Biomedical subjects

I A Teo

Publications and source records attributed to I A Teo.

12 recordsLinked to original sources

PubMed2002

Reliable and reproducible LightCycler qPCR for HIV-1 DNA 2-LTR circles.

Highly active anti-retroviral therapy (HAART) has reduced the plasma load of HIV-1 to undetectable levels. It has however failed to eliminate the virus from other body compartments. Current methods for monitoring persistent viral replication in HIV-1+ patients require a large amount of blood and/or repeated tissue biopsies. Furthermore, some of the viral reservoirs, such as brain and eye, are inaccessible for sampling. The detection of episomal HIV-1 DNA 2-LTR circles in CD4+ cells is indicative of recent, acute infection events. This paper describes a reliable and reproducible LightCycler-based assay for the quantitative measurement of HIV-1 DNA 2-LTR circles in human peripheral blood mononuclear (PBMN) cells. It details the modifications to the DNA extraction procedure and to the LightCycler PCR procedure that were required to achieve this. This new surrogate marker of persistent viral replication can now be reliably, reproducibly and robustly used to study the clinical progress of large numbers of patients whose plasma HIV-1 RNA has been reduced to undetectable levels by anti-retroviral drugs.

DNA Restriction Enzymes↗

PubMed2002

LightCycler qPCR optimisation for low copy number target DNA.

The LightCycler is a rapid air-heated thermal cycler which incorporates a fluorimeter for the detection and quantification of Polymerase Chain Reaction (PCR) amplified products. It provides real-time cycle-by-cycle analysis of product generation. Amplification occurs in glass capillary tubes. The products are detected using a fluorescent double stranded DNA binding dye or fluorescent probes. However, conditions that work well in conventional PCR reactions do not readily translate to the LightCycler. Whilst using this new technology to study an infectious pathogen in human tissue samples, several parameters were identified which can have an adverse effect on the reliable and reproducible quantification of low copy number target DNA. They included abstraction of PCR reagents on glass, primer-dimer formation, non-specific product generation, and a failure to amplify low copy number target when it is present in a high background of human chromosomal DNA. For each problem identified, several solutions are described. Novel approaches are also described to ensure that amplification of target DNA and of the quantification standards occurs with the same efficiency. With appropriate changes to the protocols currently in use, LightCycler quantitative Polymerase Chain Reaction (LC-qPCR) can be used to achieve a level of accuracy that exceeds that of an enzyme immunoassay. The LC-qPCR optimisation strategies described are of particular relevance when applying this technology to the study of pathogens in tissue samples. The technique offers the enormous potential for reliable and reproducible quantitative PCR of low copy number target DNA.

DNA Primers↗

PubMed1995

Polymerase chain reaction in situ: an appraisal of an emerging technique.

Polymerase chain reaction (PCR) in situ is a new technique which promises to enhance considerably our ability to detect a few copies of target nucleic acid sequences in fixed tissues and cells. It has an enormous potential for application in diagnostic histopathology of viral diseases and in the study of gene expression. PCR in situ is, however, technically difficult, and amplification of the target DNA is only 30-300 fold. In this article we present an overview of PCR in situ techniques used to amplify both DNA and RNA targets (RT-PCR in situ). We also identify problems which can reduce the efficiency of the technique or which can give rise to false-positive results. They include (1) the inhibitory effects of cross-linking of histones to DNA or PCR amplification, (2) abstraction of PCR reagents by tissue-bonding agents which are used to coat glass slides, (3) poor denaturation of target DNA and subsequent DNA renaturation due to extensive cross-linking of histones to DNA, or because of incorrect temperature regulation of thermal cyclers, (4) false-positive results which arise from end-labelling of DNA strand breaks by Taq polymerase, and (5) diffusion of PCR products into and out of cells leading to false-positive results. We present some of the approaches that have been used to overcome some of these difficulties and suggest new avenues for investigation to improve this technique further.

Animals↗

PubMed1995

PCR in situ: aspects which reduce amplification and generate false-positive results.

PCR in situ promises the ability to amplify and detect very low levels of target nucleic acid in tissues. Despite considerable effort, the technique is still technically difficult and has not yet proved to be reliable or reproducible. We have now identified a number of factors which can contribute to the poor amplification of the target DNA and to the generation of false-positive signals. These factors include the effects of fixation, reagent abstraction, DNA degradation, DNA end-labelling and product diffusion. We present evidence to show that formaldehyde fixation cross-links histones to DNA and thus restricts the subsequent amplification of target sequences by PCR. End-labelling of DNA occurs when direct incorporation is used to detect amplified products and this gives rise to false-positive signals. Amplified products can also diffuse out of cells and into neighbouring cells which do not contain target sequences. They can undergo re-amplification within these cells giving rise to false-positive signals. We believe considerable caution should be exercised in the interpretation of results generated using PCR in situ.

