chest symptoms.

We measured IgG-class antibodies to 12 pneumococcal antigens pre- and post-immunization with polyvalent pneumococcal vaccine in 31 children who had experienced chronic chest symptoms. The purpose of the study was to determine the relation of IgG subclasses, especially IgG2, to the subjects' antibody responses to bacterial polysaccharide antigens, to see if measuring IgG subclasses would predict these responses. Twenty-nine children (90%) had low or low-normal levels of one or more IgG subclasses, including 20 out of 31 (65%) with low or low-normal levels of IgG2. Children studied had a relatively poor increase in levels of antibody to 10 of the 12 pneumococcal vaccine antigens investigated. Both pre- and post-immunization antibody levels were related to pre-immune serum concentrations of IgG2. Pre-immunization antibody levels were strongly related to post-immunization levels; when post-immunization antibody levels were adjusted for pre-immunization levels by partial correlation, the correlation between anticapsular antibody level post-immunization and IgG2 was no longer significant. Thus, in children with chronic chest symptoms, levels of antibody measured at a random interval after natural exposure to these bacterial polysaccharide antigens are related to levels of IgG2 subclass, but antibody increases after vaccination appear to be affected more by other factors.

Adolescent↗
PubMed1990

Detection of Epstein-Barr virus by polymerase chain reaction.

The polymerase chain reaction (PCR) was used to study DNA extracted from the blood of 25 transplant patients, 5 patients with infectious mononucleosis, and 13 healthy subjects and autopsy or biopsy tissue from 29 patients with lymphoproliferative disorders. Primers were directed to conserved regions of the Epstein-Barr virus (EBV) genome encoding capsid protein gp220 and Epstein-Barr nuclear antigen 1. Specific EBV amplification was found in the blood of 11 of 25 transplant patients and all patients with infectious mononucleosis. All patients with lymphoproliferative disorders occurring in the presence of immunosuppression (eight organ transplant patients and two patients with acquired immunodeficiency syndrome) had biopsies positive for EBV by PCR. Only 1 of 19 samples from lymphomas or leukemias unrelated to immunosuppression contained EBV. PCR confirmed the very close association of EBV and lymphoproliferative disorders occurring in the presence of immunosuppression. The significance of detecting EBV sequences in the blood of transplant patients, particularly in relationship to lymphoproliferation, requires further study.

Adult↗
PubMed1990

Rapid detection of polyomavirus BK by a shell vial cell culture assay.

Polyomavirus BK (BKV) causes asymptomatic latent infection in the human host that is reactivated during periods of immune suppression. Detection by conventional tube cell culture is difficult and time consuming because BKV exhibits slow growth with late (14 to 28 days) and subtle cytopathic effects. We developed a shell vial cell culture assay (SVA) using a cross-reactive monoclonal antibody to the T antigen of simian virus 40 to detect BKV rapidly by indirect immunofluorescence. Nuclear fluorescence was seen in BKV-infected cells as early as 16 h postinoculation; 6 to 28 times more foci were present at 36 h postinoculation. Human embryonic kidney cells infected with BKV produced 7 to 42 times more fluorescent foci than MRC-5 or rhabdomyosarcoma cells did. Centrifugation enhanced the infectivity of BKV in the SVA. To define the clinical utility of SVA, urine specimens from organ transplant patients were tested. Of 27 patients, 4 (15%) were found to be positive by SVA. SVA offers a simple and rapid method for detection of BKV that can be of use in clinical studies of this virus.

Animals↗
PubMed1989

Interaction of paramyxoviruses with human basophils and their effect on histamine release.

We have demonstrated that human peripheral blood basophils released histamine on direct incubation with paramyxoviruses in vitro. Most histamine release occurred during the first 15 to 30 minutes after challenge, depending on the dose of virus used; release initiated by virus was complete by 1 hour. At a virus/cell ratio of 1:1, Sendai virus caused 41 +/- 9% histamine release, whereas parainfluenza type 3 (PI-3) virus caused 25 +/- 5% release and respiratory syncytial (RS) virus caused 19 +/- 5% release. Sendai, but not PI-3 or RS, also caused a decrease in cell number and release of lactic dehydrogenase; however, this apparent cell lysis did not account for all the histamine released. Incubation of cells with virus desensitized them to subsequent triggering by viruses but did not affect response of cells to other stimuli. Histamine release was dependent on the virus/cell ratio, temperature, and metabolic energy, but it was not strictly dependent on the presence of calcium in the extracellular medium. Histamine release was not affected by preincubation of cells with colchicine, suggesting that microtubules were not involved in the release process. Basophils desensitized by anti-IgE in the absence of calcium or treated with lactic acid to dissociate IgE molecules from membrane receptors released amounts of histamine similar to that of control basophils; thus, release was not initiated through Fc epsilon receptors. It was found, however, that histamine release by these viruses was greatly reduced when concanavalin A was used for desensitization. These data demonstrate that the respiratory viruses studied can cause direct nonimmunologic release of histamine from human basophils. Our findings provide evidence for another mechanism by which respiratory viruses can initiate inflammation.

Adult↗