Biomedical subjects

A P Butler

Publications and source records attributed to A P Butler.

At least 19 recordsLinked to original sources

PubMed2004

Stochastic modelling of landfill leachate and biogas production incorporating waste heterogeneity. Model formulation and uncertainty analysis.

A mathematical model simulating the hydrological and biochemical processes occurring in landfilled waste is presented and demonstrated. The model combines biochemical and hydrological models into an integrated representation of the landfill environment. Waste decomposition is modelled using traditional biochemical waste decomposition pathways combined with a simplified methodology for representing the rate of decomposition. Water flow through the waste is represented using a statistical velocity model capable of representing the effects of waste heterogeneity on leachate flow through the waste. Given the limitations in data capture from landfill sites, significant emphasis is placed on improving parameter identification and reducing parameter requirements. A sensitivity analysis is performed, highlighting the model's response to changes in input variables. A model test run is also presented, demonstrating the model capabilities. A parameter perturbation model sensitivity analysis was also performed. This has been able to show that although the model is sensitive to certain key parameters, its overall intuitive response provides a good basis for making reasonable predictions of the future state of the landfill system. Finally, due to the high uncertainty associated with landfill data, a tool for handling input data uncertainty is incorporated in the model's structure. It is concluded that the model can be used as a reasonable tool for modelling landfill processes and that further work should be undertaken to assess the model's performance.

Biodegradation, Environmental↗

PubMed2004

Stochastic modelling of landfill processes incorporating waste heterogeneity and data uncertainty.

A landfill is a very complex heterogeneous environment and as such it presents many modelling challenges. Attempts to develop models that reproduce these complexities generally involve the use of large numbers of spatially dependent parameters that cannot be properly characterised in the face of data uncertainty. An alternative method is presented, which couples a simplified microbial degradation model with a stochastic hydrological and contaminant transport model. This provides a framework for incorporating the complex effects of spatial heterogeneity within the landfill in a simplified manner, along with other key variables. A methodology for handling data uncertainty is also integrated into the model structure. Illustrative examples of the model's output are presented to demonstrate effects of data uncertainty on leachate composition and gas volume prediction.

Environmental Pollutants↗

PubMed2003

Soil transport and plant uptake of radio-iodine from near-surface groundwater.

This paper describes a 12-month experiment designed to study the extent of upward migration of (125)I (as a surrogate for (129)I) from near-surface groundwater, through a 50-cm column of soil and into perennial ryegrass. The water table was established at a depth of 45 cm below the soil surface. By 3 months, (125)I had migrated about half way up the soil column. After this, it tended to accumulate just above this mid-point, with only very small amounts being transported to the upper 20 cm of soil. This behaviour seemed to be explained well by soil moisture and redox conditions. The experiment indicated that (125)I was mobile only within the saturated/low redox zone at the base of the soil column and accumulated in the zone of transition between anoxic and oxic soil conditions. Uptake of (125)I by the ryegrass was found to be low.

Environmental Monitoring↗

PubMed2001

The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X.

We constructed maps for eight chromosomes (1, 6, 9, 10, 13, 20, X and (previously) 22), representing one-third of the genome, by building landmark maps, isolating bacterial clones and assembling contigs. By this approach, we could establish the long-range organization of the maps early in the project, and all contig extension, gap closure and problem-solving was simplified by containment within local regions. The maps currently represent more than 94% of the euchromatic (gene-containing) regions of these chromosomes in 176 contigs, and contain 96% of the chromosome-specific markers in the human gene map. By measuring the remaining gaps, we can assess chromosome length and coverage in sequenced clones.

Chromosomes, Human, Pair 1↗

PubMed2001

Core promoter involvement in the induction of rat ornithine decarboxylase by phorbol esters.

Overexpression of ornithine decarboxylase (ODC) is an important oncogenic event in tumorigenesis. Although ODC was one of the first genes described whose product is inducible by 12-O-tetradecanoylphorbol-13-acetate (TPA), the mechanisms of ODC transcriptional regulation have remained elusive. In this study, we systematically analyzed the rat ODC core promoter region for novel TPA response elements. Analysis of linker scanning mutants of the ODC promoter from the TATA box to the transcription start site demonstrated that mutation of the TATA box reduced the TPA induction ratio by 40%, while the basal ODC promoter activity was not significantly changed. A novel region between nt - 20 to - 10 was shown to be critical for both basal promoter activity and induction by TPA. Random mutagenesis of this region showed that conversion of the GC-rich wild-type sequence into a T-rich sequence could either substantially increase the basal promoter activity and decrease the TPA induction ratio or dramatically reduce the basal promoter activity, depending on the T content. Mutant R5, containing an ATTT sequence at nt - 15 to - 12, caused a more than twofold increase of basal promoter activity and 80% reduction of TPA induction ratio. We suggest that this region interacts with components of the general transcription machinery and that the strength of this interaction is mediated by the T-content in this region.