Autoradiography↗

PubMed1993

Identification and analysis of the transport/capsid assembly protein (tp/cap) gene of human herpesvirus-6 (HHV6).

The transport/capsid assembly protein (tp/cap) gene of human herpesvirus 6 (HHV6) strain U1102 has been identified and localized on the restriction enzyme map of the viral genome, to the EcoRI-Q fragment. The complete DNA sequence of the tp/cap gene was determined. The tp/cap gene encodes a protein product of 726 amino acids and has the strongest similarity with the homologous gene (HCMV UL56) from HCMV. Upstream of the tp/cap open reading frame is the gene for the major DNA binding protein (mdbp) and downstream is the glycoprotein B (gB) gene. This gene block arrangement is common to all herpesviruses.

Amino Acid Sequence↗

PubMed1991

Characterization of the DNA polymerase gene of human herpesvirus 6.

The construction of a recombinant bacteriophage lambda library containing overlapping clones covering 155 kbp of the 161-kbp genome of the Ugandan U1102 isolate of human herpesvirus 6 (HHV-6) is described. The use of degenerate-primer polymerase chain reaction allowed the isolation of a DNA probe for the DNA polymerase gene of HHV-6, which was subsequently used to isolate and position the pol gene on the physical map of the viral genome. A 4.4-kbp EcoRI DNA restriction fragment containing the pol gene was isolated and sequenced. The open reading frames flanking the pol gene code for the HHV-6 glycoprotein B gene and the human cytomegalovirus UL53 homolog. This arrangement is different from that seen in the alpha and gamma herpesvirus families, lending further support to the notion that HHV-6 is a member of the beta herpesvirus group.

Amino Acid Sequence↗

PubMed1987

Proteolytic processing of the Ada protein that repairs DNA O6-methylguanine residues in E. coli.

In extracts of E. coli treated with an adapting regime of MNNG, the induced 39kd Ada protein having O6-MeG-DNA methyltransferase activity is processed to a 19kd active domain corresponding to the C-terminal half of the intact protein. This proteolytic processing has been followed on Western immunoblots using antisera raised against the 19kd fragment. Initial processing at 25 degrees C or 37 degrees C mainly generates a fragment of mol. wt. 24kd which then undergoes a slower second cleavage to generate the 19kd active domain. Preceding this second cleavage site is a sequence of amino acids Thr- -Gly-Met-Thr- -Lys that also occurs at another site in the N-terminal half of the 39kd methyltransferase. It is proposed that this sequence is a recognition site for proteolytic activity. On the basis of cleavage of the Ada protein at either one or both of these sites, fragments may be generated of mol. wt. 24kd and 19kd containing the active site for O6-methylguanine and O4-methylthymine repair, and 15kd and 20kd, containing the active site for methylphosphotriester repair. These observations explain previous reports by others on the existence in cell extracts of multiple methyltransferase activities of different sizes recognizing O-methyl lesions in DNA. The cellular protease involved is resistant to a wide range of protease inhibitors.

Bacterial Proteins↗

PubMed1983

Multiple hypersensitivity to mutagens in a cell strain (46BR) derived from a patient with immuno-deficiencies.

46BR is a fibroblast cell strain established from an individual with hypogammaglobulinaemia. The cells are unique in showing hypersensitivity to the lethal effects of a wide range of DNA-damaging agents. Thus they are hypersensitive to gamma- and 254-nm UV-irradiation and show a limited capacity to repair potentially lethal gamma-irradiation damage when compared with fibroblasts from normal individuals. A slight hypersensitivity to mitomycin C was also revealed but we were not able to discriminate 46BR from normals with 4-nitroquinoline oxide. The cells were hypersensitive to the alkylating agents, dimethyl sulphate, methyl methanesulphonate, ethyl methanesulphonate, N-methyl-N'-nitro-N-nitrosoguanidine and N-methyl-N-nitrosourea but not N-ethyl-N-nitrosourea. A consideration of the spectra of DNA lesions produced by these alkylating agents together with the sensitivity to ionising radiation and mitomycin C suggests that 46BR cells are defective in a repair step that is common to all agents. We suggest that the cells are defective in DNA polymerisation or ligation. Support for this suggestion comes from the absence of any hypersensitivity to N-ethyl-N-nitrosourea since its major reaction products are not removed by excision pathways that require polymerisation and ligation.

4-Nitroquinoline-1-oxide↗

PubMed1983

A biochemical defect in the repair of alkylated DNA in cells from an immunodeficient patient (46BR).

