Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts:   Target Concepts:
Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Strand displacement amplification (SDA) is an isothermal, enzymatic method for the exponential synthesis of target nucleic acids which traditionally requires two pairs of oligoprimers. One pair, described as "bumpers", serves to generate target specific single stranded DNA after heat denaturation of double stranded DNA subsequent to primer annealing and extension. We report here the in situ (IS) application of SDA (IS-SDA) using nicked DNA targets which eliminate the need for heat denaturation and bumpers. Productive nicking can be generated by restriction endonuclease activity, exposure to dry heat, paraffin embedding, or mild depurination. IS-SDA, followed by in situ hybridization (ISH) allows for the routine detection of single copy HIV-1 DNA as well as HPV DNA in both cell lines and tissue sections. Detection of hepatitis C RNA in liver biopsy specimens using reverse transcription IS-SDA (RT-IS-SDA) was performed with direct incorporation of the reporter nucleotide. The amplification of RNA targets does require bumper primers, although not an initial denaturation step. Extensive analyzes demonstrated that SDA-ISH is as sensitive as polymerase chain reaction (PCR)-ISH and that each are more sensitive than in situ hybridization coupled to catalyzed signal amplification (CSA). Moreover. SDA-ISH is technically much simpler than PCR-ISH because it is isothermal and does not require an initial denaturation.
Diagn Mol Pathol 2000 Dec
PMID:In situ strand displacement amplification: an improved technique for the detection of low copy nucleic acids. 1112 43

The backbone assignments, secondary structure, topology, and dynamics of the single-chain hepatitis C virus NS3 protease NS4A cofactor complex have been determined by NMR spectroscopy. Residues I34 to S181 of NS3 and the central three residues of the NS4A cofactor were assigned and the secondary structure was verified for these residues. In several X-ray structures of NS4A-bound NS3 protease, residues 1 to 28 are stabilized by crystal packing, which allows for the formation of the A0 strand and alpha0 helix. In solution, these N-terminal residues are largely unassigned and no evidence of a well-structured A0 strand or alpha0 helix was detected. NOEs between residues in the E1-F1 loop (containing D81) and the alpha1 helix (containing H57) together with the detection of a D81-H57 hydrogen bond indicate that in solution the catalytic triad (D81, H57, S139) of the protease is better ordered in the presence of the NS4A cofactor. This is consistent with the earlier crystallographic results and may explain the observed increase in catalytic activity of the enzyme due to NS4A binding. A model-free analysis of our relaxation data indicates substantial exchange rates for residues V51-D81, which comprise the upper part of the N-terminal beta-barrel. A comparison of chemical-shift differences between NS3 protease and the NS3 protease-NS4A complex shows extensive chemical-shift changes for residues V51-D81 indicating that non-local structural changes occur upon NS4A binding to the NS3 protease that are propagated well beyond the protease-cofactor interaction site. This is consistent with crystallographic data that reveal large structural rearrangements of the strand and loop regions formed by residues V51-D81 as a result of NS4A binding. The coincidence of large exchange rates for the NS3 protease-NS4A complex with chemical-shift differences due to NS4A binding suggests that residues V51-D81 of the NS3 protease NS4A complex are in slow exchange with a NS4A-free conformation of NS3 protease.
J Mol Biol 2001 Feb 02
PMID:Solution structure and dynamics of the single-chain hepatitis C virus NS3 protease NS4A cofactor complex. 1116 17

The eukaryotic mRNA 3' poly(A) tail acts synergistically with the 5' cap structure to enhance translation. This effect is mediated by a bridging complex, composed of the poly(A) binding protein (PABP), eIF4G, and the cap binding protein, eIF4E. PABP-interacting protein 1 (Paip1) is another factor that interacts with PABP to coactivate translation. Here, we describe a novel human PABP-interacting protein (Paip2), which acts as a repressor of translation both in vitro and in vivo. Paip2 preferentially inhibits translation of a poly(A)-containing mRNA, but has no effect on the translation of hepatitis C virus mRNA, which is cap- and eIF4G-independent. Paip2 decreases the affinity of PABP for polyadenylate RNA, and disrupts the repeating structure of poly(A) ribonucleoprotein. Furthermore, Paip2 competes with Paip1 for PABP binding. Thus, Paip2 inhibits translation by interdicting PABP function.
Mol Cell 2001 Jan
PMID:Translational repression by a novel partner of human poly(A) binding protein, Paip2. 1117 25

