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Biomedical subjects

T F Smith

Publications and source records attributed to T F Smith.

At least 109 records · Page 6Linked to original sources
PubMed1994

The ancient regulatory-protein family of WD-repeat proteins.

WD proteins are made up of highly conserved repeating units usually ending with Trp-Asp (WD). They are found in all eukaryotes but not in prokaryotes. They regulate cellular functions, such as cell division, cell-fate determination, gene transcription, transmembrane signalling, mRNA modification and vesicle fusion. Here we define the common features of the repeating units, and criteria for grouping such proteins into functional subfamilies.

Amino Acid Sequence↗
PubMed1994

Protein classification by stochastic modeling and optimal filtering of amino-acid sequences.

The prediction of a protein's tertiary structural class from its amino-acid sequence is formulated as a signal-processing problem. The amino-acid sequence is treated as a "time series" of symbols containing signals that determine the protein's structural class. A methodology is described for building detailed stochastic signal models for recognized structural classes of single-domain proteins. We solve the problem of determining that model, from a set of candidates, which is the most probable generator of a protein's entire amino-acid sequence. The solution employs a nonlinear, optimal filtering algorithm, which is suited for implementation on parallel computer architectures. Previous approaches have only been able to classify correctly 80% of single-domain proteins within three very broad structural types, while our approach achieves this level across twelve much more detailed classes.

Amino Acid Sequence↗
PubMed1994

Modeling protein cores with Markov random fields.

A mathematical formalism is introduced that has general applicability to many protein structure models used in the various approaches to the "inverse protein folding problem." The inverse nature of the problem arises from the fact that one begins with a set of assumed tertiary structures and searches for those most compatible with a new sequence, rather than attempting to predict the structure directly from the new sequence. The formalism is based on the well-known theory of Markov random fields (MRFs). Our MRF formulation provides explicit representations for the relevant amino acid position environments and the physical topologies of the structural contacts. In particular, MRF models can readily be constructed for the secondary structure packing topologies found in protein domain cores, or other structural motifs, that are anticipated to be common among large sets of both homologous and nonhomologous proteins. MRF models are probabilistic and can exploit the statistical data from the limited number of proteins having known domain structures. The MRF approach leads to a new scoring function for comparing different threadings (placements) of a sequence through different structure models. The scoring function is very important, because comparing alternative structure models with each other is a key step in the inverse folding problem. Unlike previously published scoring functions, the one derived in this paper is based on a comprehensive probabilistic formulation of the threading problem.

Amino Acid Sequence↗
PubMed1994

Cytokine response to respiratory syncytial virus stimulation of human peripheral blood mononuclear cells.

A key impediment to developing respiratory syncytial virus (RSV) vaccines is a lack of understanding of enhanced disease that occurred in children who received a formalin-inactivated RSV (FI-RSV) vaccine. Studies in mice have suggested that the FI-RSV vaccine induces a TH2 and live RSV induces a TH1 memory T cell response. In this study, the cytokine mRNA response of peripheral blood mononuclear cells (PBMC) from adults and children with and without previous RSV infection was characterized using a semiquantitative polymerase chain reaction (PCR). PBMC from 22 subjects previously infected with RSV usually had RSV-specific increases in TH1 cytokine-specific mRNA (interferon-gamma [IFN-gamma] mRNA, 20; interleukin [IL]-2 mRNA, 12; IL-5 mRNA, 6; and IL-4 mRNA, 0). PBMC from RSV antibody-negative children had no RSV-specific increases in IFN-gamma, IL-2, or IL-4 mRNA; 1 of 7 had an increase in IL-5 mRNA. These data indicate that naturally acquired RSV induces a TH1 memory T cell response.

Adolescent↗
PubMed1994

The spectrum of cutaneous granulomatous vasculitis: histopathologic report of eight cases with clinical correlation.