The fibroblast cell strain 46BR, derived from an immunodeficient individual, is hypersensitive to the lethal effects of a variety of DNA-damaging agents, this effect being particularly marked for monofunctional methylating agents. After u.v. irradiation 46BR cells show normal unscheduled DNA synthesis, daughter strand repair, and recovery of DNA and RNA synthesis. The inhibition of DNA replicative synthesis by u.v. is slightly less than that of normal cells. After gamma-irradiation the rejoining of strand breaks is normal as are the kinetics of replicative DNA synthesis. Following treatment with dimethylsulphate, replicative DNA synthesis is affected in a similar way to normal cells, unscheduled DNA synthesis may be increased relative to normal cells, but more strand breaks persist in 46BR than in normal cells. In addition 46BR cells are hypersensitive to the toxic effects of 3-aminobenzamide, an inhibitor of ADP-ribosyl transferase. This enzyme is involved in the ligation step of repair of alkylation damage. A hypothesis is presented suggesting that 46BR may be defective in DNA ligase I.

Benzamides↗

PubMed1983

Similar rate of O6-ethylguanine elimination from DNA in normal human fibroblast and xeroderma pigmentosum cell strains not transformed by SV40.

Using a highly specific rabbit antiserum (E3) directed against O6-ethyldeoxyguanosine in a competitive radioimmunoassay, we have measured the kinetics of removal of this alkylation product from the DNA of human fibroblasts treated with the N-nitroso carcinogen N-ethyl-N-nitrosourea. A very similar rate of elimination from DNA was found in two normal human fibroblast strains (GM730 and 54BR) and in the nonvirus-transformed xeroderma pigmentosum fibroblast strains XP2BI and XP3BR. This is in contrast to the SV40-transformed xeroderma pigmentosum fibroblast strain XP12RO-SV40 which had previously been shown to be defective in its ability to remove O6-ethylguanine from DNA.

Cell Line↗

PubMed1982

The response of a variety of human fibroblast cell strains to the lethal effects of alkylating agents.

The sensitivities of fifteen human fibroblast cell strains to the lethal effects of alkylation damage produced by N-methyl-N-nitrosourea (MNU) and N-ethyl-N-nitrosourea (ENU) have been investigated. Nine cell strains were also investigated for their sensitivities to N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Included in our survey are representative strains derived from donors with the repair defective syndromes xeroderma pigmentosum (XP) and ataxia-telangiectasia (A-T), as well as strains derived from patients with Cockayne's syndrome, Bloom's syndrome, Huntington's disease and strains derived from individuals with unclassified syndromes. On the basis of our survival data we report that hypersensitivity to MNU is shown by two A-T strains (AT3BI and AT5BI), an XP strain (XP3BR), and strain 46BR derived from a patient with hypogammaglobulinaemia. This sensitivity to methylating agents is also shown by strains 46BR and XP3BR when treated with MNNG, but not for strain AT5BI. Sensitivity to ENU is shown by strain 11961 (derived from a sun-sensitive individual), XP3BR and a single Cockayne's syndrome strain CS697CTO. Of the strains studied only XP3BR was sensitive to both ethylating and methylating agents and only 46BR showed a greater than two-fold increase in sensitivity compared to normal.

Alkylating Agents↗

PubMed1982

Excision of O6-methylguanine from DNA by human fibroblasts determined by a sensitive competition method.

A new, simple and relatively inexpensive assay for measuring O6-methylguanine (O6-MeG) in methylated DNA is described. This assay used the property of suicide inactivation of Escherichia coli methyltransferase. When crude extracts of methyltransferase are incubated with DNA containing O6-MeG, transfer of the methyl group to a cysteine residue on the protein occurs and the protein is subsequently inactivated. Each protein molecular has been shown to act only once. In our assay, methylated DNA is first incubated with a fixed amount of the extract. The O6-MeG present in this DNA proportionally inactivates a part of the methyltransferase activity. The remaining activity is then incubated with a fixed amount of O6-[3H]MeG substrate of known specific activity and precipitated with acid. Hydrolysis of the acid precipitable fraction releases the unaltered O6-[3H]MeG enabling the amount of O6-MeG present in the unknown sample to be calculated. This method enables the accurate measurement of as little as 0.1 pmol of O6-MeG in methylated DNA and compares favourably with current radiochemical and immunological techniques. We have used this assay to measure O6-MeG produced in the DNA of human fibroblasts treated with N-methyl-N'-nitro-N-nitrosoguanidine. We have also studied the kinetics of removal of this lesion. We confirm previous reports of a rapid repair system for the removal of O6-MeG from DNA by human fibroblasts.

DNA↗