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At least 739 records · Page 41Linked to original sources
PubMed2006

[Early detection of hepatitis C virus infection using a new combined antigen-antibody detection assay: potential use in HIV co-infected individuals].

BACKGROUND: The aim of this study was to determine the clinical benefit of a new combined antigen-antibody immunoenzymatic assay (Monolisa HCV Ag-Ab Ultra, Biorad) in the setting of acute HCV infection in HIV infected patients. PATIENTS AND METHODS: The performance of this assay was first evaluated in 160 HIV positive samples from uninfected and chronically HCV infected patients. To assess the performance of the Ag-Ab assay in the context of acute hepatitis C, 94 stored frozen serums from 20 recently diagnosed cases were retrospectively tested for HCV-RNA and presence of anti-HCV antibodies, in parallel with the new assay. RESULTS: In HIV infected patients, the sensitivity and specificity of the Ultra assay was 100% with a strong discrimination between positive and negative samples. In HCV acutely infected patients, the Ag-Ab assay significantly reduced the seronegative period, allowing an earlier diagnosis compared to a 3rd generation ELISA in 65% of the cases. The combined assay became positive on the same bleed as the first HCV-RNA detection for 13 patients out of 20. Nevertheless, in one case, characterized by an absence of seroconversion over one year but a continuous viral replication above 1 million IU/ml, the combined assay did not improve HCV infection diagnosis. CONCLUSION: Use of this new assay as a first line screening would significantly reduce the long seronegative window period seen in HCV infection allowing earlier HCV diagnosis and rapid clinical management. However, in case of clinical acute hepatitis C, sensitive HCV-RNA detection should remain the gold standard.

Antigen-Antibody Complex↗
PubMed2002

Novel evolutionary analyses of full-length HIV type 1 subtype C molecular clones from Cape Town, South Africa.

Understanding the origin, distribution, and evolving dominance of HIV-1 subtype C strains is an important component in the design and evaluation of a globally effective AIDS vaccine. To better understand subtype C viruses, we constructed complete molecular clones of primary, CCR-5-using isolates from South Africa and analyzed the molecular phylogenies of these clones using best fitting evolutionary substitution models. Analyses were performed on three full-length sequences, and on the individual genes. All clones were nonrecombinant, and although two of three had open reading frames and intact splice sites, they were not infectious. At the genomic level, the models demonstrated the increasing variability of subtype C in South Africa. At the subgenomic level, they revealed marked differences in the evolutionary patterns of individual genes, a finding that suggests that the genes are under different selective pressures and constraints. These data underscore the dynamic nature of the subtype C epidemic and emphasize the need for continuous monitoring of local strains.

Acquired Immunodeficiency Syndrome↗
PubMed2006

N88D facilitates the co-occurrence of D30N and L90M and the development of multidrug resistance in HIV type 1 protease following nelfinavir treatment failure.

Nelfinavir was once one of the most commonly used protease inhibitors (PIs). To investigate the genetic mechanisms of multidrug resistance in protease isolates with the primary nelfinavir resistance mutation D30N, we analyzed patterns of protease mutations in 582 viruses with D30N from 460 persons undergoing HIV-1 genotypic resistance testing at Stanford University Hospital from 1997 to 2005. Three patterns of mutational associations were identified. First, D30N was positively associated with N88D but negatively associated with N88S. Second, D30N and L90M were negatively associated except in the presence of N88D, which facilitated the co-occurrence of D30N and L90M. Third, D30N+N88D+L90M formed a stable genetic backbone for the accumulation of additional protease inhibitor (PI) resistance mutations. In 16 patients having isolates with more than one combination of mutations at positions 30, 88, and 90, all exhibited one of the steps in the following progression: D30N-->D30N+N88D-->D30N+N88D+L90M-->D30N+N88D+L90M+(L33F+/-I84V or M46I/L+/-I54V). Although nelfinavir is now used less frequently than other PIs, the well-delineated mutational pathway we describe is likely to influence patterns of cross-resistance in viruses from persons who experience virologic failure while receiving this PI.

