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T F Smith

Publications and source records attributed to T F Smith.

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

Granulomatous vasculitis associated with herpes virus: a persistent, painful, postherpetic papular eruption.

Cutaneous granulomatous vasculitis manifesting as a postherpetic reaction pattern is uncommon hand has previously been reported as a delayed complication of varicella-zoster virus infection. We describe three patients who had persistent, painful, postherpetic papules in a zosteriform distribution that histologically demonstrated a small vessel granulomatous vasculitis. Herpes simplex virus DNA detected by the polymerase chain reaction technique was demonstrated in two cases.

Aged↗
PubMed1997

Beta-turn new classification and its some features in proteins.

An inspection of the phi-psi angle distribution strongly suggests that protein folding is highly constrained. A number of researchers have even suggested that a relatively small set of discrete phi-psi regions might be sufficient to describe most protein conformation. The total of 541 tight turns from 101 non-identical proteins were extracted form Brookhaven DataBank. The dihedral values of tight turns were scattered into the seven regions on the Ramachandran plot. These seven regions were called A1, A2, B1, B2, B22, T1 and T2. A1 and A2 are the traditional alpha-helix regions, B1, B2 and B22 the beta-strand regions, T1 and T2 the beta-turn regions. The A2 and T2 regions were not defined as "discrete" or single points but rather as one dimensional extended states. Based on the geometry of the two central residues of the tight turns, the new classification of beta-turn was defined. This classification of the majority of beta-turns fell into only six of the possible forty nine region combinations and were identifiable with the traditional nomenclature of Venkatachalam(1), but much simpler. The function of beta-turn in the conformation of proteins was studied. The hydrophobicity for different type turns was discussed. It shows that beta-turns have very strong hydrophilic property, so they are usually situated at the folding protein surface. The features of beta-turn and its amino acid distribution in this 541 beta-turn group and different type beta-turn were given.

Amino Acid Sequence↗
PubMed1996

Analysis of the physical properties and molecular modeling of Sec13: A WD repeat protein involved in vesicular traffic.

WD repeat proteins are a family of proteins that contain a series of highly conserved internal repeat motifs, usually ending with WD (Trp-Asp). The G beta subunit of heterotrimeric guanine nucleotide binding protein is a member of this family, and its crystal structure has been recently solved at high resolution (Wall et al. (1995) Cell 83, 1047-1058; Sondek et al. (1996) Nature 379, 369-374). Based on the coordinates of G beta, we have constructed a model for the structure of Sec13, a 33 kDa WD repeat protein from Saccharomyces cerevesiae essential for vesicular traffic. The model has been tested using a combination of biophysical and biochemical methods. Sec13 was expressed in Escherichia coli as a hexa-His-tagged protein (H6Sec13) and purified to homogeneity. In contrast to some other WD repeat proteins that are unable to fold into monomeric structures when expressed in E. coli, H6Sec13 was soluble and monomeric in the absence of detergent. The far-UV circular dichroism (CD) spectra of H6Sec13 indicated less than 10% alpha-helix consistent with the model which predicts primarily beta-sheets. H6Sec13 shows a cooperative and irreversible thermal denaturation curve consistent with a tightly packed structure. The CD spectrum shows an unusual positive ellipticity at 229 nm that was attributed to interactions of surface tryptophans since the 229 nm maximum could be abolished by modification of 6.3 +/- 0.3 (n = 3) tryptophans (out of 15 total in the molecule) with N-bromosuccinimide. Our model predicts that three sets of tryptophans are clustered near the surface. As predicted by the model, purified H6Sec13 was completely resistant to trypsin digestion. The concordance of the model of Sec13 presented in this paper with the biochemical and biophysical studies suggests that this model can be useful as a guide to further experiments designed to elucidate the function of Sec13 in vesicular traffic.

Amino Acid Sequence↗
PubMed1996

Folding of proteins with WD-repeats: comparison of six members of the WD-repeat superfamily to the G protein beta subunit.

