30 results on '"Chappell, SA"'
Search Results
2. Loss of heterozygosity at the mannose 6-phosphate insulin-like growth factor 2 receptor gene correlates with poor differentiation in early breast carcinomas
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Chappell, SA, primary, Walsh, T, additional, Walker, RA, additional, and Shaw, JA, additional
- Published
- 1997
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3. Loss of heterozygosity at chromosome 6q in preinvasive and early invasive breast carcinomas
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Chappell, SA, primary, Walsh, T, additional, Walker, RA, additional, and Shaw, JA, additional
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- 1997
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4. Microsatellite instability in early sporadic breast cancer
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Shaw, JA, primary, Walsh, T, additional, Chappell, SA, additional, Carey, N, additional, Johnson, K, additional, and Walker, RA, additional
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- 1996
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5. Smart Simple Design
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Chappell, Sam, Col and Korba, Doug
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SPARE PARTS ,STANDARDIZATION AND INTEROPERABILITY - Published
- 1999
6. Engineering a Mesoporous Silicon Nanoparticle Cage to Enhance Performance of a Phosphotriesterase Enzyme for Degradation of VX Nerve Agent.
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Lu YS, Moreno ER, Huang Y, Fan R, Tucker AT, Wright LK, Evans RA, Ahern BM, Owens DE, Chappell SA, Christensen DJ, Dresios J, and Sailor MJ
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- Animals, Rabbits, Porosity, Chemical Warfare Agents metabolism, Enzymes, Immobilized chemistry, Enzymes, Immobilized metabolism, Hydrolysis, Phosphoric Triester Hydrolases metabolism, Phosphoric Triester Hydrolases chemistry, Organothiophosphorus Compounds metabolism, Organothiophosphorus Compounds chemistry, Nanoparticles chemistry, Silicon chemistry, Nerve Agents metabolism, Nerve Agents chemistry
- Abstract
The organophosphate (OP)-hydrolyzing enzyme phosphotriesterase (PTE, variant L7ep-3a) immobilized within a partially oxidized mesoporous silicon nanoparticle cage is synthesized and the catalytic performance of the enzyme@nanoparticle construct for hydrolysis of a simulant, dimethyl p-nitrophenyl phosphate (DMNP), and the live nerve agent VX is benchmarked against the free enzyme. In a neutral aqueous buffer, the optimized construct shows a ≈2-fold increase in the rate of DMNP turnover relative to the free enzyme. Enzyme@nanoparticles with more hydrophobic surface chemistry in the interior of the pores show lower catalytic activity, suggesting the importance of hydration of the pore interior on performance. The enzyme@nanoparticle construct is readily separated from the neutralized agent; the nanoparticle is found to retain DMNP hydrolysis activity through seven decontamination/recovery cycles. The nanoparticle cage stabilizes the enzyme against thermal denaturing and enzymatic (trypsin) degradation conditions relative to free enzyme. When incorporated into a topical gel formulation, the PTE-loaded nanoparticles show high activity toward the nerve agent VX in an ex vivo rabbit skin model. In vitro acetylcholinesterase (AChE) assays in human blood show that the enzyme@nanoparticle construct decontaminates VX, preserving the biological function of AChE when exposed to an otherwise incapacitating dose., (© 2024 The Author(s). Advanced Science published by Wiley‐VCH GmbH.)
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- 2024
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7. Considerations in the Use of Codon Optimization for Recombinant Protein Expression.
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Mauro VP and Chappell SA
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- Animals, Evolution, Molecular, Genetic Engineering, Humans, RNA, Messenger genetics, RNA, Messenger metabolism, Codon genetics, Genetic Code genetics, Recombinant Proteins genetics, Recombinant Proteins metabolism
- Abstract
Codon optimization is a gene engineering approach that is commonly used for enhancing recombinant protein expression. This approach is possible because (1) degeneracy of the genetic code enables most amino acids to be encoded by multiple codons and (2) different mRNAs encoding the same protein can vary dramatically in the amount of protein expressed. However, because codon optimization potentially disrupts overlapping information encoded in mRNA coding regions, protein structure and function may be altered. This chapter discusses the use of codon optimization for various applications in mammalian cells as well as potential consequences, so that informed decisions can be made on the appropriateness of using this approach in each case.
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- 2018
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8. A cell-free expression and purification process for rapid production of protein biologics.
