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Viral load quantitation has become the major prognostic marker for disease prognosis and outcome of antiretroviral therapy in the treatment of HIV-infected individuals. The three major methodologies for viral load quantitation: the reverse transcriptase-polymerase chain reaction (RT-PCR; Amplicor HIV-1 Monitor Test, Roche Diagnostic Systems, Pleasanton, CA), the nucleic acid sequence-based amplification (NASBA; NucliSens HIV-1 QT Test, Organon Teknika, Bostel, The Netherlands); and a signal amplification methodology termed branchedchain DNA (bDNA) technique (Quantiplex HIV-1 RNA test, Bayer Diagnostics, Emeryville, CA) are briefly reviewed here.

A multiplex 'real-time' polymerase chain reaction (PCR) has been established as a general technique for the quantitation of proviral human T-lymphotrophic virus types 1 and 2 (HTLV-I/II). The technology utilizes fluorescence to measure amplification products from the tax gene of Human T-cell lymphotropic virus type 1 or the 5' long terminal repeat of Human T-cell lymphotropic virus type 2. The quantitative amplification of the standard was linear across four orders of magnitude with nearly identical amplification efficiencies for monoplex or the biplex format from 1.4 copes/assay (60 copies proviral DNA/0.5 micrograms human DNA) to 6000 copies/assay (240000 proviral copies/0.5 micrograms human DNA). The human beta-globin gene was used to normalize for human DNA input to determine the proviral DNA load. Three hundred fifty-six specimens received by Specialty Laboratories for HTLV I/II detection provided identical results in the detection of HTLV I/II proviral DNA. No additional positive specimens were identified with the biplex assay format. The coefficient of variation for the proviral DNA load was less than 30% for HTLV I or II quantitation (n=5). For spiked specimens, two groups of five separate 0.25 ml blood specimens (20 total) were spiked, respectively, with 0, 9.6, 48, 240 and 1200 copies of HTLV I or HTLV II DNA standards. The specimens were amplified with the HTLV I/II multiplex format. Twenty of twenty expected negative HTLV I or HTLV II specimens were negative (100% specificity) and 14/16 specimens spiked with 48 copies or more HTLV I were detected (87.5% sensitivity). Thirteen of sixteen HTLV II spiked specimens (>48 copies of HTLV II standard per 10 assays) were detected (81.2%). The real-time detection provides accurate and reliable results in a single amplification for both HTLV (I or II) targets with a more rapid turnaround time and a decrease in material required for results.

A rapid method based on fluorescence resonance energy transfer and real-time polymerase chain reaction (PCR) is used to identify the Factor V genotype or to identify the bacterial species Bartonella qunitana or Bartonella henselae. Allelic discrimination was performed on the post-PCR product. Thermal cyclers other than the 7700 sequence detection system can be used for PCR, after which the products can be transferred to the 7700 sequence detection system for measurement of fluorescence. The Delta R (the change in fluorescence) for each dye can be collected at the final thermal cycle and an xy scatterplot used to identify the specific genotype based on graph location. There are many advantages to this method. A maximum of 96 samples can be genotyped in less than 2 h. The method tolerates a wide range of DNA concentrations and can be determined without prior DNA determination. Fluorescence is very sensitive, with a low failure rate for allelic discrimination., (Copyright 2001 Elsevier Science (USA).)

Previously, studies of CNS infection have indicated substantially greater prevalence of HSV1 than HSV2. In reviewing unexpectedly high numbers of HSV2 infections among CSF specimens submitted to our laboratories for PCR testing, we discovered an age and gender bias suggesting a need to examine the demographics of those patients whose specimens tested positive for HSV. Some 3200 CSF specimens submitted for HSV testing were randomly selected for analysis. HSV1 was detected in 26 specimens (nine male, 17 female; average age 51 years) and HSV2 in 36 specimens (13 male, 23 female; average age 34 years). In general, there were almost twice as many HSV1 and HSV2 infections detected in females as in males. The entire group (22 male, 40 female) exhibited a preponderance of HSV2 over HSV1 infections (36:26). In contrast, the ratio of HSV2 to HSV1 infection was 3:13 in the over 60 age group of our study (11 of the 13 HSV1 infections in this age group occurred in females). In the subgroup of 21 patients aged 15-40 years (six male, 15 female), the ratio of HSV2 to HSV1 was 16:5. In the 15 infections in the group aged 41-60 years, the ratio of HSV2 to HSV1 was 12:4. In summary, our data indicate extraordinary differences in the relative frequency of HSV1 vs HSV2 CNS infections in teenagers, young adults (15-40 years), middle age (41-60) and in the elderly (>60 years), including a particular bias for HSV1 CNS infection in females over age 70 years., (Copyright 2001 Academic Press.)