Animals↗

PubMed2001

Genetic analysis of susceptibility to spontaneous and UV-induced carcinogenesis in Xiphophorus hybrid fish.

Xiphophorus interspecies hybrids provide genetically controlled models of tumor formation. Spontaneous melanomas form in first-generation backcross (BC(1)) hybrids produced from backcrossing F(1) hybrids derived from the platyfish X. maculatus Jp 163 A and the swordtail X. helleri to the X. helleri parental strain (the Gordon-Kosswig hybrid cross). Nodular melanomas originate in the dorsal fin from cells constituting the spotted dorsal (Sd) pigment pattern. A parallel genetic cross, with X. maculatus Jp 163 B, exhibits the spotted side (Sp) pigment pattern instead of Sd, and produces BC(1) hybrids exhibiting a much lower frequency of spontaneous melanoma formation. These hybrids are susceptible to melanoma development if irradiated with UV light as fry. Other hybrids involving these two strains of X. maculatus and different swordtail and platyfish backcross parents also have been investigated as potential tumor models, and show differing susceptibilities to UV-induced and spontaneous melanomas. Genotyping of individual BC(1) hybrids from several Xiphophorus crosses has implicated a locus, CDKN2X (a Xiphophorus homologue of the mammalian CDKN2 gene family, residing on Xiphophorus linkage group V), in enhancing pigmentation and the susceptibility to spontaneous and UV-induced melanoma formation in BC(1) hybrids from some crosses, but not others. Homozygosity for X. helleri and X. couchianus CDKN2X alleles in BC(1) hybrids can predispose individuals to melanoma, but this susceptibility is modified in other crosses depending both on the contributing sex-linked pigment pattern locus from X. maculatus (Sd or Sp), and the genetic constitution of the backcross parent. Xiphophorus BC(1) hybrids constitute unique genetic models offering the potential to analyze the contributions of specific genes to spontaneous and induced tumor formation in different, but comparable genetic backgrounds.

Journal Article↗

PubMed2000

A negative regulatory element within the proximal promoter region of the rat ornithine decarboxylase gene.

A putative Ets site with a core of GGAA located at nt -88 to -85 of the rat ornithine decarboxylase (ODC) gene was characterized by site-directed mutagenesis and transient expression assays. Mutation of this site, when in pODClux2m, which contains a cluster of four Sp1-binding sites, resulted in a 2.6-fold increase in basal promoter activity in untreated cells, whereas the ratio of activity in 12-O-tetradecanoylphorbol-13-acetate (TPA)-treated cells relative to the ratio in untreated cells (the induction ratio) remained largely unchanged. However, when the mutation was in pODClux168, which contains only a single Sp1-binding site (GC box V), it caused little alteration to either basal promoter activity or TPA induction ratio. A protein of 55-60 kDa was found specifically bound to this site, as shown by ultraviolet cross-linking assay. In competition assay and methylation interference assay, this protein was shown to occupy the GGAA core, although it showed no antigenic relation to c-Ets-1 in an supershift assay. We suggest that this protein binds specifically to the GGAA core and functions to inhibit activation of the ODC promoter by distal elements, including the upstream Sp1 sites.

Animals↗

PubMed1999

Enhanced Sp1 DNA-binding activity in murine keratinocyte cell lines and epidermal tumors.