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Sullivan CJ, Pendleton ED, Sasmor HH, Hicks WL, Farnum JB, Muto M, Amendt EM, Schoborg JA, Martin RW, Clark LG, Anderson MJ, Choudhury A, Fior R, Lo YH, Griffey RH, Chappell SA, Jewett MC, Mauro VP, and Dresios J
- Subjects
- Biological Products isolation & purification, Bioreactors, Cell-Free System, Erythropoietin biosynthesis, Erythropoietin genetics, Erythropoietin isolation & purification, Granulocyte-Macrophage Colony-Stimulating Factor biosynthesis, Granulocyte-Macrophage Colony-Stimulating Factor genetics, Granulocyte-Macrophage Colony-Stimulating Factor isolation & purification, Humans, Metabolic Engineering methods, Recombinant Proteins genetics, Recombinant Proteins isolation & purification, Biological Products metabolism, Recombinant Proteins biosynthesis, Technology, Pharmaceutical methods
- Abstract
Cell-free protein synthesis has emerged as a powerful technology for rapid and efficient protein production. Cell-free methods are also amenable to automation and such systems have been extensively used for high-throughput protein production and screening; however, current fluidic systems are not adequate for manufacturing protein biopharmaceuticals. In this work, we report on the initial development of a fluidic process for rapid end-to-end production of recombinant protein biologics. This process incorporates a bioreactor module that can be used with eukaryotic or prokaryotic lysates that are programmed for combined transcription/translation of an engineered DNA template encoding for specific protein targets. Purification of the cell-free expressed product occurs through a series of protein separation modules that are configurable for process-specific isolation of different proteins. Using this approach, we demonstrate production of two bioactive human protein therapeutics, erythropoietin and granulocyte-macrophage colony-stimulating factor, in yeast and bacterial extracts, respectively, each within 24 hours. This process is flexible, scalable and amenable to automation for rapid production at the point-of-need of proteins with significant pharmaceutical, medical, or biotechnological value., (Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
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- 2016
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9. A critical analysis of codon optimization in human therapeutics.
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Mauro VP and Chappell SA
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- Animals, Gene Expression Regulation, Humans, Peptides genetics, Peptides metabolism, Peptides therapeutic use, Protein Engineering, RNA Editing, RNA, Messenger genetics, RNA, Transfer chemistry, Recombinant Proteins genetics, Recombinant Proteins metabolism, Codon, Genetic Engineering methods, Genetic Therapy, Recombinant Proteins therapeutic use
- Abstract
Codon optimization describes gene engineering approaches that use synonymous codon changes to increase protein production. Applications for codon optimization include recombinant protein drugs and nucleic acid therapies, including gene therapy, mRNA therapy, and DNA/RNA vaccines. However, recent reports indicate that codon optimization can affect protein conformation and function, increase immunogenicity, and reduce efficacy. We critically review this subject, identifying additional potential hazards including some unique to nucleic acid therapies. This analysis highlights the evolved complexity of codon usage and challenges the scientific bases for codon optimization. Consequently, codon optimization may not provide the optimal strategy for increasing protein production and may decrease the safety and efficacy of biotech therapeutics. We suggest that the use of this approach is reconsidered, particularly for in vivo applications., (Copyright © 2014 Elsevier Ltd. All rights reserved.)
- Published
- 2014
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10. Verocytotoxigenic Escherichia coli O157 in camelids.
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Featherstone CA, Foster AP, Chappell SA, Carson T, and Pritchard GC
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- Animals, Disease Reservoirs veterinary, Escherichia coli Infections epidemiology, Escherichia coli Infections transmission, Humans, Public Health, Zoonoses, Camelids, New World microbiology, Escherichia coli Infections veterinary, Escherichia coli O157 pathogenicity, Sentinel Surveillance veterinary
- Published
- 2011
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11. Analysis of ribosomal shunting during translation initiation in eukaryotic mRNAs.
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Mauro VP, Chappell SA, and Dresios J
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- Animals, Base Pairing, Cell-Free System, Genes, Reporter physiology, Mice, RNA Caps metabolism, RNA, Ribosomal, 18S physiology, Saccharomyces cerevisiae metabolism, Two-Hybrid System Techniques, Peptide Chain Initiation, Translational physiology, RNA, Messenger metabolism, Ribosomes physiology
- Abstract
In eukaryotes, translation initiation involves recruitment of ribosomal subunits at either the 5' m7G cap structure or at an internal ribosome entry site (IRES). For most mRNAs, the initiation codon is located some distance downstream, necessitating ribosomal movement to this site. Although the mechanistic details of this movement remain to be fully resolved, it appears to be nonlinear for some mRNAs (i.e., ribosomal subunits appear to bypass [shunt] segments of the 5' leader as they move to the initiation codon). This chapter describes various experimental approaches to assess ribosomal shunting and to identify mRNA elements (shunt sites) that facilitate shunting. In addition, we provide an overview of approaches that can be used to investigate the mechanism used by individual shunt sites, along with a detailed protocol for investigating putative base pairing interactions between shunt sites and 18S rRNA.
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- 2007
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12. Ribosomal tethering and clustering as mechanisms for translation initiation.
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Chappell SA, Edelman GM, and Mauro VP
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- Codon, Initiator genetics, Multigene Family genetics, RNA Caps genetics, Ribosomes genetics, Peptide Chain Initiation, Translational, RNA Caps metabolism, Ribosomes metabolism
- Abstract
Eukaryotic mRNAs often recruit ribosomal subunits some distance upstream of the initiation codon; however, the mechanisms by which they reach the initiation codon remain to be fully elucidated. Although scanning is a widely accepted model, evidence for alternative mechanisms has accumulated. We previously suggested that this process may involve tethering of ribosomal complexes to the mRNA, in which the intervening mRNA is bypassed, or clustering, in which the initiation codon is reached by dynamic binding and release of ribosomal subunits at internal sites. The present studies tested the feasibility of these ideas by using model mRNAs and revealed that translation efficiency varied with the distance between the site of ribosomal recruitment and the initiation codon. The present studies also showed that translation could initiate efficiently at AUG codons located upstream of an internal site. These observations are consistent with ribosomal tethering at the cap structure and clustering at internal sites.
