Can a participatory approach contribute to food chain risk analysis?

We consider food chain risks and specifically address stakeholder participation in the risk analysis process. We combine social and natural science perspectives to explore the participation process in relation to food risks and, in particular, to consider how some specific participation processes might be scientifically evaluated and how stakeholder participation in general might be incorporated into food risk decision making. We have built considerations based on three large integrative case studies that examine aspects of participatory processes. Here we use the case studies collectively to illustrate observations and beliefs concerning the nature of the interaction of stakeholders with established quantitative risk methodologies. This account is not supported by any large volume of analysis. The views in the report are expressed in relation to an accepted risk analysis framework and also with respect to probabilistic modeling of risks and are illustrated where possible with anecdotal reports of actual case study events.

Evaluation of plasmid DNA for in vivo gene therapy: factors affecting the number of transfected fibers

Gene transfer by intramuscular injection of plasmid DNA has potential application in gene therapy. We examined factors affecting the number of expressing fibers, in contrast to total expression, following injection of plasmid DNA. Barium chloride proved effective in inducing muscle necrosis and regeneration in mice, and this increased the number of fibers expressing a reporter gene. Coinjection of ion-channel modulators did not increase the number of positive fibers, but increasing dose and repeated administration of plasmid did. Importantly, the plasmid size (7-16 kb) did not affect the number of fibers expressing the transgene, in both normal and regenerating muscle.

Pulsed-field gel electrophoresis

Pulsed-field gel electrophoresis (PFGE) was originally developed as a technique for providing electrophoretic karyotypes of micro-organisms. Since then the technique has evolved and diversified in many new directions. This review traces the evolution of PFGE, summarizes our understanding of its theoretical basis, and provides a comprehensive description of the methodology. Established and novel applications are explored and the reader is provided with an extensive list of references.

Immune responses, not promoter inactivation, are responsible for decreased long-term expression following plasmid gene transfer into skeletal muscle

Long-term high-level in vivo gene expression appears to depend on the promoter chosen to drive the gene of choice. In many cases the promoter appears to 'switch off' some time after in vivo gene transfer. We demonstrate that, following intramuscular injection of beta-galactosidase reporter plasmids, promoter 'switch off' is due to elimination of fibres expressing the transferred reporter gene by activation of a Th1 (cytotoxic) immune response. This finding, in the absence of stimulation of the immune system by viral vector proteins, has implications not only for gene transfer experiments but for the future of muscle-directed gene therapy.

Human repeat-mediated integration of selectable markers into somatic cell hybrids

We describe a strategy to introduce preferentially the dominant selectable marker neoR into the human chromosome within a monochromosome hybrid cell line. Integration of a construct containing the marker is mediated by human-specific repeat elements that promote multilocus human-specific integration with a single targeting vector. We tested two classes of repeat elements: the Alu family of SINE repeats and the Line1 repeat family. We show that Alu sequences alone are insufficient to direct human-specific integration but when used in combination with a Line1 element, or when only Line1 elements are included, integration of the vector into the human component of a monochromosome somatic cell hybrid is favored. The vectors also carry sequences that facilitate mapping and selective cloning of the targeted region. This strategy provides a means to generate selectable human subchromosomal fragments that can be used for localization of genes through positional cloning and, more important, for the identification of functional units through DNA transfer.

Extensive telomere repeat arrays in mouse are hypervariable

In this study we have analysed mouse telomeres by Pulsed Field Gel Electrophoresis (PFGE). A number of specific restriction fragments hybridising to a (TTA-GGG)4 probe in the size range 50-150kb can be detected. These fragments are devoid of sites for most restriction enzymes suggesting that they comprise simple repeats; we argue that most of these are likely to be (TTAGGG)n. Each discrete fragment corresponds to the telomere of an individual chromosome and segregates as a Mendelian character. However, new size variants are being generated in the germ line at very high rates such that inbred mice are heterozygous at all telomeres analysable. In addition we show that specific small (approximately 4-12kb) fragments can be cleaved within some terminal arrays by the restriction enzyme MnII which recognises 5'(N7)GAGG3'. Like the complete telomere-repeat arrays (TRA's) these fragments form new variants at high rates and possibly by the same process. We speculate on the mechanisms that may be involved.