Altered regulation of ornithine decarboxylase (ODC) is frequently observed in epidermal tumors. We have shown that the transcription factor Sp1 is one of the regulators of ODC expression and that Sp3 antagonizes this Sp1-mediated activation of ODC expression. These results led us to examine the levels and binding activity of Sp1 and Sp3 in nuclear extracts prepared from cultured murine keratinocytes, transformed keratinocyte cell lines and epidermal tumors. Here we show that the Sp1 DNA-binding activity is higher in established keratinocyte cell line extracts than in primary keratinocyte extracts. Sp1 message levels and Sp1 DNA-binding activity was found to be low in 20-week papillomas and high in squamous cell carcinomas. These results suggest that increased levels of Sp1 and enhanced Sp1 DNA binding activity are correlated with epidermal tumor progression. Based on these results, we propose that increased Sp1 DNA binding may augment the proliferative capacity of tumor cells through overexpression of Sp1-responsive genes, possibly including ODC.

Animals↗

PubMed1998

Serum responsive gene expression mediated by Sp1.

We compared the Sp1 binding activity of Rat2 fibroblasts in nuclear extracts prepared from quiescent cells and cells stimulated with 20% serum. Increased DNA-binding activity was observed in extracts from serum-stimulated cells when an Sp1 oligonucleotide was used as radiolabeled probe in electrophoretic mobility shift assays. This increase in Sp1 DNA-binding activity is not due to changes in the amount of Sp1 in the nucleus as shown by immunoblot analysis. The transcriptional activity of a reporter construct containing six Sp1 sites upstream of a minimal adenovirus promoter or an Sp1-dependent promoter such as ornithine decarboxylase (ODC) containing Sp1 sites was enhanced following serum stimulation in transient transfection assays. Dephosphorylation of the nuclear extracts with potato acid phosphatase abolished the Sp1 DNA-binding activity, demonstrating a possible correlation between phosphorylation of Sp1 and DNA-binding activity. These results implicate a potential role for Sp1 in mediating signal transduction pathways in response to mitogenic signals.

Acid Phosphatase↗

PubMed1997

Transcription factor Sp3 antagonizes activation of the ornithine decarboxylase promoter by Sp1.

Ornithine decarboxylase (ODC) expression is important for proliferation and is elevated in many tumor cells. We previously showed that Sp1 is a major positive regulator of ODC transcription. In this paper we have investigated transcriptional regulation of rat ODC by the closely related factor Sp3. While over-expression of Sp1 caused a dramatic activation of the ODC promoter, over-expression of Sp3 caused little or no activation in either Drosophila SL2 cells (lacking endogenous Sp1 or Sp3) or in H35 rat hepatoma cells. Furthermore, co-transfection studies demonstrated that Sp3 abolished trans -activation of the ODC promoter by Sp1. DNase I footprint studies and electrophoretic mobility shift assays demonstrated that both recombinant Sp1 and Sp3 bind specifically to several sites within the ODC promoter also protected by nuclear extracts, including overlapping GC and CT motifs located between -116 and -104. This CT element is a site of negative ODC regulation. Mutation of either element reduced binding, but mutation of both sites was required to eliminate binding of either Sp1 or Sp3. These results demonstrate that ODC is positively regulated by Sp1 and negatively regulated by Sp3, suggesting that the ratio of these transcription factors may be an important determinant of ODC expression during development or transformation.

Animals↗

PubMed1997

Disruption of transcription in vitro and gene expression in vivo by DNA adducts derived from a benzo[a]pyrene diol epoxide located in heterologous sequences.

Previous studies indicated a high affinity of the transcription factor Sp1 for DNA adducts derived from benzo[a]pyrene diol epoxide (BPDE) in sequences that are not normal binding sites for Sp1. We tested for functional effects of this phenomenon in three systems in which transcription is Sp1-dependent. In an in vitro, Sp1-dependent transcription system addition of heterologous plasmid DNA containing BPDE adducts abolished production of a specific run-off transcript. This inhibition was not seen with unmodified plasmid DNA, and could be overcome by addition of purified Sp1 protein. In SL2 insect cells, high-level expression of an Sp1-dependent reporter gene, which was dependent on co-transfection of an Sp1 expression vector, was inhibited >95% by co-transfection of heterologous DNA containing BPDE adducts. This inhibition could be partially overcome by increasing the amount of the Sp1 expression vector in the transfections. In human C33A cells, expression of a transfected reporter gene driven by a GC box containing fragment of the human E2F1 promoter was enhanced by co-transfection of an Sp1 expression plasmid. Expression was inhibited 3-6-fold by co-transfection of heterologous DNA containing BPDE-DNA adducts. A similar inhibition was seen in human SAOS-2 cells, which lack functional p53 protein. These data are consistent with functionally significant sequestration of the Sp1 transcription factor by BPDE-DNA adducts in all three systems. Altered availability of transcription factors such as Sp1 in carcinogen-treated cells may disrupt patterns of gene expression.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗

PubMed1997

From long range mapping to sequence-ready contigs on human chromosome 6.