Base Sequence↗
PubMedDate not supplied

[Bacterial pneumonia as a risk marker for new bacterial diseases in patients with HIV infection].

BACKGROUND: Bacterial pneumonias are a main cause of morbidity and mortality among patients infected by the HIV. Furthermore, recent data suggest that, under certain circumstances, they can be prognostic markers. METHODS: The evolution of a cohort of HIV-infected patients, prospectively defined by having suffered a pneumonia, was studied with regards to the occurrence of a new pneumonia or death from a bacterial disease; the evolution of a control cohort of patients matched according to sex, CD4-cell count, previous HIV-disease and zidovudine-treatment was compared to the former cohort by means of survival-analysis techniques. RESULTS: Forty-nine patients in each group were followed up for a total of 1389 and 1893 patient-months respectively. In the first group, 17 new first pneumonia episodes were diagnosed, as compared to 7 in the second group (relative-risk: 3.23, 95% confidence interval: 1.34 to 7.79, p = 0.005). Eight of the 31 deaths that occurred in the first group were attributed to a bacterial disease, as compared to none of the 24 deaths in the second group (p = 0.007, Fisher's exact test) (in five of those cases, a bacteria was isolated which was thought to be directly related to the death). CONCLUSIONS: HIV-infected patients who suffer a bacterial pneumonia have an increased risk of suffering new severe bacterial diseases (pneumonia or fatal diseases) as compared to HIV-infected patients with similar prognostic features but no previous episodes of pneumonia.

Adolescent↗
PubMed2002

Complexities in ETS-domain transcription factor function and regulation: lessons from the TCF (ternary complex factor) subfamily. The Colworth Medal Lecture.

The ETS-domain transcription factor family can be divided into a series of subfamilies. Elk-1 represents the founding member of the ternary complex factor (TCF) subfamily. By focusing on the TCF subfamily, we can demonstrate the complexities that exist in the function and regulation of ETS-domain transcription factors. This article focuses on Elk-1 in detail and summarizes the functions of other TCFs. The key themes covered include the domain structure of the TCFs, the mechanisms of complex formation with serum response factor, regulation of TCFs by mitogen-activated protein kinase cascades, and transcriptional regulatory properties of the TCFs. Finally, the emerging role of the TCFs in vivo is discussed. A picture is developing indicating that, while these proteins exhibit significant sequence and functional conservation, key differences in their structure and regulation are being identified which may relate to unique functions of these proteins in vivo.

Amino Acid Sequence↗
PubMedDate not supplied

Effect of HCV infection on THP-1 monocytoid cells.

Hepatitis C virus (HCV) is the main cause of hepatocellular carcinoma in industrialized countries. HCV-HIV-1 co-infection occurs frequently among users of illicit intravenous drugs, thereby increasing the severity of HIV disease and the evolution of chronic active hepatitis towards cirrhosis and hepatocellular carcinoma. The present work shows that THP-1 monocytoid cells are susceptible to HCV infection, of strain 1b, and that this strain can induce cellular modifications in this cell line. Infection of HCV was demonstrated by positivity for the E2 antigen within THP-1 cells and by indirect immunofluorescence; moreover, HCV-RNA was detected in supernatants of THP-1 cells from day 7 post-inoculation. Cell shape and membrane surface antigens varied upon viral infection, which is also capable of inducing oxygen radicals. In particular we underline the relevant intracellular accumulation of ferritin that paralleled an increase of cell surface expression of the transferrin receptor. Evaluation of cellular events upon HCV infection in THP-1 cells may represent a useful tool with which to identify alteration in monocytes metabolism and to study therapeutic approaches for such alterations.

12E7 Antigen↗
PubMed2004

Evolution of genotypic and phenotypic resistance to Enfuvirtide in HIV-infected patients experiencing prolonged virologic failure.