The family of WD-repeat proteins comprises over 30 different proteins that share a highly conserved repeating motif [Neer, E. J., Schmidt, C. J., Nambudripad, R., & Smith, T. F. (1994) Nature 371, 297-300]. Members of this family include the signal-transducing G protein beta subunit, as well as other proteins that regulate signal transduction, transcription, pre-mRNA splicing, cytoskeletal organization, and vesicular fusion. The crystal structure of one WD-repeat protein (G beta) has now been solved (Wall et al., 1995; Sondek et al, 1996) and reveals that the seven repeating units form a circular, propeller-like structure with seven blades each made up of four beta strands. It is very likely that all WD-repeat proteins form a similar structure. If so, it will be possible to use information about important surface regions of one family member to predict properties of another. If WD proteins form structures similar to G beta, their hydrodynamic properties should be those of compact, globular proteins, and they should be resistant to cleavage by trypsin. However, the only studied example of a WD-repeat protein, G beta, synthesized in vitro in a rabbit reticulocyte lysate, is unable to fold into a native structure without its partner protein G gamma. The non-WD-repeat amino terminal alpha helix of G beta does not inhibit folding because G beta does not fold even when this region is removed. It is not known whether all WD-repeat proteins are unable to fold when synthesized in an in vitro system. We synthesized seven members of the family in a rabbit reticulocyte lysate, determined their Stokes radius, sedimentation coefficient, and frictional ratio, and assayed their stability to trypsin. Our working definition of folding was that the proteins from globular, trypsin-resistant structures because, except for G beta gamma, their functions are not known or cannot be assayed in reticulocyte lysates. We chose proteins that include amino and carboxyl extensions as well as proteins that are made up entirely of WD-repeats. We show that unlike G beta, several proteins with WD-repeats are able to fold into globular proteins in a rabbit reticulocyte lysate. One protein, beta Trcp, formed large aggregates like G beta, suggesting that it may also require a partner protein. Despite the presence of many potential tryptic cleavage sites, all of the proteins that did fold gave stable large products on tryptic proteolysis, as predicted on the basis of the structure of G beta. These studies suggest that other WD-repeat proteins are likely to form propeller structures similar to G beta.

1-Alkyl-2-acetylglycerophosphocholine Esterase↗
PubMed1996

Global optimum protein threading with gapped alignment and empirical pair score functions.

We describe a branch-and-bound search algorithm for finding the exact global optimum gapped sequence-structure alignment ("threading") between a protein sequence and a protein core or structural model, using an arbitrary amino acid pair score function (e.g. contact potentials, knowledge-based potentials, potentials of mean force, etc.). The search method imposes minimal conditions on how structural environments are defined or the form of the score function, and allows arbitrary sequence-specific functions for scoring loops and active site residues. Consequently the search method can be used with many different score functions and threading methodologies; this paper illustrates five from the literature. On a desktop workstation running LISP, we have found the global optimum protein sequence-structure alignment in NP-hard search spaces as large as 9.6 x 10(31), at rates ranging as high as 6.8 x 10(28) equivalent threadings per second (most of which are pruned before they ever are examined explicitly). Continuing the procedure past the global optimum enumerates successive candidate threadings in monotonically increasing score order. We give efficient algorithms for search space size, uniform random sampling, segment placement probabilities, mean, standard deviation and partition function. The method should prove useful for structure prediction, as well as for critical evaluation of new pair score functions.

Algorithms↗
PubMed1996

Multiple domain protein diagnostic patterns.

We have implemented an iterative algorithm for the identification of diagnostic patterns from sets of multiple-domain proteins, where domains need not be common to all the proteins in the defining set. Our algorithm was applied to sequences gathered using a variety of methods, including BLAST, common keywords, and common E.C. numbers. In all cases, useful diagnostic patterns were obtained, possessing both high sensitivity and specificity. The patterns were found to correlate in several cases with both functional and structural domains. Patterns generated from a large number of sequence families were analyzed for probable multiple-domain structure.

Algorithms↗
PubMed1996

Reconstruction of ancient molecular phylogeny.

Support for contradictory phylogenies is often obtained when molecular sequence data from different genes is used to reconstruct phylogenetic histories. Contradictory phylogenies can result from many data anomalies including unrecognized paralogy. Paralogy, defined as the reconstruction of a phylogenetic tree from a mixture of genes generated by duplications, has generally not been formally included in phylogenetic reconstructions. Here we undertake the task of reconstructing a single most likely evolutionary relationship among a range of taxa from a large set of apparently inconsistent gene trees. Under the assumption that differences among gene trees can be explained by gene duplications, and consequent losses, we have developed a method to obtain the global phylogeny minimizing the total number of postulated duplications and losses and to trace back such individual gene duplications to global genome duplications. We have used this method to infer the most likely phylogenetic relationship among 16 major higher eukaryotic taxa from the sequences of 53 different genes. Only five independent genome duplication events need to be postulated in order to explain the inconsistencies among these trees.