Our aim is to construct physical clone maps covering those regions of chromosome 6 that are not currently extensively mapped, and use these to determine the DNA sequence of the whole chromosome. The strategy we are following involves establishing a high density framework map of the order of 15 markers per Megabase using radiation hybrid (RH) mapping. The markers are then used to identify large-insert genomic bacterial clones covering the chromosome, which are assembled into sequence-ready contigs by restriction enzyme fingerprinting and sequence tagged site (STS) content analysis. Contig gap closure is performed by walking experiments using STSs developed from the end sequences of the clone inserts.

Chromosomes, Human, Pair 6↗

PubMed1997

Off-axis output factors for 6MV and 18MV photons.

A series of in-air measurements showed that collimator scatter (Sc) did not change significantly for 6MV photons when the centre of the field was moved away from the central axis. This result enabled a model to be developed for the off-axis Effective Output Factor (EOF) which was then verified for 6MV and 18MV photons on a Varian 2100c accelerator and for 6MV photons on a Varian 600c accelerator. Thus off-axis output factors may be predicted, for a range of rectangular asymmetric fields, using only the Primary Off-Centre Ratio (POCR) in air and the on-axis output factor. Depth doses were also investigated off-axis and found to have no clinically significant differences compared with on-axis depth doses, for depths less than 7.5 cm for 6MV and 12.5 cm for 18MV photons. The model is simple to implement and avoids the need for a measurement for each patient, thus saving accelerator time.

Biophysical Phenomena↗

PubMed1996

Involvement of a pertussis-toxin sensitive G protein in the induction of gene expression by insulin.

Binding of insulin to its receptor triggers multiple cellular responses, including changes in metabolism and in gene expression, resulting from the activation of multiple signalling pathways. Pertussis toxin has been shown to block an insulin-stimulated phospholipase C, resulting in an inhibition of the synthesis of phospholipid second messengers by insulin. In the present study, we investigated the significance of this pathway for the induction of growth-related genes by insulin treatment of H35 hepatoma cells. We found that pertussis toxin dramatically inhibits the induction of c-fos mRNA by insulin. Although c-jun and ornithine decarboxylase induction were also inhibited by pertussis toxin, they were much less sensitive than c-fos. These results indicate an important for lipid second messengers in mitogenic signalling by insulin and further demonstrate distinct roles for this pathway in the induction of c-fos and c-jun.

Animals↗

PubMed1996

Physical mapping of chromosome 6: a strategy for the rapid generation of sequence-ready contigs.

The development of radiation hybrid (RH) mapping (Cox et al., 1990) and the availability of large numbers of STS markers, together with extensive bacterial clone resources provided a means to accelerate the process of mapping a human chromosome and preparing bacterial clone contigs ready to sequence. Our aim is to construct physical clone maps covering those regions of chromosome 6 that are not currently extensively mapped, and use these to determine the DNA sequence of the whole chromosome. We report here a strategy which initially involves establishing a high density framework map using RH mapping. The framework markers are then used for the identification of bacterial genomic clones covering the chromosome. The bacterial clones are analysed by restriction enzyme fingerprinting and STS-content analysis to identify sequence-ready contigs. Contig gap closure will also be performed by clone walking.

Chromosome Mapping↗

PubMed1995

Regulation of rat ornithine decarboxylase promoter activity by binding of transcription factor Sp1.

Ornithine decarboxylase (ODC) is the rate-limiting enzyme of polyamine biosynthesis. We investigated the transcriptional regulation of the rat ODC gene using transient expression assays. The 5'-flanking region (-1156 to +13) of the ODC gene was sufficient to mediate strong basal expression of a luciferase reporter. Sequences between -345 and -93 contributed to basal promoter activity. This region, containing five potential Sp1 binding sites, was analyzed by electrophoretic mobility shift assays. Three specific DNA-protein complexes were identified using H35 nuclear extracts and the -345/-93 ODC probe. Binding to all three was eliminated by competition with an oligonucleotide containing an Sp1 binding site, but not by a mutant Sp1 oligonucleotide. Preincubation with an antibody against Sp1 supershifted complexes associated with one or more of Sp1 binding sites 1-4 as well as with site 5. DNase I footprinting revealed two protected regions: PR-I (-92 to -130) and PR-II (-304 to -332). PR-I contains a putative binding site for Sp1 that was protected by recombinant Sp1 protein. Transfection studies in Schneider SL2 cells demonstrated that the ODC promoter is transactivated up to 350-fold by Sp1 and that this transactivation is dependent on the presence of Sp1 binding sites 1-4. Thus, although the ODC promoter binds multiple nuclear proteins, Sp1 or a related protein appears to be a critical determinant of ODC transcription, possibly through cooperative interactions between Sp1 and additional transcription factors.

