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Biomedical subjects

Ian Roberts

Publications and source records attributed to Ian Roberts.

At least 37 records · Page 2Linked to original sources
PubMed2005

Generation of "neoheparin" from E. coli K5 capsular polysaccharide.

Heparin remains a major drug in prevention of thromboembolic disease. Concerns related to its animal source have prompted search for heparin analogues. The anticoagulant activity of heparin depends on a specific pentasaccharide sequence that binds antithrombin. We report the generation of a product with antithrombin-binding, anticoagulant, and antithrombotic properties similar to those of heparin, through combined chemical and enzymatic modification of a bacterial (E. coli K5) polysaccharide. The process is readily applicable to large-scale production.

Animals↗
PubMed2005

Somatic genetic changes accompanying lung tumor development.

Carcinomas are believed to develop by incremental steps of increasingly abnormal morphology driven by accumulating somatic genetic changes. This process is often difficult to study, as the early stages are undetectable. We used fluorescence bronchoscopy, which enhances detection of preinvasive bronchial lesions, and have obtained sequential biopsies of carcinoma in situ (CIS) from a patient with no detectable tumor and from a squamous cell carcinoma that developed 19 months after presentation at the site of one of the previous CIS lesions. Biopsies of preinvasive CIS, which follow-up showed had different pathologic outcomes, and tumor were microdissected to obtain enriched cell populations and DNA prepared from them. Molecular characteristics of these biopsies were compared by loss of heterozygosity analysis, TP53 mutation analysis, and comparative genomic hybridization. Although all lesions examined had the same TP53 mutation and almost identical allelotypes, differences were observed. Loss in 5q21 and amplification of 3q25-26 were associated with the lesion that progressed and the subsequent carcinoma. Allele loss at 4p16 was detected in the tumor but not in any of the CIS lesions, suggesting it was a late event associated with tumor invasion. Amplification at 4q12 was specifically observed in the tumor and in the CIS at the site of eventual tumor formation. Although these findings may be unique to this one patient, the successful demonstration of sequential genetic changes raises the possibility that this approach, unencumbered by interpatient variability between lesions, will greatly facilitate the identification of molecular events driving the invasive process

Adult↗
PubMed2005

Post-licence driver education for the prevention of road traffic crashes: a systematic review of randomised controlled trials.

The effectiveness of post-licence driver education for preventing road traffic crashes was quantified using a systematic review and meta-analyses of randomised controlled trials. Searches of appropriate electronic databases, the Internet and reference lists of relevant papers were conducted. The searches were not restricted by language or publication status. Data were pooled from 21 randomised controlled trials, including over 300,000 full licence-holding drivers of all ages. Nineteen trials reported subsequent traffic offences, with a pooled relative risk of 0.96 (95% confidence interval 0.94, 0.98). Fifteen trials reported traffic crashes with a pooled relative risk of 0.98 (0.96, 1.01). Four trials reported injury crashes with a pooled relative risk of 1.12 (0.88, 1.41). The results provide no evidence that post-licence driver education is effective in preventing road injuries or crashes. Although the results are compatible with a small reduction in the occurrence of traffic crashes, this may be due to selection biases or bias in the included trials.

Accidents, Traffic↗
PubMed2005

The effect of scientific misconduct on the results of clinical trials: a Delphi survey.

OBJECTIVES: To discover what types of scientific misconduct are most likely to influence the results of a clinical trial. DESIGN: Delphi survey of expert opinion with three rounds of consultation. SETTING: Non-industry clinical trial "community". PARTICIPANTS: Experts identified from invitees to a previous MRC consultation on clinical trials. 32 out of the 40 experts approached agreed to participate. RESULTS: We identified thirteen forms of scientific misconduct for which there was majority agreement (>50%) that they would be likely or very likely to distort the results and majority agreement (>50%) that they would be likely or very likely to occur. Of these, the over-interpretation of 'significant' findings in small trials, selective reporting and inappropriate subgroup analyses were the main themes. CONCLUSIONS: According to this expert group, the most important forms of scientific misconduct in clinical trials are selective reporting and the opportunistic use of the play of chance. Data fabrication and falsification were not rated highly because it was considered that these were unlikely to occur. Registration and publication of detailed clinical trial protocols could make an important contribution to preventing scientific misconduct.