Cutaneous granulomatous vasculitis is an uncommon histopathologic finding that has been associated with lymphoproliferative disorders, systemic vasculitis, autoimmune inflammatory diseases, and infection. To define further the concept of cutaneous granulomatous vasculitis and to emphasize its clinical importance, we reviewed biopsy material from 8 patients seen from 1985 through 1992. All biopsies showed evidence of blood vessel damage with fibrinoid change or hemorrhage (or both) and granulomatous inflammation in and around vessel walls. Special stains for microorganisms were negative in all cases. Associated medical disorders included neuropathy (2 patients), sarcoid-like disease (2), systemic vasculitis (1), lymphoma and suspected lymphoma (1 each), and associated herpes simplex virus (1). T-cell gene-rearrangement studies were negative in a patient with suspected lymphoma. Granulomatous cutaneous vasculitis is most commonly associated with lymphoma and systemic vasculitis. In selected cases, infection should be considered as an underlying cause.

Aged↗
PubMed1994

Detection of cytomegalovirus DNA in sera of liver transplant recipients.

We prospectively studied the utility of the amplification of cytomegalovirus (CMV) DNA in the sera of liver transplant recipients in order to predict symptomatic CMV infection, thus enabling preemptive therapy with antiviral agents. Serum samples obtained at biweekly intervals from 20 sequential liver transplant recipients for at least 8 weeks following transplantation were tested by the PCR amplification procedure. Results were correlated with blood and urine cultures, histopathological findings from infected organs, and clinical manifestations. Six patients (30%) developed symptomatic CMV infection; in five (83%) of these patients, CMV DNA was detected prior to symptomatic CMV infection, and in one (17%) of these patients, CMV DNA was detected at the time of symptomatic CMV infection. CMV DNA was detected a mean of 13 days (range, 0 to 23 days) prior to the onset of symptomatic CMV infection. In addition, CMV DNA was detected in the sera of four of five patients with asymptomatic viremia and two patients with asymptomatic viruria. Lastly, the PCR was negative for sera from seven patients with no evidence of CMV infection. We found that PCR was able to detect the presence of CMV DNA in the sera of liver transplant recipients at a sensitivity of 92% and a specificity of 100% for CMV infection, while the sensitivity and specificity for symptomatic infection were 100 and 57%, respectively.

Base Sequence↗
PubMed1993

Structural analysis of the CD11b gene and phylogenetic analysis of the alpha-integrin gene family demonstrate remarkable conservation of genomic organization and suggest early diversification during evolution.

CD11b is a member of the beta 2 subfamily of the human leukocyte integrins. Its expression is limited to mature myeloid and NK cells and is up-regulated during the course of granulocytic and monocytic differentiation. The CD11b/CD18 (Mo1) heterodimer promotes adhesion of granulocytes and monocytes to C3bi-coated bacteria and endothelial cells. In an attempt to relate the exon structure to the known functional domains, as well as to identify and study cis-acting elements that are involved in its tissue-specific expression, we have isolated genomic clones encoding CD11b, deduced the exon/intron organization, and determined the transcriptional start site. The CD11b gene spans 55 kb and is encoded by 30 exons. Its structure closely resembles that of CD11c, another of the three leukocyte integrin alpha-chains, and suggests that these two genes arose by a gene duplication event. Furthermore, comparison of the CD11b gene structure with that of platelet glycoprotein IIb and Drosophila PS2 suggest how the human leukocyte integrins evolved and dispersed during the course of evolution.

Amino Acid Sequence↗
PubMed1993

Polymerase chain reaction (PCR) identification of human papillomavirus (HPV) DNA in verrucous carcinoma of the larynx.

The incidence of human papillomavirus (HPV) DNA in archival formalin-fixed, paraffin-embedded tissue sections from verrucous carcinoma of the larynx was determined using polymerase chain reaction (PCR) with consensus primers and by in situ hybridization designed to detect HPV types 6/11, 16/18, 31/33/35. HPV DNA was detected in 17 (85%) of 20 tissue samples by PCR; none of the 20 samples were positive for the seven genotype types tested by in situ hybridization. PCR is a valuable tool to detect HPV and therefore will significantly clarify the importance of HPV in squamous mucosal disorders.

Adult↗
PubMed1993

The binding domain structure of retinoblastoma-binding proteins.