Semiconductor-controlled contour-clamped homogeneous electric field apparatus

The design and construction of a transistor-driven hexagonal contour-clamped homogeneous electric field (CHEF) apparatus is discussed in detail. The addition of computer control of pulsed-field timings and experiment duration gives rise to an efficient electrophoresis tool designed to achieve separation of DNA molecules in different size groupings. In particular, pulse time regimes which lead to the monotonic separation of DNA molecules ranging from 90 kbp to over a megabase pair are demonstrated. Theoretical treatment of electric field clamping with transistor-driven multiple electrodes is supported by measurements and by the actual performance of electrophoretic separation of yeast chromosomes. The large sample capacity of gels run in this apparatus coupled with the modest power requirements necessary to provide a homogeneous electric field offer significant advantages over earlier CHEF designs.

Role for the Wilms tumor gene in genital development?

Detailed molecular definition of the WAGR region at chromosome 11p13 has been achieved by chromosome breakpoint analysis and long-range restriction mapping. Here we describe the molecular detection of a cytogenetically invisible 1-megabase deletion in an individual with aniridia, cryptorchidism, and hypospadias but no Wilms tumor (WT). The region of overlap between this deletion and one associated with WT and similar genital anomalies but no aniridia covers a region of 350-400 kilobases, which is coincident with the extent of homozygous deletion detected in tumor tissue from a sporadic WT. A candidate WT gene located within this region has recently been isolated, suggesting nonpenetrance for tumor expression in the first individual. The inclusion within the overlap region of a gene for WT predisposition and a gene for the best-documented WT-associated genitourinary malformations leads us to suggest that both of these anomalies result from a loss-of-function mutation at the same locus. This in turn implies that the WT gene exerts pleiotropic effect on both kidney and genitourinary development, a possibility supported by the observed expression pattern of the WT candidate gene in developing kidney and gonads.

Specificities of IncF plasmid conjugation genes

The conjugation regions of IncF plasmids are closely related in that they share extensive DNA homology, and that they specify related pili. Variations between individual conjugation gene products of different IncF plasmids have, however, been noted. We have extended these observations by carrying out a systematic survey of twelve such plasmids, to examine the numbers and the groupings of the plasmid-specific alleles of several genes required for conjugation and its control.

Using vector plasmids carrying cloned origins of transfer (oriT), four different specificities were recognized, and these were correlated with the specificities of the genes with products that may act at this site (traM, traYandtraZ). ThetraYgene is the first gene of the major transfer operon, and is therefore located close to the site at which thetraJprotein acts to induce expression of the operon: correspondingly, correlation was observed between theoriT/traMYZandtraJspecificities in most of the plasmids. In turn,traJis negatively regulated by thefinOandfinPproducts acting in concert: thefinOproduct was relatively non-specific, but sixfinPalleles were identified, again with specificities correlated with those oftraJ. Our explanation for this unexpectedly large number offinPalleles derives from the concept that thefinPproduct is an RNA molecule rather than a protein. Although the conjugative pili encoded by IncF plasmids are closely related, they confer different efficiencies of plating of the various F-specific bacteriophages. We distinguished four groups on this basis, presumably resulting from differences in the primary amino-acid sequences of the pilin proteins. These groups could be related to the surface exclusion system specificities, consistent with the hypothesis that surface exclusion acts at least in part by preventing interaction between the pilus and the recipient cell surface.

From these data, information about the evolutionary relationships between the twelve IncF plasmids can be deduced.