Bias↗
PubMed2005

Evaluation of 3 methods of whole-genome amplification for subsequent metaphase comparative genomic hybridization.

A common aim in cancer research is to investigate mechanisms of malignant progression by genetic analysis of key stages, including pre-malignancy, microinvasion, and micrometastases. As such lesions are small and require microdissection from clinical samples, the amount of DNA that can be recovered is limited and frequently inadequate for commonly used techniques of genomic analysis, such as comparative genomic hybridization (CGH). There is a critical requirement for techniques of whole-genome amplification that minimize representation bias in the amplified sample. Several techniques have been described, although their relative suitability for CGH has not been examined adequately. Here we compare the abilities of degenerate oligonucleotide-primed PCR (DOP-PCR), multiple-strand displacement amplification (MDA), and balanced PCR accurately to amplify limited amounts of template DNA for use in CGH. Amplification by DOP-PCR and MDA, but not balanced PCR faithfully preserved the original genomic content following amplification, as evidenced by generally concordant CGH copy number karyograms. Whereas the amplification products of DOP-PCR were immediately available for labeling and hybridization, the products of MDA required a further digestion step to produce optimal-sized probes for CGH. Moreover, MDA was less reliable overall than DOP-PCR at the lowest starting amount of 10 pg of template DNA. We conclude that DOP-PCR is the method of choice for whole-genome amplification of minute quantities of DNA to enable global genomic analysis to be performed on limited clinical samples.

Metaphase↗
PubMed2005

Meta-analysis of randomised trials of monetary incentives and response to mailed questionnaires.

STUDY OBJECTIVE: To quantify the increase in mailed questionnaire response attributable to a monetary incentive. DESIGN: A systematic search for randomised controlled trials of monetary incentives and mailed questionnaire response was conducted. For each trial identified, logistic regression was used to estimate the odds ratio for response per 0.01 dollars incentive increase. Odds ratios were pooled in a series of random effect meta-analyses stratified by the minimum and maximum amounts offered. Piecewise logistic regression was used to estimate the odds ratio for response per $0.01 increase given in each of five incentive ranges. SETTING: Populations in several developed countries, predominantly the USA. PARTICIPANTS: 85,671 randomised participants from 88 trials. MAIN RESULTS: The pooled odds ratios for response per 0.01 dollars incentive decreased monotonically as the maximum amount of incentive offered increased. The piecewise logistic regression model estimated that for incentive amounts up to 0.50 dollars, each additional 0.01 dollars increased the odds of response by about 1% (pooled OR = 1.012, 95%CI 1.007 to 1.016). The effects on response above 0.50 dollars were smaller and decreased monotonically in the ranges: 0.50-0.99 dollars, 1-1.99 dollars, 2-4.99 dollars, 5.00 dollars and over, but remained statistically significant up to 5 dollars. CONCLUSIONS: This meta-analysis of the best available evidence shows that monetary incentives increase mailed questionnaire response. Researchers should include small amounts of money with mailed questionnaires rather than give no incentive at all.

Health Services Research↗
PubMed2004

Acquisition of high-level chromosomal instability is associated with integration of human papillomavirus type 16 in cervical keratinocytes.

Whereas two key steps in cervical carcinogenesis are integration of high-risk human papillomavirus (HR-HPV) and acquisition of an unstable host genome, the temporal association between these events is poorly understood. Chromosomal instability is induced when HR-HPV E7 oncoprotein is overexpressed from heterologous promoters in vitro. However, it is not known whether such events occur at the "physiologically" elevated levels of E7 produced by deregulation of the homologous HR-HPV promoter after integration. Indeed, an alternative possibility is that integration in vivo is favored in an already unstable host genome. We have addressed these issues using the unique human papillomavirus (HPV) 16-containing cervical keratinocyte cell line W12, which was derived from a low-grade squamous intraepithelial lesion and thus acquired HPV16 by "natural" infection. Whereas W12 at low passage contains HPV16 episomes only, long-term culture results in the emergence of cells containing integrated HPV16 only. We show that integration of HPV16 in W12 is associated with 3' deletion of the E2 transcriptional repressor, resulting in deregulation of the homologous promoter of the integrant and an increase in E7 protein levels. We further demonstrate that high-level chromosomal instability develops in W12 only after integration and that the forms of instability observed correlate with the physical state of HPV16 DNA and the level of E7 protein. Whereas intermediate E7 levels are associated with numerical chromosomal abnormalities, maximal levels are associated with both numerical and structural aberrations. HR-HPV integration is likely to be a critical event in cervical carcinogenesis, preceding the development of chromosomal abnormalities that drive malignant progression.