We developed a homogeneous format reverse transcription-polymerase chain reaction assay for quantitating hepatitis C virus (HCV) RNA based on the TaqMan principle, in which signal is generated by cleaving a target-specific probe during amplification. The test uses two probes, one specific for HCV and one specific for an internal control, containing fluorophores with different emission spectra. Titers are calculated in international units (IU)/ml by comparing the HCV signal generated by test samples to that generated by a set of external standards. Endpoint titration experiments demonstrated that samples containing 28 IU/ml give positive results 95% of the time. Based on these data, the limit of detection was set conservatively at 40 IU/ml. All HCV genotypes were amplified with equal efficiency and accurately quantitated: when equal quantities of RNA were tested, each genotype produced virtually identical fluorescent signals. The test exhibited a linear range extending from 64 to 4,180,000 IU/ml and excellent reproducibility, with coefficients of variation ranging from 21.6 to 30.4%, which implies that titers that differ by a factor of twofold (0.3 log10) are statistically significant (P = 0.005). The test did not react with other organisms likely to co-infect patients with hepatitis C and exhibited a specificity of 99% when evaluated on a set of samples from HCV seronegative blood donors. In interferon-treated patients, the patterns of viral load changes revealed by the TaqMan HCV quantitative test distinguished responders from nonresponders and responder-relapsers. These data indicate that the TaqMan quantitative HCV test provides an attractive alternative for measuring HCV viral load and should prove useful for prognosis and for monitoring the efficacy of antiviral treatments.
J Mol Diagn 2000 Aug
PMID:Performance characteristics of a quantitative, homogeneous TaqMan RT-PCR test for HCV RNA. 1122 21

The identification of HHV-8 has opened the way for numerous epidemiological studies aimed at determining both the prevalence of HHV-8 in various sub-groups of the population (affected or not by KS) and at identifying possible cofactors necessary for the development of KS. We set up a study to evaluate the prevalence of HHV-8 in the South of Italy in KS cases, hospital patients and blood donors and to verify the role of immunosuppression in KS. In KS patients the prevalence of lytic and latent antigens were both 91% (29 positive cases). Lytic and latent antigens have prevalence rates of 20% and 15% respectively in hospital patients. In the donor group the rates were 16% for lytic antigens and 2% for latent antigens. The most recurrent chronic pathology in KS patients was cardiopathy (5 cases). The pathological case histories report 4 cases of Herpes Zoster, 6 of diabetes, one case of hepatitis C who had also had gonorrea. There was also a case, negative to HHV-8, who had had malaria after residing for three years in Oristano in Sardinia (a zone with high endemic malaria). Our study confirms that in Southern Italy there are relatively high prevalences of HHV-8 both in the general population and in blood donors and that immunodysregulation may be involved in the pathogenesis of KS. Other studies are necessary to confirm the sexual transmission of the HHV-8 virus and to better understand the natural history of HHV-8 infection.
Int J Mol Med 2001 May
PMID:HHV-8 prevalence, immunosuppression and Kaposi's sarcoma in South Italy. 1129 17

Efficient translation of most eukaryotic mRNAs results from synergistic cooperation between the 5' m(7)GpppN cap and the 3' poly(A) tail. In contrast to such mRNAs, the polyadenylated genomic RNAs of picornaviruses are not capped, and translation is initiated internally, driven by an extensive sequence termed IRES (for internal ribosome entry segment). Here we have used our recently described poly(A)-dependent rabbit reticulocyte lysate cell-free translation system to study the role of mRNA polyadenylation in IRES-driven translation. Polyadenylation significantly stimulated translation driven by representatives of each of the three types of picornaviral IRES (poliovirus, encephalomyocarditis virus, and hepatitis A virus, respectively). This did not result from a poly(A)-dependent alteration of mRNA stability in our in vitro translation system but was very sensitive to salt concentration. Disruption of the eukaryotic initiation factor 4G-poly(A) binding protein (eIF4G-PABP) interaction or cleavage of eIF4G abolished or severely reduced poly(A) tail-mediated stimulation of picornavirus IRES-driven translation. In contrast, translation driven by the flaviviral hepatitis C virus (HCV) IRES was not stimulated by polyadenylation but rather by the authentic viral RNA 3' end: the highly structured X region. X region-mediated stimulation of HCV IRES activity was not affected by disruption of the eIF4G-PABP interaction. These data demonstrate that the protein-protein interactions required for synergistic cooperativity on capped and polyadenylated cellular mRNAs mediate 3'-end stimulation of picornaviral IRES activity but not HCV IRES activity. Their implications for the picornavirus infectious cycle and for the increasing number of identified cellular IRES-carrying mRNAs are discussed.
Mol Cell Biol 2001 Jul
PMID:Eukaryotic initiation factor 4G-poly(A) binding protein interaction is required for poly(A) tail-mediated stimulation of picornavirus internal ribosome entry segment-driven translation but not for X-mediated stimulation of hepatitis C virus translation. 1139 Jun 39