The role of hepatitis G virus (HGV) infection in acute non-A-E hepatitis was investigated in adults with viral hepatitis. HGV RNA was present in 1 of 28 patients with non-A-E hepatitis but 9 of 22 with hepatitis C (P < .003). HGV RNA-positive patients (HGV-infected and HGV-hepatitis C virus [HCV]-coinfected) developed light-to-moderate jaundice. Clinical and biochemical features of HGV-positive and HCV-positive patients and patients with non-A, non-G hepatitis were similar. Three patients with HGV-HCV coinfection, tested within 18 months after disease onset, have remained HGV RNA-positive but have become HCV RNA-negative. Only 1 non-A-E hepatitis patient was confirmed as being infected with HGV alone, suggesting that HGV is not the main etiologic agent of non-A-E hepatitis. Although HGV RNA was significantly associated with hepatitis C, patients with mixed HCV-HGV infections did not demonstrate a more severe course of disease than did patients with HCV infection.

Background: Viral infections have been implicated in the pathogenesis of a variety of autoimmune diseases., Objective: This investigation was undertaken to determine the presence or absence of viral genomes in the depigmented and uninvolved skin of patients with vitiligo., Methods: A polymerase chain reaction assay was used to detect viral genomes in paraffin-embedded skin biopsy specimens. Twenty-nine patients with vitiligo and 22 control subjects were included. Biopsy specimens were screened in a blinded fashion for a panel of DNA and RNA viruses including herpes simplex, varicella-zoster, cytomegalovirus (CMV), Epstein-Barr, HIV, and human T-cell lymphotropic virus., Results: CMV DNA was identified in 38% of the patients studied. Twenty-one percent had indeterminate results. Results in all control subjects were negative. Polymerase chain reaction screening for identification of other viral genomes was negative. Although not statistically significant, data trends suggested a correlation between the presence of CMV DNA in biopsy specimens and active vitiligo of relatively brief duration. In addition, CMV-positive patients had a statistically significant increased frequency of other concurrent autoimmune diseases., Conclusion: CMV DNA in the depigmented and uninvolved skin of some patients with vitiligo and its absence in control subjects suggest that vitiligo may indeed be triggered by a viral infection in select patients.

A clinical procedure for rapid detection of human immunodeficiency virus type 1 (HIV-1) by DNA amplification is demonstrated. The rapid procedure reduces handling requirements and amplification time and eliminates use of radioactivity for the detection of the amplification product. Total leukocyte lysates are the amplification substrates. Two conserved regions in the HIV-1 genome are amplified by 45 cycles of a two-temperature thermal cycle and the amplification products are detected by ultraviolet light after electrophoresis on agarose gels. Twenty-four specimens clinically diagnosed by detection of antibody (IgG) to HIV-1 were confirmed by the rapid DNA amplification procedure. In a blind study, 56 samples positive for HIV-1 DNA were detected in 503 individuals by the current classical polymerase chain reaction method; the same 56 positive samples were also detected by the rapid amplification protocol. No false-positive or false-negative results were obtained. The turnaround time for analysis has been reduced to < 24 h without compromising test results.

The sensitivity and application of the polymerase chain reaction (PCR) for the diagnosis of parvovirus B19 (B19) infection was investigated by simultaneously assaying a collection of 279 consecutively received samples for presence of anti-B19 IgM and IgG antibodies by Western blot and for B19 DNA by PCR and dot-blot hybridization (dot-blot); samples were sera from patients with suspected B19 infection. PCR and dot-blot detected B19 DNA in 9% (16/179) and 1% (2/179), respectively of Ab-positive samples (IgM+/IgG-, IgM+IgG+, IgM-IgG+), and in 28% (15/54) and 2% (1/54), respectively, of IgM+ samples. PCR also detected B19 DNA in 2% (2/100) of IgM-/IgG- samples, both of which had normal total IgG and IgM levels. PCR is of unique value because it permits diagnosis of B19 infection even in the absence of specific acute phase (IgM) and in the presence or absence of convalescent-phase (IgG) Ab.