Cells, Cultured↗
PubMed2004

Paint-assisted microdissection-FISH: Rapid and simple mapping of translocation breakpoints in the embryonal rhabdomyosarcoma cell line RD.

BACKGROUND: Spectral karyotyping and multiple fluorophore fluorescence in situ hybridisation (M-FISH) facilitate identification of inter-chromosomal rearrangements, but are of low cytogenetic resolution in mapping translocation breakpoints. Reverse chromosome painting yields increased cytogenetic information but isolation of aberrant chromosomes is technically difficult. We have developed the technique of paint-assisted microdissection FISH (PAM-FISH), which enables microdissection of aberrant chromosomes to be carried out easily and rapidly using relatively simple apparatus. METHODS: A selected chromosome paint is hybridised to abnormal metaphases to label a chromosome of interest, which is then microdissected, amplified, labelled by polymerase chain reaction (PCR), and reverse painted onto extended normal metaphases. RESULTS: PAM-FISH was used to reassess structural chromosomal abnormalities identified by molecular cytogenetics in the rhabdomyosarcoma cell line RD. PAM-FISH improved the analysis of virtually all structural abnormalities, identifying six novel translocations and indicating that seven previously described rearrangements were in fact not present in RD. Accuracy of the breakpoint mapping obtained was confirmed by bacterial artificial chromosome-FISH. CONCLUSIONS: PAM-FISH is ideally suited to analysis of tumour metaphases as it is not affected by poor chromosome morphology. Reagents generated by PAM-FISH are also suitable for other investigations, such as mapping using sequence tagged-site PCR or genomic microarrays. PAM-FISH is technically straightforward and could readily be adopted in a routine cytogenetics laboratory for accurate high-throughput analysis of chromosome breakpoints.

Cell Line, Tumor↗
PubMed2004

Follow-up by mail in clinical trials: does questionnaire length matter?

In large clinical trials where outcome assessment is possible using questionnaires, it may be more cost-effective to mail them to patients than to conduct interviews in-person. However, nonresponse to mailed questionnaires reduces the effective sample size and can introduce bias. We conducted a systematic review and meta-analysis of randomized controlled trials evaluating the effect of questionnaire length on response rates. We searched 14 electronic bibliographic databases, the reference lists of relevant trials, and we contacted the authors of eligible trials to ask about unpublished data. For each trial identified, we used logistic regression to estimate the odds ratio for response per one page increase in the number of pages included in the questionnaire. We pooled the regression coefficients in a random effects meta-analysis. Heterogeneity among the coefficients was assessed using a chi-square test at a 5% significance level. We specified a priori that the reduction in the odds of response per one page increase would be greatest among trials comparing relatively short questionnaires. We used meta regression to examine the relationships between the regression coefficients, the length of the questionnaires used in each trial, and other study characteristics. A total of 38 randomized controlled trials were identified where participants were allocated to questionnaires of differing lengths and where the number of pages used was known. There was significant heterogeneity between the regression coefficients estimated from each trial. In meta regression, most of the heterogeneity was explained by variation in the length of the questionnaires used in each trial. Among trials in which the shortest questionnaire was a postcard, the odds of response were more than halved for each additional page used (0.39; 95% CI 0.34 to 0.45). In the remaining trials, pooled effect sizes were much smaller. In trials of one page compared with either two or three pages, the odds of response per one page increase was 1.01 (95% CI 0.82 to 1.24). For one page compared with four or more pages, and for two or more pages compared with longer alternatives, the odds ratios per one page increase were 0.90 (95% CI 0.83 to 0.98) and 0.98 (95% CI 0.96 to 0.99), respectively. There were no statistically significant associations between trial results and other study characteristics. It appears that response can be increased by using a shorter questionnaire. Moderate changes to the length of shorter questionnaires will be more effective than moderate changes to the length of longer questionnaires. If a choice of follow-up questionnaire exists for a clinical trial, the shorter one should be used. If a new follow-up questionnaire is to be designed, it should be made as short as possible without compromising the data collection requirements of the trial.