- Published
- 2006
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13. Ribosomal shunting mediated by a translational enhancer element that base pairs to 18S rRNA.
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Chappell SA, Dresios J, Edelman GM, and Mauro VP
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- Animals, Cell Line, Mice, RNA, Ribosomal, 18S chemistry, Base Pairing, Enhancer Elements, Genetic genetics, Protein Biosynthesis genetics, RNA, Ribosomal, 18S genetics, Ribosomes metabolism
- Abstract
In eukaryotes, 40S ribosomal subunits move from their recruitment site on the mRNA to the initiation codon by an as yet poorly understood process. One postulated mechanism involves ribosomal shunting, in which ribosomal subunits completely bypass regions of the 5' leader. For some mRNAs, shunting has been shown to require various mRNA elements, some of which are thought to base pair to 18S rRNA; however, the role of base pairing has not yet been tested directly. In earlier studies, we demonstrated that a short mRNA element in the 5' leader of the Gtx homeodomain mRNA functioned as a ribosomal recruitment site by base pairing to the 18S rRNA. Using a model system to assess translation in transfected cells, we now show that this intermolecular interaction also facilitates ribosomal shunting across two types of obstacles: an upstream AUG codon in excellent context or a stable hairpin structure. Highly efficient shunting occurred when multiple Gtx elements were present upstream of the obstacles, and a single Gtx element was present downstream. Shunting was less efficient, however, when the multiple Gtx elements were present only upstream of the obstacles. In addition, control experiments with mRNAs lacking the upstream elements showed that these results could not be attributed to recruitment by the single downstream element. Experiments in yeast in which the mRNA elements and 18S rRNA sequences were both mutated indicated that shunting required an intact complementary match. The data obtained by this model system provide direct evidence that ribosomal shunting can be mediated by mRNA-rRNA base pairing, a finding that may have general implications for mechanisms of ribosome movement.
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- 2006
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14. An mRNA-rRNA base-pairing mechanism for translation initiation in eukaryotes.
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Dresios J, Chappell SA, Zhou W, and Mauro VP
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- Animals, Base Sequence, Enhancer Elements, Genetic genetics, Homeodomain Proteins genetics, Mice, Mutation genetics, Transcription Factors genetics, Base Pairing, Peptide Chain Initiation, Translational, RNA, Messenger chemistry, RNA, Messenger genetics, RNA, Ribosomal chemistry, RNA, Ribosomal genetics, Saccharomyces cerevisiae genetics
- Abstract
Base-pairing of messenger RNA to ribosomal RNA is a mechanism of translation initiation in prokaryotes. Although analogous base-pairing has been suggested to affect the translation of various eukaryotic mRNAs, direct evidence has been lacking. To test such base-pairing, we developed a yeast system that uses ribosomes containing a mouse-yeast hybrid 18S rRNA. Using this system, we demonstrate that a 9-nucleotide element found in the mouse Gtx homeodomain mRNA facilitates translation initiation by base-pairing to 18S rRNA. Various point mutations in the Gtx element and in either the hybrid or wild-type yeast 18S rRNAs confirmed the requirement for an intact complementary match. The presence of the Gtx element in various mRNAs suggests that this element affects the translation of groups of mRNAs. We discuss the possibility that other mRNA elements affect translation by base-pairing to different sites in the 18S rRNA.
- Published
- 2006
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15. Biochemical and functional analysis of a 9-nt RNA sequence that affects translation efficiency in eukaryotic cells.
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Chappell SA, Edelman GM, and Mauro VP
- Subjects
- 5' Untranslated Regions chemistry, 5' Untranslated Regions genetics, 5' Untranslated Regions metabolism, Base Pairing, Base Sequence, Eukaryotic Cells metabolism, Genes genetics, Protein Binding, Protein Subunits, RNA, Ribosomal, 18S chemistry, RNA, Ribosomal, 18S genetics, RNA, Ribosomal, 18S metabolism, Ribosomes chemistry, Protein Biosynthesis genetics, Regulatory Sequences, Ribonucleic Acid genetics, Ribosomes metabolism
- Abstract
We previously identified an internal ribosome entry site (IRES) within the 5' leader of the mRNA encoding the Gtx homeodomain protein and showed that shorter nonoverlapping segments of this 5' leader could enhance the translation of a second cistron in a dicistronic mRNA. One of these segments was 9 nt in length, and when multiple copies of this IRES module were linked together, IRES activity was greatly enhanced. To further expand the potential uses of these synthetic constructs and facilitate analyses of the mechanism by which they affect translation, we show here that an IRES containing five linked copies of the 9-nt sequence can also enhance translation in the 5' leader of a monocistronic mRNA. Moreover, a search for interactions of the IRES module with cellular factors revealed specific binding to 40S ribosomal subunits but not to other cellular components. Based on the results of earlier studies suggesting that this sequence could bind to a complementary segment of 18S rRNA, we tested various sequences for possible links between the length of the complementary match, their binding to ribosomes, and their influence on translational efficiency. We found that the length of the complementary match was directly correlated with the ability of RNA probes to bind to ribosomes. In addition, translation was maximally enhanced ( approximately 8-fold) by a 7-nt segment of the 9-nt element; the enhancement declined progressively as the complementary stretches became progressively longer or shorter. The results suggest that the Gtx 9-nt sequence affects translation efficiency by a mechanism that involves base pairing to 18S rRNA.