The retinoblastoma gene product (Rb), a cellular growth suppressor, complexes with viral and cellular proteins that contain a specific binding domain incorporating three invariant residues: Leu-X-Cys-X-Glu, where X denotes a nonconserved residue. Hydrophobic and electrostatic properties are strongly conserved in this segment even though the nonconserved amino acids vary considerably from one Rb-binding protein to another. In this report, we present a diagnostic computer pattern for a high-affinity Rb-binding domain featuring the three conserved residues as well as the conserved physico-chemical properties. Although the pattern encompasses only 10 residues (with only 4 of these explicitly defined), it exhibits 100% sensitivity and 99.95% specificity in database searches. This implies that a certain pattern of structural and physico-chemical properties encoded by this short sequence is sufficient to govern specific Rb binding. We also present evidence that the secondary structural conformation through this region is important for effective Rb binding.

Amino Acid Sequence↗
PubMed1993

Structural analysis based on state-space modeling.

A new method has been developed to compute the probability that each amino acid in a protein sequence is in a particular secondary structural element. Each of these probabilities is computed using the entire sequence and a set of predefined structural class models. This set of structural classes is patterned after Jane Richardson's taxonomy for the domains of globular proteins. For each structural class considered, a mathematical model is constructed to represent constraints on the pattern of secondary structural elements characteristic of that class. These are stochastic models having discrete state spaces (referred to as hidden Markov models by researchers in signal processing and automatic speech recognition). Each model is a mathematical generator of amino acid sequences; the sequence under consideration is modeled as having been generated by one model in the set of candidates. The probability that each model generated the given sequence is computed using a filtering algorithm. The protein is then classified as belonging to the structural class having the most probable model. The secondary structure of the sequence is then analyzed using a "smoothing" algorithm that is optimal for that structural class model. For each residue position in the sequence, the smoother computes the probability that the residue is contained within each of the defined secondary structural elements of the model. This method has two important advantages: (1) the probability of each residue being in each of the modeled secondary structural elements is computed using the totality of the amino acid sequence, and (2) these probabilities are consistent with prior knowledge of realizable domain folds as encoded in each model. As an example of the method's utility, we present its application to flavodoxin, a prototypical alpha/beta protein having a central beta-sheet, and to thioredoxin, which belongs to a similar structural class but shares no significant sequence similarity.

Flavodoxin↗
PubMed1993

The evolution of the thrombospondin gene family.

Thrombospondin-1 is an adhesive glycoprotein that is involved in cellular attachment, spreading, migration, and proliferation. To date, four genes have been identified that encode for the members of the thrombospondin gene family. These four genes are homologous to each other in the EGF-like (type 2) repeats, the calcium-binding (type 3) motifs, and the COOH-terminal. The latter has been reported to be a cell-binding domain in thrombospondin-1. Phylogenetic trees have been constructed from the multisequence alignment of thrombospondin sequences from human, mouse, chicken, and frog. Two different algorithms generate comparable results in terms of the topology and the branch lengths. The analysis indicates that an early form of the thrombospondin gene duplicated about 925 million years ago. The gene duplication that produced the thrombospondin-1 and -2 branches of the family is predicted to have occurred 583 million years ago, whereas the gene duplication that produced the thrombospondin-3 and -4 branches of the family is predicted to have occurred 644 million years ago. These results indicate that the members of the thrombospondin gene family have existed throughout the evolution of the animal kingdom and thus probably participate in functions that are common to most of its members.

Amino Acid Sequence↗
PubMed1993

Human papillomavirus infection and intraepithelial, in situ, and invasive carcinoma of penis.

