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Biomedical subjects

A Herbert

Publications and source records attributed to A Herbert.

At least 55 records · Page 3Linked to original sources
PubMed1999

Left-handed Z-DNA: structure and function.

Z-DNA is a high energy conformer of B-DNA that forms in vivo during transcription as a result of torsional strain generated by a moving polymerase. An understanding of the biological role of Z-DNA has advanced with the discovery that the RNA editing enzyme double-stranded RNA adenosine deaminase type I (ADAR1) has motifs specific for the Z-DNA conformation. Editing by ADAR1 requires a double-stranded RNA substrate. In the cases known, the substrate is formed by folding an intron back onto the exon that is targeted for modification. The use of introns to direct processing of exons requires that editing occurs before splicing. Recognition of Z-DNA by ADAR1 may allow editing of nascent transcripts to be initiated immediately after transcription, ensuring that editing and splicing are performed in the correct sequence. Structural characterization of the Z-DNA binding domain indicates that it belongs to the winged helix-turn-helix class of proteins and is similar to the globular domain of histone-H5.

Adenosine Deaminase↗
PubMed1999

RNA processing and the evolution of eukaryotes.

In eukaryotes, RNA processing events, including alternative splicing and RNA editing, can generate many different messages from a single gene. As a consequence, the RNA pool, which we refer to here as the 'ribotype', has a different information content from the genotype and can vary as circumstances change. The outcome of a single RNA processing event often regulates the outcome of another, giving rise to networks that affect the composition and expression of a particular ribotype. Successful ribotypes are determined by natural selection, and can be incorporated into the genome over time by reverse transcription. Eukaryotic evolution is therefore influenced by the alternate ways in which RNAs are processed and the continual interplay between RNA and DNA.

Animals↗
PubMed1999

Cervical intraepithelial neoplasia grade III (CIN III) and invasive cervical carcinoma: the yawning gap revisited and the treatment of risk.

In a 3-year study of the population of Southampton and south-west Hampshire there were 10 times as many cases of CIN III compared with invasive squamous carcinoma (700 compared with 70). The peak incidence of CIN III per 1000 screened women years was in those aged 25-29 years, which was 20 years earlier than the peak incidence of invasive cervical cancer per 1000 women years at risk. Ninety percent of CIN III was diagnosed in women under 50 years. There were 14 cases of cervical glandular intraepithelial neoplasia grade III (CGIN III), three coexisting with CIN III, all in women aged under 50 years: the gap between intraepithelial and invasive lesions was not seen for glandular neoplasia. Although referral was for at least moderate dyskaryosis in 86.8% of women with CIN III or CGIN III, most had been screened previously, either having had mild abnormalities requiring repeat cytology (39.8%) or negative cytology (34.5%). Only 12 women aged > or = 50 years had previous negative cytology: 21.4% compared with 35.6% of women aged < 50 years (P = 0.034). The results of this study suggest that the best opportunity for preventing invasive squamous cell carcinoma lies in screening women aged 20-39 years when the incidence of CIN III in the screened population is highest and before the peak incidence of invasive disease. The results also indicate the importance of repeated screening and follow up of minor cytological abnormalities in the detection of CIN III. The benefit of screening must be regarded as a treatment of risk, since it is almost certain that a high proportion of CIN III regresses or persists unchanged.

Adolescent↗
PubMed1999

Crystallization and preliminary studies of the DNA-binding domain Za from ADAR1 complexed to left-handed DNA.

The proteolytically defined Z-DNA binding domain Za of human adenosine deaminase type 1 (hADAR1) has been crystallized in complex with the DNA oligomer d(TCGCGCG). The crystals were obtained from a solution containing ammonium sulfate as precipitating agent and belong to the tetragonal space group P4212. A complete diffraction data set has been collected to a resolution of 2.4 A. The unit-cell dimensions are a = b = 85.9, c = 71.3 A. A Raman spectrum of the complex indicates that the DNA in the complex adopts the left-handed Z conformation.