Algorithms↗
PubMed1996

Detection of human papillomavirus DNA in primary squamous cell carcinoma of the male urethra.

OBJECTIVES: The prevalence of human papillomavirus deoxyribonucleic acid (DNA) in primary squamous cell carcinoma of the male urethra and corresponding control tissue was studied. METHODS: The technique of polymerase chain reaction DNA amplification was used to detect specific human papillomavirus DNA sequences in archival pathologic and control tissue. We analyzed 16 cases of primary squamous cell carcinoma of the male urethra and 22 specimens of normal male urethra stratified by location within the urethra. RESULTS: Primary squamous cell carcinoma of the pendulous urethra was significantly associated with human papillomavirus type 16 DNA (6 of 6 cases), but the control tissue from the pendulous urethra was not (0 of 12, P < 0.001). Primary squamous cell carcinoma of the bulbous and posterior urethra was not associated with human papillomavirus infection. CONCLUSIONS: Infection of the male urethra with human papillomavirus type 16 may have a role in the pathogenesis of primary squamous cell carcinoma of the pendulous urethra, for which it has a strong predilection, vis-à-vis the bulbous and posterior urethra.

Carcinoma, Squamous Cell↗
PubMed1996

Prognostic significance and risk factors of untreated cytomegalovirus viremia in liver transplant recipients.

To study whether cytomegalovirus (CMV) viremia is a reliable marker of impending CMV disease and thus a guide for preemptive antiviral therapy, 126 consecutive liver transplant recipients were followed by routine CMV blood cultures in the absence of antiviral prophylaxis or treatment for viremia. Seventy-three patients (58%) developed CMV infections, and 36 (29%) had more than one infection episode: 29 patients (23%) had organ involvement and 45 (36%) had viremia. Within a same episode, CMV viremia was 90% sensitive and 80% specific for predicting concurrent organ involvement but preceded organ involvement in only 9 (31%) of 29 patients. In a separate analysis, untreated isolated CMV viremia in the first CMV infection episode was followed by organ involvement in a subsequent episode in 9 (33%) of 28 patients, mainly in the donor-positive, recipient-negative (D+/R-) population. The results indicate that CMV viremia is not an ideal marker to guide preemptive antiviral treatment in liver transplant recipients but is a good marker in D+/R- patients.

Adult↗
PubMed1995

A biologically consistent model for comparing molecular phylogenies.

In the framework of the problem of combining different gene trees into a unique species phylogeny, a model for duplication/speciation/loss events along the evolutionary tree is introduced. The model is employed for embedding a phylogeny tree into another one via the so-called duplication/speciation principle requiring that the gene duplicated evolves in such a way that any of the contemporary species involved bears only one of the gene copies diverged. The number of biologically meaningful elements in the embedding result (duplications, losses, information gaps) is considered a (asymmetric) dissimilarity measure between the trees. The model duplication concept is compared with that one defined previously in terms of a mapping procedure for the trees. A graph-theoretic reformulation of the measure is derived.

Evolution, Molecular↗
PubMed1995

A prospective comparison of molecular diagnostic techniques for the early detection of cytomegalovirus in liver transplant recipients.

Forty-one consecutive liver transplant recipients were studied by polymerase chain reaction (PCR) of serum and peripheral blood mononuclear cells, reverse transcription (RT)-PCR of peripheral blood mononuclear cells, and viral blood culture for symptomatic cytomegalovirus (CMV) infection. The techniques were also used to predict the occurrence of CMV infection. For diagnosis of symptomatic CMV infection, the sensitivity and specificity of the different techniques were as follows: PCR of serum, 100% and 45%; RT-PCR, 25% and 97%; PCR of peripheral blood mononuclear cells, 83% and 35%; and blood culture, 83% and 86%, respectively. PCR of serum was positive in 83% of subjects with symptomatic infection before onset compared with 17% positive by blood culture. While viral blood culture was the best technique for the diagnosis of symptomatic CMV infection, PCR of serum was best at predicting the development of symptomatic CMV infection.