Four heavily antiretroviral-experienced HIV-infected patients had significant plasma HIV-RNA reductions (>1 log) after beginning an Enfuvirtide (ENF)-based rescue regimen. However, all had viral rebound shortly thereafter, sustaining high levels of plasma viremia over 80 weeks. These patients developed rapidly genotypic and phenotypic resistance to ENF. Mutations within the HR1 env region were selected (N43D in three and G36V/D in one), resulting in high-level phenotypic resistance to ENF. Interestingly, two patients had a sustained CD4+ T-cell increase and two maintained stable CD4+ T-cell counts despite virologic failure under ENF. The possible mechanisms involved in this response were examined. Changes in virus tropism from R5 to R5/X4 were observed in two patients, in parallel with increases in ENF phenotypic resistance. Low levels of T-cell activation, T-cell turnover, and cytotoxic T lymphocyte (CTL) activity were found in all four patients. An overall increase in the proportion of viruses released from cells of the macrophage lineage was observed. In summary, single mutations at the HR1 env region result in significant loss of susceptibility to ENF. Despite virologic failure, these patients may maintain elevated CD4+ counts through a reduction in their overall immune activation.

Amino Acid Sequence↗
PubMed2004

GEMDOCK: a generic evolutionary method for molecular docking.

We have developed an evolutionary approach for flexible ligand docking. This approval, GEMDOCK, uses a Generic Evolutionary Method for molecular DOCKing and an empirical scoring function. The former combines both discrete and continuous global search strategies with local search strategies to speed up convergence, whereas the latter results in rapid recognition of potential ligands. GEMDOCK was tested on a diverse data set of 100 protein-ligand complexes from the Protein Data Bank. In 79% of these complexes, the docked lowest energy ligand structures had root-mean-square derivations (RMSDs) below 2.0 A with respect to the corresponding crystal structures. The success rate increased to 85% if the structure water molecules were retained. We evaluated GEMDOCK on two cross-docking experiments in which each ligand of a protein ensemble was docked into each protein of the ensemble. Seventy-six percent of the docked structures had RMSDs below 2.0 A when the ligands were docked into foreign structures. We analyzed and validated GEMDOCK with respect to various search spaces and scoring functions, and found that if the scoring function was perfect, then the predicted accuracy was also essentially perfect. This study suggests that GEMDOCK is a useful tool for molecular recognition and may be used to systematically evaluate and thus improve scoring functions.

Algorithms↗
PubMed2000

Are RNA viruses adapting or merely changing?

RNA viruses and retroviruses fix substitutions approximately 1 million-fold faster than their hosts. This diversification could represent an inevitable drift under purifying selection, the majority of substitutions being phenotypically neutral. The alternative is to suppose that most fixed mutations are beneficial to the virus, allowing it to keep ahead of the host and/or host population. Here, relative sequence diversification of different proteins encoded by viral genomes is found to be linear. The examples encompass a wide variety of retroviruses and RNA viruses. The smoothness of relative divergence spans quasispeciation following clonal infection, to variation among different isolates of the same virus, to viruses from different species or those associated with different diseases, indicating that the majority of fixed mutations likely reflects drift. This held for both mammalian and plant viruses, indicating that adaptive immunity doesn't necessarily shape the relative accumulation of amino acid substitutions. When compared to their hosts RNA viruses evolution appears conservative.

Adaptation, Physiological↗
PubMed2006

Characterization and application of aptamers for Taq DNA polymerase selected using an evolution-mimicking algorithm.

Using an evolution-mimicking algorithm (EMA), we have recently identified DNA aptamers that inhibit Taq DNA polymerase. In the present study, we have attempted to improve further the inhibitory activities of aptamers, as well as to characterize those aptamers with the most potent inhibitory activities. To characterize the most potent aptamer and demonstrate its applicability, the abilities to inhibit Tth DNA polymerase and to modulate specific amplification in PCR were investigated. This aptamer inhibited both Tth DNA polymerase and Taq DNA polymerase and improved the specificity of detection of a low-copy-number target gene in PCR using these DNA polymerases.