Adenosine Deaminase↗
PubMed1998

Spectroscopic characterization of a DNA-binding domain, Z alpha, from the editing enzyme, dsRNA adenosine deaminase: evidence for left-handed Z-DNA in the Z alpha-DNA complex.

Double-stranded RNA adenosine deaminase (ADAR1) is an ubiquitous enzyme in metazoa that edits pre-mRNA changing adenosine to inosine in regions of double-stranded RNA. Zalpha, an N-terminal domain of human ADAR1 encompassing 76 amino acid residues, shows apparent specificity for the left-handed Z-DNA conformation adopted by alternating (dGdC) polymers modified by bromination or methylation, as well as for (dGdC)13 inserts present in supercoiled plasmids. Here, a combination of circular dichroism, fluorescence, and gel-retardation studies is utilized to characterize recombinant Zalpha peptide and to examine its interaction with DNA. Results from laser-Raman spectroscopy experiments provide direct evidence for the existence of Z-DNA in peptide-DNA complexes.

Adenosine Deaminase↗
PubMed1998

The Zalpha domain from human ADAR1 binds to the Z-DNA conformer of many different sequences.

Z-DNA, the left-handed conformer of DNA, is stabilized by the negative supercoiling generated during the movement of an RNA polymerase through a gene. Recently, we have shown that the editing enzyme ADAR1 (double-stranded RNA adenosine deaminase, type 1) has two Z-DNA binding motifs, Zalpha and Zbeta, the function of which is currently unknown. Here we show that a peptide containing the Zalpha motif binds with high affinity to Z-DNA as a dimer, that the binding site is no larger than 6 bp and that the Zalpha domain can flip a range of sequences, including d(TA)3, into the Z-DNAconformation. Evidence is also presented to show that Zalpha and Zbeta interact to form a functional DNA binding site. Studies with atomic force microscopy reveal that binding of Zalpha to supercoiled plasmids is associated with relaxation of the plasmid. Pronounced kinking of DNA is observed, and appears to be induced by binding of Zalpha. The results reported here support a model where the Z-DNA binding motifs target ADAR1 to regions of negative supercoiling in actively transcribing genes. In this situation, binding by Zalpha would be dependent upon the local level of negative superhelicity rather than the presence of any particular sequence.

Adenosine Deaminase↗
PubMed1998

Double-stranded RNA-specific adenosine deaminase: nucleic acid binding properties.

The RNA-specific adenosine deaminase (ADAR1, herein referred to as ADAR) is an interferon-inducible RNA-editing enzyme. ADAR catalyzes the C-6 deamination of adenosine in double-stranded (ds) structures present in viral RNAs and cellular pre-mRNAs as well as synthetic dsRNA substrates. ADAR possesses three functionally distinct copies of the highly conserved double-stranded RNA binding R motif (RI, RII, RIII) implicated in the recognition of dsRNA structures within the substrate RNAs. ADAR is also a Z-DNA-binding protein. Two Z-DNA binding motifs (Zalpha and Zbeta) present in ADAR correspond to repeated regions homologous to the N-terminal region of the vaccinia virus E3L protein. Here we describe assay methods for measurement of ADAR enzymatic activity, dsRNA binding activity, and Z-DNA binding activity.

Adenosine Deaminase↗
PubMed1998

A case-control study of true-positive versus false-negative cervical smears in women with cervical intraepithelial neoplasia (CIN) III.

Cervical smears (n = 150) from five departments showing high-grade dyskaryosis were examined by three cytologists. All the smears came from patients with biopsy-proven CIN III. One hundred had been correctly reported (true positives) but 50 had originally been reported as negative and had been found to be positive only on review (false negatives). There were significant differences between the two sets in the characteristics of the dyskaryotic cell population. The false-negative smears tended to have fewer than 200 dyskaryotic cells. The nuclei of the dyskaryotic cells tended to have fine rather than coarse nuclear chromatin. A smear with fewer than 50 dyskaryotic cells is 26 times more likely to be reported as negative than one with more than 200 dyskaryotic cells. The results suggest that there is a type of severely dyskaryotic smear that is inherently likely to be missed on routine screening.