Animals↗

PubMed1995

Expression of epidermal ornithine decarboxylase and nuclear proto-oncogenes in phorbol ester tumor promotion-sensitive and -resistant mice.

This study was undertaken to assess the effects of a single or two sequential topical applications of 12-O-tetradecanoylphorbol-13-acetate (TPA) on the expression of c-fos, c-jun, junB, c-myc, and ornithine decarboxylase (ODC) in promotion-sensitive SSIN mice and the relatively promotion-resistant C57BL/6 strain. Northern blot analysis demonstrated that a single promoting dose of TPA induced ODC mRNA expression 10- to 15-fold in both strains. Treatment of each strain with a second dose of TPA, 48 h (in C57BL/6 mice) or 72 h (in SSIN mice) after the first, led to hyperinduction of ODC activity. Although this involved transcription of new ODC mRNA, the hyperinduction of ODC enzyme activity was primarily posttranscriptional. Induction of c-fos mRNA or protein was maximal about 3 h after a single treatment in either strain but was sustained for at least 6 h in C57BL/6 mice. In contrast, two treatments of SSIN mice with TPA caused a rapid, strong c-fos induction 1-2 h after treatment, whereas C57BL/6 mice responded no more strongly than after a single treatment. c-jun mRNA and protein were induced only slightly in either strain, but junB was induced about fivefold in SSIN mice and tenfold in C57BL/6 mice. Although c-myc was induced to comparable levels in both strains, the response was more prolonged in C57BL/6 mice. Compared with SSIN mice, C57BL/6 mice responded to TPA treatment, in general, with changes in proto-oncogene mRNA to a higher level or for longer or both. Thus, although small differences in the expression of these genes were observed, they were not positively correlated with the differential sensitivity of SSIN and C57BL/6 mice toward tumor promotion by phorbol esters, with the possible exception of c-fos.

Animals↗

PubMed1995

Characterization of novel phorbol ester- and serum-responsive sequences of the rat ornithine decarboxylase gene promoter.

Ornithine decarboxylase (ODC), the key regulatory enzyme in mammalian polyamine biosynthesis, is rapidly induced by mitogens and tumor promoters. We used transient expression assays and DNA-protein binding studies to examine the regulation of ODC promoter activity by phorbol esters and serum growth factors. A fragment of the ODC 5' flanking region (nt-1156 to +13) was sufficient to confer 12-O-tetradecanoylphorbol-13-acetate (TPA)-responsive expression to a luciferase reporter gene when transfected into H35 cells. However, induction by TPA was not observed in Rat2 fibroblasts, although refeeding of serum-starved Rat2 cells with fresh serum-containing medium rapidly induced a fivefold to sixfold increase in ODC promoter activity, maximal about 8 h after refeeding. Deletion analysis demonstrated that several sequences contributed to basal ODC promoter activity but that nt -92 to +13 was sufficient for induction by TPA or by serum. This sequence lacked canonical TPA-responsive elements, and an activator protein-1 (AP-1) consensus oligonucleotide failed to compete effectively for proteins binding to this region. Two of four protein complexes observed by gel-shift analysis of nt -92 to +13 were competitively inhibited by wild-type but not mutant oligonucleotides encompassing a variant cyclic AMP-response element (CRE) (ODC nt -50 to -42); however, a consensus CRE did not compete. Mutagenesis of this site demonstrated that it contributes to basal expression of the ODC promoter but not to TPA or serum responsiveness. Thus, we conclude that the proximal ODC promoter (nt -92 to +13) responds to TPA and serum stimulation in a cell-type-specific manner that is not mediated by canonical AP-1 elements.

Animals↗