Chemical composition of liver chromatin was determined for rats fed a complete stock diet, or a diet lacking protein or fat. High carbohydrate, fat-free (diet 1) and low carbohydrate, protein-free (diet 2) diets were selected because they elicit structural alteration in chromatin as measured by incubation with micrococcal nuclease (E.C. 3.1.4.7). In the present study, either dietary treatment caused an increase in mass ratios of RNA:DNA and nonhistone:DNA, relative to control ratios. The nonhistone-DNA ratios in liver of rats fed diet 1 or diet 2 were 2.4-fold and 3.5-fold, respectively, larger than control ratios. The histone:DNA ratio remained relatively constant among all three dietary treatments. Liver nuclei were purified from rats fed each dietary treatment and were solubilized in 9 M urea. The nuclear proteins were analyzed by two-dimensional electrophoresis and visualized with a silver treatment that stains proteins in color. The electrophoretograms presented show preferentially proteins with low molecular weights and acidic pIs, two characteristics of nonhistones. The two-dimensional protein patterns are nearly identical for nuclear proteins from all three treatments. Analysis of the electrophoretograms indicates that the diet-induced increased nonhistone:DNA ratios are apparently not attributable to new species of protein, but rather to increased relative abundance of many proteins in the existing populations.

Native rat liver NHC protein-DNA interactions have been investigated by use of a nitrocellulose filter assay sensitive in detection of protein-DNA complexes. Optimal conditions for DNA-protein interactions occurs at low ionic strength conditions (110 mM phosphate buffer). A fraction of NHC proteins was enriched 25-fold by their affinity for rat DNA immobilized on cellulose columns under these conditions. At higher ionic strength (260 mM-0.04M phosphate buffer and 0.15 M sodium chloride), this fraction binds approximately sevenfold less to rat DNA but with a substantial increase in stability of the complexes. Equilibrium competition experiments indicate that at the higher ionic strength there is a considerable DNA sequence specificity of the rat DNA binding NHC protein. Since rat DNA contains three components as defined by their reassociation kinetics: single copy DNA (C0t1/2pure = 1.6 times 103); middle repetitive DNA (C0t1?1PURE = 1.1); and highly repetitive (C0t1/2pure smaller than 0.02). The two former were isolated and employed in the DNA binding assays. At the high ionic strength criterion, the rat DNA binding NHC proteins showed a substantial preference for a subset of middle repetitive DNA sequences. This suggests a preferential interaction between a class of NHC proteins and a class of middle repetitive DNA sequences.

We demonstrate by messenger RNA (mRNA) . complementary DNA (cDNA) hybridization that nutrient variation can alter 1) the frequency in which entire classes or families of liver polyadenylated mRNAs [poly(A)+ mRNAs] are present within the cell and 2) the sequence complexity of those transcripts. Feeding a carbohydrate-rich, fat-free diet to rats for 5 days resulted in an increased sequence complexity of rare and moderately abundant liver poly(A)+ mRNAs when compared with poly(A)+ mRNA from rats fed high fat or basal diets. In addition, the frequency of reiteration of abundant sequences increased approximately 10 times compared with the abundant poly(A)+ mRNAs of rats fed high fat or basal diet. The results indicate that the functionality of the template is influenced by nutrient concentrations and may be one means by which complex organisms achieve homeostasis.

The higher order structure of rat liver chromatin from nuclei of animals fed stock or semi-synthetic diets for 5 days was investigated by a specific enzymatic probe, micrococcal nuclease (EC 3.1.4.7). Micrococcal nuclease digests 50% of DNA in eukaryotic chromatin into acid-soluble nucleotides while 50% of the DNA is resistant to digestion because of associated nucleoproteins. This selective digestion of DNA reflects higher orders of structure of the universal chromatin subunit, the nucleosome, found in lower eukaryotes, plants and animals. When rats were fed a commercial stock diet, 50.3% of the DNA in liver chromatin was digested by micrococcal nuclease. However, when rats were fed various semi-synthetic diets, the amount of DNA susceptible to micrococcal nuclease digestion varied as a function of diet (P less than 0.0001). Differences in the amount of DNA susceptible to micrococcal nuclease ranged from 71.4% for chromatin of rats fed a high carbohydrate/fat-free diet to 38.8% for chromatin of those fed a low carbohydrate/protein-free diet. DNA fragments generated by brief micrococcal nuclease digestion were analyzed by electrophoresis on 2.5% polyacrylamide--0.5% agarose gels. Chromatin from rats fed the high carbohydrate/fat-free diet was more rapidly digested to the monomer nucleosomin-free diet. To our knowledge, these diet-induced alterations in the higher order structure of chromatin are the first to be reported as occurring by in vivo modulation.