Case-Control Studies↗
PubMed1998

Investigation of the effect of occult invasive cancer on progress towards successful cervical screening.

OBJECTIVES: To describe the effect of occult invasive disease on progress towards meeting the Health of the Nation target for reducing the incidence of cervical cancer, and to investigate the possible effect of a higher risk of cervical cancer in women born since 1940. SETTING: Southampton and South West Hampshire (SSWH), with a total female population of 218,549 in 1990, the midpoint of a study period covering 1985 to 1995. METHODS: Incidence was calculated per 100,000 women years at risk in overlapping three year periods for symptomatic and screen detected cancers. The same methods was used for cohorts of women born before and after 1940. Screen detected stage Ia1 cancers were identified as a subgroup. RESULTS: The incidence of invasive cervical cancer fell by 27.4%, from 16.8 to 12.2 per 100,000 women years at risk between 1985-87 and 1993-95, which was a significant linear trend (chi 2 = 4.494, df = 1, p = 0.034). The corresponding figures adjusted for age in a standardised European population were 16.3 and 11.5: a fall greater than required to meet the Health of the Nation target set for the year 2000. Incidence remained relatively high until screen detected cancers, more than one third of which were stage Ia1, had passed a peak in 1992. When screen detected stage Ia1 cancers were excluded, incidence fell by 41.2%, from 16.5 to 9.7 per 100,000 women years at risk: a highly significant linear trend (chi 2 = 12.391, df = 1, p < 0.001). The incidence in the first three years of the study was higher in women born between 1940 and 1954 than in those born between 1925 and 1939, though the reverse would be expected by age and the natural history of the disease. In the 1940-54 birth cohort 44% (23/52) of screen detected cancers were stage Ia1, with a peak in 1992. When these were excluded, incidence fell by 57.1%, from 31.7 to 13.6 per 100,000 women years at risk: a highly significant linear trend (chi 2 = 13.704, df = 1, p < 0.001), whereas an increase would be expected for a cohort aged from 30-45 to 40-55. In the 1925-39 cohort only 24% (8/33) of screen detected cancers were stage Ia1. When these were excluded, incidence fell by 35.3%, from 24.9 to 16.1, which was not a significant linear trend (chi 2 = 0.409, df = 1, p = 0.522). CONCLUSION: An overall decline in incidence was not achieved until prevalent occult invasive disease had been detected by improved screening. The data confirm the effectiveness of screening, particularly in a high risk cohort of women born between 1940 and 1954.

Adolescent↗
PubMed1997

Construction of a Z-DNA-specific restriction endonuclease.

Novel restriction enzymes can be created by fusing the nuclease domain of FokI endonuclease with defined DNA binding domains. Recently, we have characterized a domain (Z alpha) from the N-terminal region of human double-stranded RNA adenosine deaminase (hADAR1), which binds the Z-conformation with high specificity. Here we report creation of a conformation-specific endonuclease, Z alpha nuclease, which is a chimera of Z alpha and FokI nuclease. Purified Z alpha nuclease cleaves negatively supercoiled plasmids only when they contain a Z-DNA forming insert, such as (dC-dG)13. The precise location of the cleavage sites was determined by primer extension. Cutting has been mapped to the edge of the B-Z junction, suggesting that Z alpha nuclease binds within the Z-DNA insert, but cleaves in the nearby B-DNA, by using a mechanism similar to type IIs restriction enzymes. These data show that Z alpha binds Z-DNA in an environment similar to that in a cell. Z alpha nuclease, a structure-specific restriction enzyme, may be a useful tool for further study of the biological role of Z-DNA.

Cloning, Molecular↗
PubMed1997

A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase.