- Published
- 2004
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16. Prevalence of faecal excretion of verocytotoxigenic Escherichia coli O157 in cattle in England and Wales.
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Paiba GA, Wilesmith JW, Evans SJ, Pascoe SJ, Smith RP, Kidd SA, Ryan JB, McLaren IM, Chappell SA, Willshaw GA, Cheasty T, French NP, Jones TW, Buchanan HF, Challoner DJ, Colloff AD, Cranwell MP, Daniel RG, Davies IH, Duff JP, Hogg RA, Kirby FD, Millar MF, Monies RJ, Nicholls MJ, and Payne JH
- Subjects
- Animals, Bacteriophage Typing veterinary, Cattle, Cattle Diseases microbiology, DNA, Bacterial analysis, England epidemiology, Escherichia coli Infections epidemiology, Escherichia coli O157 classification, Feces microbiology, Female, Male, Polymerase Chain Reaction veterinary, Prevalence, Random Allocation, Seasons, Shiga Toxins analysis, Surveys and Questionnaires, Wales epidemiology, Cattle Diseases epidemiology, Escherichia coli Infections veterinary, Escherichia coli O157 isolation & purification
- Abstract
During the decade to 1999, the incidence of human infections with the zoonotic pathogen verocytotoxin-producing Escherichia coli O157 (VTEC O157) increased in England and Wales. This paper describes the results of a survey of 75 farms to determine the prevalence of faecal excretion of VTEC O157 by cattle, its primary reservoir host, in England and Wales. Faecal samples were collected from 4663 cattle between June and December 1999. The prevalence of excretion by individual cattle was 4.2 per cent (95 per cent confidence interval [CI] 2.0 to 6.4) and 10.3 per cent (95 per cent CI 5.8 to 14.8) among animals in infected herds. The within-herd prevalence on positive farms ranged from 1.1 to 51.4 per cent. At least one positive animal was identified on 29 (38.7 per cent; 95 per cent CI 28.1 to 50.4) of the farms, including dairy, suckler and fattening herds. The prevalence of excretion was least in the calves under two months of age, peaked in the calves aged between two and six months and declined thereafter. The phage types identified most widely were 4, 34 and 2, which were each found on six of the 29 positive farms.
- Published
- 2003
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17. The internal ribosome entry site (IRES) contained within the RNA-binding motif protein 3 (Rbm3) mRNA is composed of functionally distinct elements.
- Author
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Chappell SA and Mauro VP
- Subjects
- 3T3 Cells, Amino Acid Motifs, Animals, Base Sequence, Binding Sites, Cell Line, Cell-Free System, Cytoplasm metabolism, DNA metabolism, DNA Mutational Analysis, Gene Deletion, Humans, Luciferases metabolism, Mice, Molecular Sequence Data, Mutation, Open Reading Frames, Protein Binding, Protein Biosynthesis, RNA, Messenger metabolism, RNA-Binding Proteins chemistry, Rats, Ribosomes metabolism, Transfection, Tumor Cells, Cultured, RNA-Binding Proteins physiology, Ribosomes chemistry
- Abstract
Although the internal ribosome entry sites (IRESes) of viral mRNAs are highly structured and comprise several hundred nucleotides, there is a variety of evidence indicating that very short nucleotide sequences, both naturally occurring and synthetic, can similarly mediate internal initiation of translation. In this study, we performed deletion and mutational analyses of an IRES contained within the 720-nucleotide (nt) 5' leader of the Rbm3 mRNA and demonstrated that this IRES is highly modular, with at least 9 discrete cis-acting sequences. These cis-acting sequences include a 22-nt IRES module, a 10-nt enhancer, and 2 inhibitory sequences. The 22-nt sequence was shown to function as an IRES when tested in isolation, and we demonstrated that it did not enhance translation by functioning as a transcriptional promoter, enhancer, or splice site. The activities of all 4 cis-acting sequences were further confirmed by their mutation in the context of the full IRES. Interestingly, one of the inhibitory cis-acting sequences is contained within an upstream open reading frame (uORF), and its activity seems to be masked by translation of this uORF. Binding studies revealed that all 4 cis-acting sequences could bind specifically to distinct cytoplasmic proteins. In addition, the 22-nt IRES module was shown to bind specifically to 40 S ribosomal subunits. The results demonstrate that different types of cis-acting sequences mediate or modulate translation of the Rbm3 mRNA and suggest that one of the IRES modules contained within the 5' leader facilitates translation initiation by binding directly to 40 S ribosomal subunits.
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- 2003
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18. Faecal carriage of verocytotoxin-producing Escherichia coli O157 in cattle and sheep at slaughter in Great Britain.