Characterisation of a lambda transducing phage carrying the F conjugation gene traG

A lambda transducing phage carrying the traGSTD genes of the E. coli K12 factor F was isolated by an in vivo technique, and characterized in tra complementation tests, by determining its restriction endonuclease fragment sizes, and by measuring heteroduplex molecules. The size and location on the F physical map of the tra transducing segment was thereby determined. Comparison of the proteins synthesized in UV-irradiated cells by this phage and by a derivative carrying the amber traG79 mutation, allowed the traG product to be identified as a protein of molecular weight 100,000. In the same experiments, the sizes of the traT and traD products made by the phage were also measured, being 25,000 and 85,000 daltons respectively.

Investigations of the F conjugation gene traI:traI mutants and lambdatraI transducing phages

A series of traI point and deletion mutants of Flac, and a traM mutant, were characterised. Complementation tests with an amber Flac traI mutant confirmed their genotypes, and in addition all the traI mutants, but not the traM mutant, were complemented by pRS31 (PSC101 traDI) and EDlambda109 (lambdatraI). Judging from the efficiencies of plating of F-specific phages, none of the mutations affected pilus formation. The traI products of F and of the F-like plasmid R1 were interchangeable with each other but not with that of R100, while the traM product of F could not be replaced by those of R1 or of R100. Neither traI nor traM were needed for conjugal transfer of ColE1. Three lambda transducing phages carrying traI were isolated by in vivo or in vitro techniques, and characterised by genetic complementation tests, by analysis of the fragments produced by restriction endonucleases, and by measurement of heteroduplex molecules. The genetic structures together with the sizes and F coordinates, of the transfer regions carried by the phages were thereby determined. Comparison of the proteins synthesised in UV-irradiated cells by one of the lambdatraI phages with those made by a derivative carrying an amber traI mutation, allowed the traI product to be identified as a protein of molecular weight 174,000. In addition, the molecular weights of the traD (84,000), traS (18,000), and traT (25,000) products made by the lambdatraSTD1 phage EDlambda107 were measured. The possible roles of the traI and traM products in conjugation are discussed.

The genetic locations of traO, finP and tra-4 on the E. coli K12 sex factor F

Using a series of Hfr and F prime deletion strains, the F transfer inhibition genefinPhas been mapped betweenoriandtraJ. Marker rescue experiments with the Hfr deletion strains further showed thattraO, the site of action of the transfer inhibitor, is located immediately to the left of, or possibly within,traJ, and that the polar mutationtra-4lies intraK.

Interactions between the surface exclusion systems of some F-like plasmids

Four surface exclusion systems have been identified amongst a group of F-like plasmids inE. coli: SfxI(F), SfxII(ColV2 and R538-1fin−), SfxIII(ColVBtrpand R1-19) and SfxIV(R100-1 and R136fin−). None of these systems was expressed in stationary phase cells or, except for ColVBtrp, duringfin+transfer inhibition, showing that the surface exclusion gene(s) is usually co-controlled with the transfer genes.

Recipient cells carrying two plasmids specifying different surface exclusion systems did not always express both of these: the overall pattern suggested that the four systems and/or their sites of action are related. There was no surface exclusion between donor cells carrying two plasmids determining different surface exclusion systems and recipient cells carrying a plasmid determining either one of these. Our hypothesis to explain this and other results is that surface exclusion prevents interaction between the tip of the pilus on the donor cell and a receptor site on the recipient cell surface. Pili (probably mixed) with two types of tips would be present on cells carrying two different plasmids, the one unresponsive to the single surface exclusion system of the recipient cells allowing transfer of both plasmids.

Surface exclusion by ColV-K94

Measurement of ColEl transfer by ColV2, inE. coliK12, showed that ColV2 specifies a surface exclusion system. This system is different from those specified by Flac, and by ColVBtrpand Rl-19. Like these other two systems, the ColV2 surface exclusion system is subject to inhibition by the appropriate transfer inhibitor, and is not expressed in stationary phase cells.