The role of human papillomavirus (HPV) infection and other reported cofactors in the genesis, evolution, and clinical manifestations of precancerous and cancerous squamous cell lesions of the penis were studied in 34 men. Clinically, all lesions demonstrated aceto-whitening. Histologic changes of HPV infection formed a field-of-change that involved the components of the preputial cavity in all patients. These changes were associated with minor grades of penile intraepithelial neoplasia (PIN I and II) in 19 patients, major grades of PIN/carcinoma in situ (PIN III/Tis) in 7, and invasive squamous cell carcinoma (SCCa, Stages T2 and T3) in 8. Most of the patients (79.4%) were heavy smokers; 52.9 percent had a history of HPV infection, PIN, or invasive penile SCCa; and 60 percent of 30 patients had female sexual partners who had HPV-related genital neoplasia. A pilot virologic study of specimens obtained from 20 representative patients utilizing polymerase chain reaction amplification detected HPV DNA in 80 percent. Laser therapy was aimed at the entire field-of-change in 30 patients; recurrent minor-grade PIN or SCCa developed in 2 of 23 patients (8.7%) followed for up to three years. Of the 4 remaining patients treated with local excision or partial penectomy, 3 (75%) had development of recurrent minor-grade PIN when followed for up to four years. The combination of the host of carcinogenic factors and currently rampant immunologic disorders will likely lead to an increase in the historically low incidence of SCCa of the penis in the United States.

Adult↗
PubMed1993

Risk factors for cytomegalovirus and severe bacterial infections following liver transplantation: a prospective multivariate time-dependent analysis.

Risk factors for cytomegalovirus and severe bacterial infections were studied prospectively by univariate, multivariate and time-dependent Cox model analysis in 79 consecutive liver transplant patients treated with selective bowel decontamination. Cytomegalovirus infection occurred in 39 patients (49%) and was symptomatic in 22 patients. Twenty-six patients (33%) developed at least one of 43 documented severe bacterial infections. In a multivariate analysis of risk factors for all cytomegalovirus infections, the cytomegalovirus seronegative recipient-cytomegalovirus seropositive donor group was the highest risk group (P < 0.001). Using the same analysis for risk factors for symptomatic cytomegalovirus infections, a prolonged prothrombin time (P < 0.005), a diagnosis of acute fulminant hepatitis as the underlying liver disease (P < 0.01) and a cytomegalovirus seronegative patient receiving a liver from a seropositive donor (P < 0.001) were significant. The treatment with OKT3 therapy (P < 0.008) and hepatic artery thrombosis (P < 0.02) were found to be significant risk factors in a time-dependent univariate analysis but were not independent risk factors when multivariate analysis was utilized. Significant risk factors for major bacterial infections (P < 0.03) using univariate analysis included a prolonged anesthesia, anhepatic and surgical times, as well as the transfusion of large amounts of fresh frozen plasma or autologous blood. In a multivariate analysis, only the transfusion of large amounts of fresh frozen plasma (P < 0.04) was a significant independent risk factor. Cytomegalovirus infection was a risk factor for the development of severe bacterial infections (P < 0.03) in a multivariate time-dependent analysis.

Adult↗
PubMed1993

Varicella-zoster virus retinitis in a patient with AIDS-related complex: case report and brief review of the acute retinal necrosis syndrome.

Retinitis reminiscent of the acute retinal necrosis syndrome was recognized in a patient with AIDS-related complex after he had experienced several episodes of a sacral, dermatomic zosteriform eruption. Varicella-zoster virus (VZV) was subsequently recovered from cell culture of retinal tissue. The literature on VZV retinitis, including that on acute retinal necrosis, is reviewed. Dissemination of VZV infection in AIDS is also reviewed. Features that differentiate the findings and course of VZV retinitis in patients with AIDS from those in otherwise healthy adults are noted and related to potentially different pathogenic mechanisms. This unusual and recently recognized complication of herpesvirus infection may be promoted by AIDS-related immunosuppression. Acute retinal necrosis and other more-recently described forms of VZV retinitis, which have primarily been subjects of the ophthalmologic literature, merit the attention of clinicians and investigators of infectious diseases.

AIDS-Related Complex↗
PubMed1993

Comparison of the major outer-membrane protein (MOMP) gene of mouse pneumonitis (MoPn) and hamster SFPD strains of Chlamydia trachomatis with other Chlamydia strains.