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Paiba GA, Gibbens JC, Pascoe SJ, Wilesmith JW, Kidd SA, Byrne C, Ryan JB, Smith RP, McLaren M, Futter RJ, Kay AC, Jones YE, Chappell SA, Willshaw GA, and Cheasty T
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- Animals, Data Collection, England, Feces microbiology, Humans, Prevalence, Rectum microbiology, Seasons, Abattoirs, Cattle, Escherichia coli Infections transmission, Escherichia coli O157 isolation & purification, Food Contamination, Sheep, Shiga Toxins biosynthesis
- Abstract
A 12-month abattoir survey was conducted between January 1999 and January 2000, to determine the prevalence of faecal carriage of verocytotoxin-producing Escherichia coli O157 (VTEC O157) in cattle and sheep slaughtered for human consumption in Great Britain. Samples of rectum containing faeces were collected from 3939 cattle and 4171 sheep at 118 abattoirs, in numbers proportional to the throughput of the premises. The annual prevalence of faecal carriage of VTEC O157 was 4.7 per cent (95 per cent confidence interval 4.1 to 5.4) for cattle and 1.7 per cent (1.3 to 2.1) for sheep, values which were statistically significantly different from each other (P < 0.001). The organisms were recovered from both cattle and sheep slaughtered throughout the year and at abattoirs in all regions of the country, but the highest prevalence was in the summer. The most frequency recovered VTEC O157 isolates were phage types 2, 8 and 21/28 in cattle and 4 and 32 in sheep, the five most frequently isolated phage types associated with illness in people in Great Britain during the same period.
- Published
- 2002
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19. Investigation of the genetic diversity among isolates of Salmonella enterica serovar Dublin from animals and humans from England, Wales and Ireland.
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Liebana E, Garcia-Migura L, Clouting C, Cassar CA, Clifton-Hadley FA, Lindsay EA, Threlfall EJ, Chappell SA, and Davies RH
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- Animals, Anti-Bacterial Agents analysis, Anti-Bacterial Agents classification, Birds, Cattle, Chickens, Cluster Analysis, Dogs, Drug Resistance, Bacterial, Electrophoresis, Gel, Pulsed-Field methods, Humans, Integrons genetics, Phylogeny, Plasmids analysis, Plasmids isolation & purification, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, Ribotyping methods, Salmonella enterica classification, Salmonella enterica isolation & purification, Sheep, Swine, Genetic Variation, Salmonella enterica genetics
- Abstract
Aims: To assess the degree of genetic diversity among animal Salmonella Dublin UK isolates, and to compare it with the genetic diversity found among human isolates from the same time period., Methods and Results: One hundred isolates (50 human and 50 animal) were typed using plasmid profiling, XbaI-pulsed field gel electrophoresis (PFGE) and PstI-SphI ribotyping. Antimicrobial resistance data to 16 antibiotics was presented, and the presence of class-I integrons was investigated by real-time PCR. Seven different plasmid profiles, 19 ribotypes and 21 PFGE types were detected. A combination of the three methods allowed clear differentiation of 43 clones or strains. Eighteen isolates were resistant to at least one antimicrobial; five of them were multi-resistant and of these, only three presented class I integrons., Conclusions: Ribotyping data suggest the existence of at least three very different clonal lines; the same distribution in well-defined groups was not evident from the PFGE data. The existence of a variety of clones in both animals and humans has been demonstrated. A few prevalent clones seem to be widely disseminated among different animal species and show a diverse geographical and temporal distribution. The same clones were found in animals and humans, which may infer that both farm and pet animals may act as potential vehicles of infection for humans. Some other clones seem to be less widely distributed. Clustering analysis of genomic fingerprints of Salmonella Dublin and Salm. Enteritidis isolates confirms the existence of a close phylogenetic relationship between both serotypes., Significance and Impact of the Study: This paper describes the utility of a multiple genetic typing approach for Salm. Dublin. It gives useful information on clonal diversity among human and animal isolates.
- Published
- 2002
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20. New ways of initiating translation in eukaryotes.
- Author
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Schneider R, Agol VI, Andino R, Bayard F, Cavener DR, Chappell SA, Chen JJ, Darlix JL, Dasgupta A, Donzé O, Duncan R, Elroy-Stein O, Farabaugh PJ, Filipowicz W, Gale M Jr, Gehrke L, Goldman E, Groner Y, Harford JB, Hatzglou M, He B, Hellen CU, Hentze MW, Hershey J, Hershey P, Hohn T, Holcik M, Hunter CP, Igarashi K, Jackson R, Jagus R, Jefferson LS, Joshi B, Kaempfer R, Katze M, Kaufman RJ, Kiledjian M, Kimball SR, Kimchi A, Kirkegaard K, Koromilas AE, Krug RM, Kruys V, Lamphear BJ, Lemon S, Lloyd RE, Maquat LE, Martinez-Salas E, Mathews MB, Mauro VP, Miyamoto S, Mohr I, Morris DR, Moss EG, Nakashima N, Palmenberg A, Parkin NT, Pe'ery T, Pelletier J, Peltz S, Pestova TV, Pilipenko EV, Prats AC, Racaniello V, Read GS, Rhoads RE, Richter JD, Rivera-Pomar R, Rouault T, Sachs A, Sarnow P, Scheper GC, Schiff L, Schoenberg DR, Semler BL, Siddiqui A, Skern T, Sonenberg N, Sossin W, Standart N, Tahara SM, Thomas AA, Toulmé JJ, Wilusz J, Wimmer E, Witherell G, and Wormington M
- Subjects
- Animals, Artifacts, Binding Sites physiology, Genes, Genetic Vectors, Humans, Peptide Initiation Factors metabolism, RNA Processing, Post-Transcriptional physiology, RNA, Messenger metabolism, RNA, Transfer metabolism, RNA, Viral metabolism, Reproducibility of Results, Research Design, Ribosomes metabolism, Eukaryotic Cells metabolism, Protein Biosynthesis physiology
- Published
- 2001
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21. A 5' Leader of Rbm3, a Cold Stress-induced mRNA, Mediates Internal Initiation of Translation with Increased Efficiency under Conditions of Mild Hypothermia.