Several approaches have been undertaken in the attempt to inhibit hepatitis C virus (HCV) translation. Antisense oligonucleotides (AS ONs) have proven to be invaluable in the characterization of the HCV internal ribosome entry site (IRES). Chemical modification of oligonucleotides has resulted in optimized stability and specificity. Artificial ribozymes have also been developed to target the HCV IRES. Both techniques have demonstrated efficacy in vitro and in vivo. Various studies have identified cellular cofactor proteins that are required for IRES function, which may present themselves as intervention targets. Recent experiments have revealed that the HCV IRES uses a novel mechanism of recruiting translational components. These new advances in understanding the mechanism of HCV translation could lead to the development of novel IRES inhibitor strategies.
Curr Opin Mol Ther 2001 Jun
PMID:Hepatitis C IRES: translating translation into a therapeutic target. 1149 52

Hepatitis C virus (HCV), a positive-sense, single-stranded RNA virus of the Flaviviridae family, is a major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma worldwide. Its RNA is difficult to study because biological materials are scarce and RNA replication is of low efficiency. This review focuses on the structure and functions of HCV RNA along with their biological and clinical significance. Despite the challenging characteristics of HCV, significant progress has been made in understanding the properties of HCV RNA and developing viral replication systems toward the improvement of antiviral therapies.
Cell Mol Life Sci 2001 Aug
PMID:Hepatitis C viral RNA: challenges and promises. 1157 84

Piecemeal necrosis, currently called interface hepatitis, is a feature of viral hepatitis as well as autoimmune hepatitis and steatohepatitis. The mechanism of liver cell loss and piecemeal necrosis needs to be determined. We hypothesize that piecemeal necrosis in hepatitis is due to a piecemeal removal of hepatocyte cytoplasm by lymphocytic ingestion. To test this hypothesis, 61 consecutive liver biopsies were examined by light microscopy, by immunohistochemistry and by electron microscopy, and the lymphocytic-hepatocytic interaction was morphologically assessed. In cases of hepatitis C, hepatitis B, autoimmune hepatitis, primary biliary cirrhosis, and steatohepatitis, piecemeal necrosis was found. Using cytokeratin stains, it was apparent that the lymphocyte-hepatocyte interaction and piecemeal necrosis leads first to binding of the lymphocyte to hepatocyte plasma membrane and then blebbing or indentation of the hepatocyte by the lymphocyte, followed by endocytosis of liver cell cellular components and digestion in the lymphocyte lysosomes. This process is repeated while the cytoplasm and the nucleus of the hepatocyte disappear bite by bite, and only nubbins of residual hepatocytic cytoplasm remain, either attached to intact hepatocytes or surrounded and sequestered within scar tissue and lymphocytes. We conclude that piecemeal necrosis is a gradual disappearance of hepatocytes as a result of lymphocyte-hepatocyte binding and ligand internalization of liver surface molecules by the lymphocyte. This gradual process leads to a slow reduction of hepatocyte size and eventual disappearance at the interface between the lobule and portal tracts. To term this new kind of necrosis, we propose the name troxis necrosis, after the Greek noun meaning "nibbling."
Exp Mol Pathol 2001 Oct
PMID:"Piecemeal" necrosis: renamed troxis necrosis. 1159 20

The Hepatitis C virus is a positive-stranded RNA virus which is the causal agent for a chronic liver infection afflicting more than 170,000,000 people world-wide. The HCV genome is approximately 9.6 kb in length and the proteome encoded is a polyprotein of a little more than 3000 amino acid residues. This polyprotein is processed by a combination of host and viral proteases into structural and non-structural proteins. The functions of most of these proteins have been established by analogy to other viruses and by sequence homology to known proteins, as well as subsequent biochemical analysis. Two of the non-structural proteins, NS4b and NS5a, are still of unknown function. The development of antivirals for this infectious agent has been hampered by the lack of robust and economical cell culture and animal infection systems. Recent progress in the molecular virology of HCV has come about due to the definition of molecular clones, which are infectious in the chimpanzee, the development of a subgenomic replicon system in Huh7 cells, and the description of a transgenic mouse model for HCV infection. Recent progress in the structural biology of the virus has led to the determination of high resolution three-dimensional structures of a number of the key virally encoded enzymes, including the NS3 protease, NS3 helicase, and NS5b RNA-dependent RNA polymerase. In some cases these structures have been determined in complex with substrates, co-factors (NS4a), and inhibitors. Finally, a variety of techniques have been used to define host factors, which may be required for HCV replication, although this work is just beginning.
J Mol Biol 2001 Oct 26
PMID:Recent advances in the molecular biology of hepatitis C virus. 1167 30


<< Previous 1 2 3 4 5 6 7 8 9 10 Next >>