Restriction fragments containing the major outer-membrane protein (MOMP) gene from two nonhuman (rodent) strains of Chlamydia trachomatis, the mouse pneumonitis (MoPn) strain and the SFPD strain isolated from hamsters with transmissible proliferative ileitis, were cloned and sequenced. The MOMP genes of both MoPn and SFPD encode an identical 22-amino acid leader peptide and mature polypeptides of 365 and 382 amino acids, respectively. Alignment of the MOMP genes of the two rodent strains revealed 91% identity. By comparison with other known chlamydial MOMP gene sequences, there was 80%-83% identity with human biovars strains of C. trachomatis, and there was 69%-70% identity with C. psittaci and C. pneumoniae strains. The main differences in these sequences were clustered into four variable domains. A minimum-length evolutionary tree was constructed on the basis of the MOMP gene variable positions by using PIMA package software. The minimum mutation distances indicated that (i) the MOMP genes of all chlamydial strains may have evolved from a common ancestor; (ii) all the strains of C. trachomatis compose one of the subtrees, and strains of C. psittaci and C. pneumoniae compose the other subtree; and (iii) in the C. trachomatis subtree, the human and the rodent strains are divided into two clusters. The branching pattern of this evolutionary tree is generally consistent with current classification based on serological, morphological, and other biological characteristics.

Amino Acid Sequence↗
PubMed1993

Dependence of polymerase chain reaction product inactivation protocols on amplicon length and sequence composition.

Specific diagnostic test results generated by polymerase chain reaction (PCR) depend upon control of amplicon contamination in the clinical laboratory. We compared photochemical (isopsoralen [IP]) and enzymatic (uracil N-glycosylase [UNG]) methods for their ability to prevent carryover of amplicons generated from genomic targets of five viruses. PCR products (amplicons) (herpes simplex virus, 342 bp; cytomegalovirus, 250 bp; Epstein-Barr virus, 240 bp) exposed to UV light in the presence of various concentrations of IP compound 10 (IP-10) resulted in apparent increased molecular sizes of the products, as indicated by migration patterns after gel electrophoresis, and were predictive of inactivation by the agent. For amplicons of < or = 100 bp, IP-10-induced electrophoretic shifts were related to the guanidine-cytidine (G + C) content of the PCR product; no apparent shift and no inactivation were observed for a 92-bp herpes simplex virus amplicon (G + C content, 65%), whereas the 100-bp human papillomavirus product (G + C content, 42%) showed a concentration-dependent shift (25 to 100 micrograms/ml) in electrophoretic migration and was partially inactivated. UNG effectively controlled amplicon carryover for target DNA of > or = 240 bp; however, this treatment did not inactivate the two amplicons of < or = 100 bp, regardless of the G + C content of the product. Larger products were inactivated efficiently by both methods, regardless of their G + C contents. We concluded that both IP and UNG effectively inactivated PCR amplicons but not short amplicons of < or = 100 bp. We recommend that with the adoption of PCR technology in clinical laboratories, primers should be designed to produce amplicons of at least 240 to 350 bp (depending on G + C content) and that at least one effective method of controlling carryover contamination should be incorporated into each PCR protocol.

Base Composition↗
PubMed1993

New developments in the diagnosis of viral diseases.

Major technical advances have occurred, especially in the last 5 years, in the laboratory diagnosis of viral infections. Immunologic detection of immediate early antigens in specimens such as bronchoalveolar lavage fluid and blood inoculated into shell vial cell cultures, particularly for herpesvirus (cytomegalovirus, herpes simplex virus, varicella-zoster virus), has provided results 16 to 48 hours after inoculation rather than the several days required for recognition of cytopathic effects in conventional tube cell cultures. Similarly, cytomegalovirus viremia can be detected directly by immunostaining of peripheral blood leukocytes with commercially available reagents the same day the specimen is submitted to the laboratory. Single-test membrane immunoassays have provided rapid (15 minutes) detection of viral antigens (respiratory syncytial virus, rotavirus, influenza virus type A). In the near future, diagnostic virology laboratories will be expected to monitor viral strains for susceptibility to the growing list of antiviral drugs. Amplification of nucleic acid sequences of viruses from cerebrospinal fluid or tissue, which generally does not yield isolates by conventional diagnostic techniques, has added a new dimension to the laboratory diagnosis of viral infection.

Adult↗