Cytomegalovirus↗
PubMed1995

Comparison of three methods for extraction of viral nucleic acids from blood cultures.

Reliable nucleic acid extraction techniques for blood specimens are required for the sensitive detection of viral DNA. Standardized procedures for processing blood specimens for the molecular detection of herpesviruses (cytomegalovirus [CMV], herpes simplex virus, varicella-zoster virus, and Epstein-Barr virus [EBV]) have not been established. Three methods were used to extract DNA from blood specimens from healthy donors and asymptomatic immunocompromised patients: (i) IsoQuick treatment of whole blood, (ii) extraction of the peripheral blood leukocytes by lysis (lysis buffer and proteinase K), and (iii) extraction of peripheral blood leukocytes with phenol-chloroform (sodium docecyl sulfate solution and proteinase K). All blood specimens from 25 healthy blood donors were negative for CMV, herpes simplex virus and varicella-zoster virus nucleic acid sequences, regardless of the extraction method, while three samples (12%) extracted by the lysis technique were positive for EBV DNA. Of 25 blood samples from asymptomatic immunocompromised patients, CMV and EBV each were detected in nine specimens by lysis extraction, four each by IsoQuick and four (CMV) and six (EBV) by the phenol-chloroform method. Our results indicate that the lysis method is optimal for the detection of CMV and EBV DNA sequences by PCR from the leukocytic fraction of blood specimens. DNA of these viruses is frequently present in blood specimens from asymptomatic immunocompromised patients and occasionally from healthy donors.

Base Sequence↗
PubMed1995

Optimization of detection of cytomegalovirus viremia in transplantation recipients by shell vial assay.

Cytomegalovirus (CMV) viremia is a widely used laboratory marker of CMV disease following transplantation and is additionally used to trigger preemptive antiviral therapy. Despite this, the optimal method for diagnosing CMV viremia in transplantation recipients remains unknown. To determine the sampling frequency and blood volume required for the optimal diagnosis of viremia by shell vial assay, a prospective study of 46 viremic transplantation recipients was conducted. Blood specimens (2.5 and 5 ml) were collected twice, 3 h apart, at a median of 1.4 days (range, 1 to 3 days) after the triggering shell vial-positive blood had been collected. Considering a single 2.5-ml specimen, an average of only 40% of previously viremic patients had documented CMV in their blood: this increased to 50% when a second 2.5-ml sample of blood was collected 3 h later. The yields of two 2.5-ml versus two 5-ml samples were 50 versus 61%, respectively. Viremia as detected by shell vial assay is intermittent, and increasing the frequency and volume of blood sampling increases its diagnosis. These results have implications in diagnosis of CMV infection and its preemptive therapy.

Bone Marrow Transplantation↗
PubMed1995

The detection of human papillomavirus deoxyribonucleic acid in intraepithelial, in situ, verrucous and invasive carcinoma of the penis.

PURPOSE: We study the prevalence of human papillomavirus deoxyribonucleic acid (DNA) in squamous cell carcinoma and control tissue of the penis. MATERIALS AND METHODS: The technique of polymerase chain reaction DNA amplification was used to detect specific human papillomavirus DNA sequences in archival pathological and control tissues. We analyzed 42 cases of invasive squamous cell carcinoma, 13 of carcinoma in situ, 12 of penile intraepithelial neoplasia, 3 of verrucous carcinoma and 25 of balanitis xerotica obliterans, as well as 29 routine neonatal circumcision specimens and 32 adult circumcision specimens. RESULTS: Overall, the detection rates for human papillomavirus DNA in the study and control tissues were 55% (23 of 42 cases) for invasive squamous cell carcinoma, 92% (12 of 13) for carcinoma in situ, 92% (11 of 12) for penile intraepithelial neoplasia, 0% (0 of 3) for verrucous carcinoma, 4% (1 of 25) for balanitis xerotica obliterans, 0% (0 of 29) for neonatal circumcision and 9% (3 of 32) for adult circumcision. In all groups human papillomavirus type 16 was the most common genotype identified. CONCLUSIONS: The prevalence of human papillomavirus DNA is significantly greater in carcinoma of the penis than in control tissue. Moreover, the prevalence is greater in noninvasive lesions (carcinoma in situ and penile intraepithelial neoplasia) than in invasive carcinoma.

Balanitis↗