Editing of RNA changes the read-out of information from DNA by altering the nucleotide sequence of a transcript. One type of RNA editing found in all metazoans uses double-stranded RNA (dsRNA) as a substrate and results in the deamination of adenosine to give inosine, which is translated as guanosine. Editing thus allows variant proteins to be produced from a single pre-mRNA. A mechanism by which dsRNA substrates form is through pairing of intronic and exonic sequences before the removal of noncoding sequences by splicing. Here we report that the RNA editing enzyme, human dsRNA adenosine deaminase (DRADA1, or ADAR1) contains a domain (Zalpha) that binds specifically to the left-handed Z-DNA conformation with high affinity (KD = 4 nM). As formation of Z-DNA in vivo occurs 5' to, or behind, a moving RNA polymerase during transcription, recognition of Z-DNA by DRADA1 provides a plausible mechanism by which DRADA1 can be targeted to a nascent RNA so that editing occurs before splicing. Analysis of sequences related to Zalpha has allowed identification of motifs common to this class of nucleic acid binding domain.

Adenosine Deaminase↗
PubMed1997

Is cervical screening working? A cytopathologist's view from the United Kingdom.

This article considers the NHS cervical screening program and the controversies which have attended the introduction of comprehensive screening in a partially screened population of women in whom the underlying risk of disease was unknown. The increase in screening coverage which has taken place since 1988 has coincided with a period of high prevalence of cervical cancer and its precursors among women in the screening age group, against which background the recent fall in mortality and incidence of the disease has been a far greater achievement than generally recognized. The success of the program is considered in the context of the expectations and limitations of the test itself, and the high standards required for screening to be effective.

Adult↗
PubMed1997

Immunohistochemical phenotype of malignant mesothelioma: predictive value of CA125 and HBME-1 expression.

Histological diagnosis of malignant mesothelioma and differentiation from adenocarcinoma is often difficult. Definitive pathological confirmation of malignant mesothelioma requires demonstration of an appropriate immunohistochemical phenotype. Selection of an optimum panel of immunohistochemical antibodies for the reliable identification of malignant mesothelioma is hindered by the absence of a specific immunohistochemical label for mesothelioma cells. Recently, we have found that the ovarian carcinoma cell antibody CA125 labels malignant mesothelioma cells, and the antibody HBME-1 has been developed as a sensitive mesothelial cell marker. We have compared the immunohistochemical staining patterns achieved with CA125 and HBME-1 to those obtained using a panel of eight further antibodies in 17 malignant mesotheliomas and 14 primary and secondary adenocarcinomas within lung and pleura. CA125 labelled malignant mesothelioma cells in 15 of 17 cases (88%), and adenocarcinoma cells in seven of 14 cases (50%). HBME-1 labelled mesothelioma cells in all 17 cases (100%) but also labelled adenocarcinoma cells in 10 of 14 cases (71%). BerEP4 positively labelled one malignant mesothelioma but was negative in the remaining 16 cases and positively labelled nine of 14 adenocarcinomas (64%). Monoclonal anti-CEA, AUA-1, CA19.9 and LeuM1 labelled no malignant mesotheliomas and were positive in 10 (71%), nine (64%), eight (57%) and six (43%) of 14 cases of adenocarcinoma, respectively. Diastase-PAS staining detected neutral mucin in none of the malignant mesotheliomas but in 10 (71%) of the 14 adenocarcinomas. We conclude that CA125 and HBME-1 do not label mesothelial cells with sufficient specificity to be useful for differentiating malignant mesothelioma from adenocarcinoma, although negative staining with HBME-1 makes a diagnosis of malignant mesothelioma unlikely. As there remains an absence of a specific positive mesothelial cell marker this distinction is still most reliably made using a panel of antibodies including at least two of the following: anti-CEA, AUA-1, BerEP4, LeuM1 and CA19.9, in combination with histochemical assessment of neutral mucin production.

Adenocarcinoma↗