The DNA-binding nonhistone proteins (NHP) have been demonstrated to fractionate the rat genome into protein-bound and unbound DNA sequences. Twenty percent of highly sheared rat DNA [approximately 350 base pair (bp)] can be retained on membrane filters as protein complexes. When extracted from the filter and retitrated with the NHP, a 4- to 5-fold enrichment of binding sites is present in the bound DNA with few, if any, sites detected in the unbound DNA. Rat DNA restricted by EcoRI endonuclease can be fractionated by its DNA-binding NHP retention characteristics. Reassociation kinetics of the bound restricted sequences indicate that 45.6% is a subset of total single-copy sequence of the rat genome an 26.9% is repetitive sequences. Cross hybridization studies indicate the repetitive sequences of the bound DNA are not enriched as much as the slow component of the rat genome. Thus a 4-fold enrichment of a subset of the rat genome has been observed via NHP-DNA interactions.

Dot hybridization of messenger RNA (mRNA) and complementary DNA (cDNA) has been used to measure the relative levels of albumin and alpha-fetoprotein mRNA in liver of rats fed for 5 d a fat-free (carbohydrate-rich) diet, a high fat diet or a basal diet, all three of which were isonitrogenous. The level of albumin mRNA in rats fed the fat-free (carbohydrate-rich) diet was 30 to 45% of the level in animals fed the basal 4% fat diet. The concentration of another mRNA, that for alpha-fetoprotein, remained unchanged. It has been established by others that albumin mRNA levels and albumin synthesis are diminished in response to low levels of dietary protein. We show that albumin mRNA levels are lower than those observed in animals fed the basal 4% fat diet, even when dietary protein is adequate (30% wt/wt), if the nonprotein calories are derived solely from carbohydrate.

A carbohydrate-rich, fat-free diet dramatically alters the higher-order chromatin structure of rat liver nuclei. In addition, the mRNA level of the phenotypic protein of liver, albumin, is reduced. Within 200 base pairs of the initiation site of the albumin mRNA, a histone H1-binding site has been mapped. Histone H1 is the higher-order architectural protein of chromosomes. The presence of H1 with nucleosomes that package albumin gene sequences implies the presence of H1 in template-active chromatin. The role histone H1 has on the architecture of active genes may be a fundamental level of gene regulation.

Interaction of rat liver histone H1 fraction with the 5'-end of the rat serum albumin gene was localized within a 346 base pair (bp) restriction fragment. Sequence analysis of the fragment showed the fragment was 72 mol % adenosine-thymidine, which is significantly greater than the mole percent adenosine-thymidine composition of the rat genome. Gel retardation assays of the histone H1-DNA interaction indicate the complex formed behaves as previously characterized H1-DNA and shows a high-affinity H1 binding site within the enriched albumin restriction site. Deoxyribonuclease I (DNase I) protection assays on the H1 binding site define three protected regions only on the template strand of the DNA fragment. The three sites lie 55 and 110 bp apart (165 bp between the first and third binding site) with a consensus binding sequence of 5'-GA-ATA-CTGGCTT-C-TT-CTA-G-3'. The sequences between the protected DNA regions are highly enriched in adenosine-thymidine bases (79.3 and 86 mol % adenosine-thymidine, respectively). The functional significance is not understood.

DNA-dependent RNA polymerase has been found to be preferentially released at 43 degrees C from the folded nucleoids of an E. coli dnaAts mutant when compared with the same nucleoids at 30 degrees C or with nucleoids of a dnaA+ strain at either 30 degrees or 43 degrees C. The polypeptides released are identical in molecular weight with those of the beta and beta' constituent polypeptides of the core enzyme of a known E. coli RNA polymerase. In addition, these polypeptides are precipitated by specific anti-RNA polymerase rabbit IgG. The implications of the interactions of RNA polymerase with the dnaA gene product are discussed.

Cloned DNA containing the first nine exons of the rat albumin gene was digested with EcoRI and HindIII, and the resulting fragments were used to screen for regions with relatively high affinity for protein. Of three restriction fragments preferentially bound, the fragment containing the first two exons of the albumin gene was consistently bound over others by heat-stable protein extracted from liver nuclei with 0.35-1.0 M NaCl. Proteins extracted with lower and higher ionic strength buffers bound the DNA fragments, but with little specificity. The DNA fragment that was preferentially bound consistently by the 1.0 M nuclear extract was subcloned into pBR325 and was used to isolate the specific DNA-binding activity. After purification, histone H1 was the polypeptide with preferential DNA-binding activity. Histone H1 has a high-affinity binding site in the 5' end of the rat albumin gene within 440 5'-flanking base pairs and the first two exons of the gene.