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Chappell SA, Owens GC, and Mauro VP
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- 3T3 Cells, Animals, Cell Line, Cell-Free System, DNA, Complementary isolation & purification, Genes, Reporter, Hypothermia, Induced, Mice, Mice, Inbred C57BL, Open Reading Frames, Protein Biosynthesis, RNA, Messenger biosynthesis, RNA-Binding Proteins genetics, Ribosomes chemistry, Sequence Analysis, RNA, Transfection, 5' Untranslated Regions analysis, RNA-Binding Proteins biosynthesis
- Abstract
Although mild hypothermia generally reduces protein synthesis in mammalian cells, the expression of a small number of proteins, including Rbm3, is induced under these conditions. In this study, we identify an Rbm3 mRNA with a complex 5' leader sequence containing multiple upstream open reading frames. Although these are potentially inhibitory to translation, monocistronic reporter mRNAs containing this leader were translated relatively efficiently. In addition, when tested in the intercistronic region of dicistronic mRNAs, this leader dramatically enhanced second cistron translation, both in transfected cells and in cell-free lysates, suggesting that the Rbm3 leader mediates cap-independent translation via an internal ribosome entry site (IRES). Inasmuch as Rbm3 mRNA and protein levels are both increased in cells exposed to mild hypothermia, the activity of this IRES was evaluated at a cooler temperature. Compared to 37 degrees C, IRES activity at 33 degrees C was enhanced up to 5-fold depending on the cell line. Moderate enhancements also occurred with constructs containing other viral and cellular IRESes. These effects of mild hypothermia on translation were not caused by decreased cell growth, as similar effects were not observed when cells were serum starved. The results suggest that cap-independent mechanisms may facilitate the translation of particular mRNAs during mild hypothermia.
- Published
- 2001
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22. Internal initiation of translation of five dendritically localized neuronal mRNAs.
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Pinkstaff JK, Chappell SA, Mauro VP, Edelman GM, and Krushel LA
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- Animals, Cell Line, Hippocampus metabolism, RNA Caps, RNA, Messenger metabolism, Rats, Dendrites metabolism, Neurons metabolism, Protein Biosynthesis, RNA, Messenger genetics
- Abstract
In neurons, translation of dendritically localized mRNAs is thought to play a role in affecting synaptic efficacy. Inasmuch as components of the translation machinery may be limiting in dendrites, we investigated the mechanisms by which translation of five dendritically localized mRNAs is initiated. The 5' leader sequences of mRNAs encoding the activity-regulated cytoskeletal protein, the alpha subunit of calcium-calmodulin-dependent kinase II, dendrin, the microtubule-associated protein 2, and neurogranin (RC3) were evaluated for their ability to affect translation in the 5' untranslated region of a monocistronic reporter mRNA. In both neural and nonneural cell lines, the activity-regulated cytoskeletal protein, microtubule-associated protein 2, and alpha-CaM Kinase II leader sequences enhanced translation, whereas the dendrin and RC3 5' untranslated regions slightly inhibited translation as compared with controls. When cap-dependent translation of these constructs was suppressed by overexpression of a protein that binds the cap-binding protein eIF4E, it was revealed that translation of these mRNAs had both cap-dependent and cap-independent components. The cap-independent component was further analyzed by inserting the 5' leader sequences into the intercistronic region of dicistronic mRNAs. All five leader sequences mediated internal initiation via internal ribosome entry sites (IRESes). The RC3 IRES was most active and was further characterized after transfection in primary neurons. Although translation mediated by this IRES occurred throughout the cell, it was relatively more efficient in dendrites. These data suggest that IRESes may increase translation efficiency at postsynaptic sites after synaptic activation.
- Published
- 2001
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23. Identification of two short internal ribosome entry sites selected from libraries of random oligonucleotides.
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Owens GC, Chappell SA, Mauro VP, and Edelman GM
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- Animals, Binding Sites, COS Cells, Chlorocebus aethiops, Gene Library, Oligonucleotides, Rats, Tumor Cells, Cultured, RNA, Complementary, RNA, Messenger, RNA, Ribosomal, 18S, Ribosomes metabolism
- Abstract
Sequences that control translation of mRNA may play critical roles in regulating protein levels. One such element is the internal ribosome entry site (IRES). We previously showed that a 9-nt segment in the 5' leader sequence of the mRNA encoding Gtx homeodomain protein could function as an IRES. To identify other short sequences with similar properties, we designed a selection procedure that uses a retroviral vector to express dicistronic mRNAs encoding enhanced green and cyan fluorescent proteins as the first and second cistrons, respectively. Expression of the second cistron was dependent upon the intercistronic sequences and was indicative of IRES activity. B104 cells were infected with two retroviral libraries that contained random sequences of 9 or 18 nt in the intercistronic region. Cells expressing both cistrons were sorted, and sequences recovered from selected cells were reassayed for IRES activity in a dual luciferase dicistronic mRNA. Two novel IRESes were identified by this procedure, and both contained segments with complementarity to 18S rRNA. When multiple copies of either segment were linked together, IRES activities were dramatically enhanced. Moreover, these synthetic IRESes were differentially active in various cell types. These properties are similar to those of the previously identified 9-nt IRES module from Gtx mRNA. These results provide further evidence that short nucleotide sequences can function as IRESes and support the idea that some cellular IRESes may be composed of shorter functional modules. The ability to identify IRES modules with specific expression properties may be useful in the design of vectors for biotechnology and gene therapy.