Algorithms↗
PubMed1990

Is the pseudo-dyad in retroviral proteinase monomers structural or evolutionary?

A pseudo-dyad was found to exist in the monomers of the crystal structures of the proteinases from Rous sarcoma virus and the human immunodeficiency virus. This dyad, also discovered earlier in pepsin-like aspartic proteinases and considered to be of probable evolutionary origin, has been shown to arise as a result of the topology and the folding of the proteinase monomers and may not therefore have much evolutionary significance.

Avian Sarcoma Viruses↗
PubMed1994

The evolution of tuberculosis infection among schoolchildren in Barcelona and the HIV epidemic.

SETTING: First grade students in primary schools in the city of Barcelona, Spain. OBJECTIVE: To estimate the prevalence of tuberculin reaction and sources of infection; to analyse trends in comparison with previous data. DESIGN: Tuberculin screening of first grade schoolchildren (1985 birth cohort) was undertaken in 1991-92 using 2 TU of PPD RT23. RESULTS: The prevalence of reactors among the 12,007 children tested from the 1985 cohort was 0.87%, varying among districts between 0.13% and 3.03%. Follow-up of positive tests was completed for 75 children, which led to the identification of 6 cases of previously unknown clinical tuberculosis among these children, while for 14 infected children index cases were found, one of whom was a confirmed HIV-infected IVDU. CONCLUSION: The comparison of results with data from previous studies suggests that tuberculosis infection among schoolchildren in Barcelona may not be declining as in previous years, especially in areas such as the inner city, where poverty combines with HIV infection and with increasing migration from countries with a higher tuberculosis prevalence.

Child↗
PubMed2002

Evaluation of structural and evolutionary contributions to deleterious mutation prediction.

Methods for automated prediction of deleterious protein mutations have utilized both structural and evolutionary information but the relative contribution of these two factors remains unclear. To address this, we have used a variety of structural and evolutionary features to create simple deleterious mutation models that have been tested on both experimental mutagenesis and human allele data. We find that the most accurate predictions are obtained using a solvent-accessibility term, the C(beta) density, and a score derived from homologous sequences, SIFT. A classification tree using these two features has a cross-validated prediction error of 20.5% on an experimental mutagenesis test set when the prior probability for deleterious and neutral cases is equal, whereas this prediction error is 28.8% and 22.2% using either the C(beta) density or SIFT alone. The improvement imparted by structure increases when fewer homologs are available: when restricted to three homologs the prediction error improves from 26.9% using SIFT alone to 22.4% using SIFT and the C(beta) density, or 24.8% using SIFT and a noisy C(beta) density term approximating the inaccuracy of ab initio structures modeled by the Rosetta method. We conclude that methods for deleterious mutation prediction should include structural information when fewer than five to ten homologs are available, and that ab initio predicted structures may soon be useful in such cases when high-resolution structures are unavailable.

Bacterial Proteins↗
PubMed2003

Optimal viral production.

Viruses reproduce by multiplying within host cells. The reproductive fitness of a virus is proportional to the number of offspring it can produce during the lifetime of the cell it infects. If viral production rates are independent of cell death rate, then one expects natural selection will favor viruses that maximize their production rates. However, if increases in the viral production rate lead to an increase in the cell death rate, then the viral production rate that maximizes fitness may be less than the maximum. Here we pose the question of how fast should a virus replicate in order to maximize the number of progeny virions that it produces. We present a general mathematical framework for studying problems of this type, which may be adapted to many host-parasite systems, and use it to examine the optimal virus production scheduling problem from the perspective of the virus.

Evolution, Molecular↗
PubMed1999

From Pan to pandemic.

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Acquired Immunodeficiency Syndrome↗