Follow-Up Studies↗
PubMed2003

Nodule initiation involves the creation of a new symplasmic field in specific root cells of medicago species.

The organogenesis of nitrogen-fixing nodules in legume plants is initiated in specific root cortical cells and regulated by long-distance signaling and carbon allocation. Here, we explore cell-to-cell communication processes that occur during nodule initiation in Medicago species and their functional relevance using a combination of fluorescent tracers, electron microscopy, and transgenic plants. Nodule initiation induced symplasmic continuity between the phloem and nodule initials. Macromolecules such as green fluorescent protein could traffic across short or long distances from the phloem into these primordial cells. The created symplasmic field was regulated throughout nodule development. Furthermore, Medicago truncatula transgenic plants expressing a viral movement protein showed increased nodulation. Hence, the establishment of this symplasmic field may be a critical element for the control of nodule organogenesis.

Biological Transport↗
PubMed2003

Effectiveness of out-of-home day care for disadvantaged families: randomised controlled trial.

OBJECTIVE: To assess the effects of providing daycare facilities for young children on the health and welfare of disadvantaged families. DESIGN: Randomised controlled trial. Eligible children from the application list to a daycare facility were randomly allocated to receive a daycare place or not. SETTING: Early Years daycare centre in Borough of Hackney, London. PARTICIPANTS: 120 mothers and 143 eligible children (aged between 6 months and 3.5 years). INTERVENTION: A place at the centre, which provided high quality day care. Control families used other child care that they secured for themselves. MAIN OUTCOME MEASURES: Maternal paid employment, household income, child health and development. RESULTS: At 18 months' follow up, 67% of intervention group mothers and 60% of control group mothers were in paid employment (adjusted risk ratio 1.23 (95% confidence interval 0.99 to 1.52)), but were no more likely to have a weekly household income of above pound 200 (risk ratio 0.88 (0.70 to 1.09)). Intervention group children had more otitis media with effusion (risk ratio 1.74 (1.02 to 2.96)) and used more health services (1.58 (1.05 to 2.38)), but both estimates were imprecise. CONCLUSION: The provision of child day care may have increased maternal employment, but it did not seem to increase household income. The results suggest that providing day care may be insufficient as a strategy to reduce poverty. The study shows how random allocation can be used to ration and evaluate interventions where demand exceeds supply.

Child Day Care Centers↗
PubMed2003

Overexpression of UDP-glucose dehydrogenase in Escherichia coli results in decreased biosynthesis of K5 polysaccharide.

The Escherichia coli K5 capsular polysaccharide (glycosaminoglycan) chains are composed of the repeated disaccharide structure: -GlcAbeta1,4-GlcNAcalpha1,4-(where GlcA is glucuronic acid and GlcNAc is N-acetyl-D-glucosamine). The GlcA, present in most glycosaminoglycans, is donated from UDP-GlcA, which, in turn, is generated from UDP-glucose by the enzyme UDP-glucose dehydrogenase (UDPGDH). The formation of UDP-GlcA is critical for the biosynthesis of glycosaminoglycans. To investigate the role of UDPGDH in glycosaminoglycan biosynthesis, we used K5 polysaccharide biosynthesis as a model. E. coli was transformed with the complete gene cluster for K5 polysaccharide production. Additional transformation with an extra copy of UDPGDH resulted in an approx. 15-fold increase in the in vitro UDPGDH enzyme activity compared with the strain lacking extra UDPGDH. UDP-GlcA levels were increased 3-fold in overexpressing strains. However, metabolic labelling with [14C]glucose showed, unexpectedly, that overexpression of UDPGDH lead to decreased formation of K5 polysaccharide. No significant difference in the K5 polysaccharide chain length was observed between control and overexpressing strains, indicating that the decrease in K5-polysaccharide production most probably was due to synthesis of fewer chains. Our results suggest that K5-polysaccharide biosynthesis is strictly regulated such that increasing the amount of available UDP-GlcA results in diminished K5-polysaccharide production.

Bacterial Capsules↗