- Published
- 2001
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24. Expression of oestrogen receptor alpha variants in non-malignant breast and early invasive breast carcinomas.
- Author
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Chappell SA, Johnson SM, Shaw JA, and Walker RA
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- Adult, Breast pathology, Carcinoma, Ductal, Breast metabolism, Estrogen Receptor alpha, Female, Humans, Hyperplasia metabolism, Middle Aged, Neoplasm Proteins genetics, Point Mutation genetics, Polymorphism, Single-Stranded Conformational, RNA, Messenger analysis, Receptors, Estrogen genetics, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, DNA, Breast metabolism, Breast Neoplasms metabolism, Fibrocystic Breast Disease metabolism, Neoplasm Proteins metabolism, Receptors, Estrogen metabolism
- Abstract
Oestrogen receptor (ER) alpha variants have been described in normal breast and breast carcinomas, but their presence in a range of benign conditions and in small early invasive breast carcinomas has not been considered. Cryostat tissue sections from 19 normal and proliferative breast lesions and 44 carcinomas 15 mm and less in size detected by mammographic screening were screened for ERalpha splice variants using reverse transcriptase-nested PCR. The carcinomas were assessed for mutation by single-stranded conformational polymorphism analysis and variant forms/band shifts were sequenced. ERalpha was detected in all 19 non-malignant cases and exon 7-deleted variants were found in 16 of them. Three cases showed weak expression of exon 5, and two of exon 3 variants. There was no relationship between the presence of variants and the extent of proliferative change, ER status or age. ERalpha mRNA was not detected in two carcinomas; exon 3 deletions were found in four (9. 5%) of the other carcinomas, exon 5 in two (4.8%), and exon 7 in 11 (26.2%), with two variants in four carcinomas and a total of 29.5% of all cases having detectable variants. Two point mutations were found in one, which was a tubular carcinoma. Variant forms were identified in carcinomas of all sizes (bar<10 mm) but were more frequent in those of 15 mm. There was no relationship with type, grade or receptor status. The main difference between non-malignant breast and early invasive cancers related to exons 3 and 5. The findings suggest that ERalpha variants are not involved in breast cancer development but occur with tumour progression and may be a consequence rather than a cause., (Copyright 2000 John Wiley & Sons, Ltd.)
- Published
- 2000
- Full Text
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25. A mutation in the c-myc-IRES leads to enhanced internal ribosome entry in multiple myeloma: a novel mechanism of oncogene de-regulation.
- Author
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Chappell SA, LeQuesne JP, Paulin FE, deSchoolmeester ML, Stoneley M, Soutar RL, Ralston SH, Helfrich MH, and Willis AE
- Subjects
- 5' Untranslated Regions, Base Sequence, Bone Marrow physiology, Cell Line, Gene Expression Regulation, Neoplastic, Humans, Molecular Sequence Data, Protein Biosynthesis, Proto-Oncogene Mas, Proto-Oncogene Proteins c-myc metabolism, Recombinant Proteins genetics, Recombinant Proteins metabolism, Multiple Myeloma genetics, Point Mutation, Proto-Oncogene Proteins c-myc genetics, Regulatory Sequences, Nucleic Acid, Ribosomes
- Abstract
The 5' untranslated region of the proto-oncogene c-myc contains an internal ribosome entry segment (IRES) (Nanbru et al., 1997; Stoneley et al., 1998) and thus c-myc protein synthesis can be initiated by a cap-independent as well as a cap-dependent mechanism (Stoneley et al., 2000). In cell lines derived from patients with multiple myeloma (MM) there is aberrant translational regulation of c-myc and this correlates with a C-T mutation in the c-myc-IRES (Paulin et al., 1996). RNA derived from the mutant IRES displays enhanced binding of protein factors (Paulin et al., 1998). Here we show that the same mutation is present in 42% of bone marrow samples obtained from patients with MM, but was not present in any of 21 controls demonstrating a strong correlation between this mutation and the disease. In a tissue culture based assay, the mutant version of the c-myc-IRES was more active in all cell types tested, but showed the greatest activity in a cell line derived from a patient with MM. Our data demonstrate that a single mutation in the c-myc-IRES is sufficient to cause enhanced initiation of translation via internal ribosome entry and represents a novel mechanism of oncogenesis.
- Published
- 2000
- Full Text
- View/download PDF
26. A 9-nt segment of a cellular mRNA can function as an internal ribosome entry site (IRES) and when present in linked multiple copies greatly enhances IRES activity.
- Author
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Chappell SA, Edelman GM, and Mauro VP
- Subjects
- 5' Untranslated Regions genetics, Animals, Cell Line, Genes, Reporter, Homeodomain Proteins genetics, Humans, Mice, Oligoribonucleotides genetics, RNA, Ribosomal, 18S genetics, Rats, Sequence Deletion, Transfection, RNA, Messenger genetics, Ribosomes genetics
- Abstract
This study addresses the properties of a newly identified internal ribosome entry site (IRES) contained within the mRNA of the homeodomain protein Gtx. Sequential deletions of the 5' untranslated region (UTR) from either end did not define distinct IRES boundaries; when five nonoverlapping UTR fragments were tested, four had IRES activity. These observations are consistent with other cellular IRES analyses suggesting that some cellular IRESes are composed of segments (IRES modules) that independently and combinatorially contribute to overall IRES activity. We characterize a 9-nt IRES module from the Gtx 5' UTR that is 100% complementary to the 18S rRNA at nucleotides 1132-1124. In previous work, we demonstrated that this mRNA segment could be crosslinked to its complement within intact 40S subunits. Here we show that increasing the number of copies of this IRES module in the intercistronic region of a dicistronic mRNA strongly enhances IRES activity in various cell lines. Ten linked copies increased IRES activity up to 570-fold in Neuro 2a cells. This level of IRES activity is up to 63-fold greater than that obtained by using the well characterized encephalomyocarditis virus IRES when tested in the same assay system. When the number of nucleotides between two of the 9-nt Gtx IRES modules was increased, the synergy between them decreased. In light of these findings, we discuss possible mechanisms of ribosome recruitment by cellular mRNAs, address the proposed role of higher order RNA structures on cellular IRES activity, and suggest parallels between IRES modules and transcriptional enhancer elements.
- Published
- 2000
- Full Text
- View/download PDF
27. c-Myc protein synthesis is initiated from the internal ribosome entry segment during apoptosis.
- Author
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Stoneley M, Chappell SA, Jopling CL, Dickens M, MacFarlane M, and Willis AE
- Subjects
- Apoptosis drug effects, Apoptosis genetics, Apoptosis Regulatory Proteins, Genes, myc, Half-Life, HeLa Cells, Humans, Membrane Glycoproteins pharmacology, Mitogen-Activated Protein Kinases metabolism, Protein Synthesis Inhibitors pharmacology, Proto-Oncogene Mas, Proto-Oncogene Proteins c-myc genetics, RNA, Messenger genetics, RNA, Messenger metabolism, Staurosporine pharmacology, TNF-Related Apoptosis-Inducing Ligand, Tumor Necrosis Factor-alpha pharmacology, Apoptosis physiology, Proto-Oncogene Proteins c-myc biosynthesis, Ribosomes metabolism
- Abstract
Recent studies have shown that during apoptosis protein synthesis is inhibited and that this is in part due to the proteolytic cleavage of eukaryotic initiation factor 4G (eIF4G). Initiation of translation can occur either by a cap-dependent mechanism or by internal ribosome entry. The latter mechanism is dependent on a complex structural element located in the 5' untranslated region of the mRNA which is termed an internal ribosome entry segment (IRES). In general, IRES-mediated translation does not require eIF4E or full-length eIF4G. In order to investigate whether cap-dependent and cap-independent translation are reduced during apoptosis, we examined the expression of c-Myc during this process, since we have shown previously that the 5' untranslated region of the c-myc proto-oncogene contains an IRES. c-Myc expression was determined in HeLa cells during apoptosis induced by tumor necrosis factor-related apoptosis-inducing ligand. We have demonstrated that the c-Myc protein is still expressed when more than 90% of the cells are apoptotic. The presence of the protein in apoptotic cells does not result from either an increase in protein stability or an increase in expression of c-myc mRNA. Furthermore, we show that during apoptosis initiation of c-myc translation occurs by internal ribosome entry. We have investigated the signaling pathways that are involved in this response, and cotransfection with plasmids which harbor either wild-type or constitutively active MKK6, a specific immediate upstream activator of p38 mitogen-activated protein kinase (MAPK), increases IRES-mediated translation. In addition, the c-myc IRES is inhibited by SB203580, a specific inhibitor of p38 MAPK. Our data, therefore, strongly suggest that the initiation of translation via the c-myc IRES during apoptosis is mediated by the p38 MAPK pathway.
- Published
- 2000
- Full Text
- View/download PDF
28. A single nucleotide change in the c-myc internal ribosome entry segment leads to enhanced binding of a group of protein factors.
- Author
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Paulin FE, Chappell SA, and Willis AE
- Subjects
- Base Sequence, Blotting, Northern, Blotting, Western, Cell Line, Cytoplasm metabolism, DNA Primers, Protein Binding, RNA, Messenger genetics, RNA, Messenger metabolism, RNA-Binding Proteins metabolism, RNA-Binding Proteins radiation effects, Ultraviolet Rays, Genes, myc, Point Mutation, Ribosomes metabolism
- Abstract
A 340 nucleotide section of the c- myc 5' untranslated region (UTR) contains an internal ribosome entry segment. We have described previously a mutation in this region of RNA in cell lines derived from patients with multiple myeloma (MM) which exhibit increased expression of c- myc protein by an aberrant translational mechanism. In this study we show by electrophoretic mobility shift assays (EMSA), north-western blotting and UV cross-linking that radiolabelled c- myc 5' UTR RNA transcripts which harbour the mutation cause enhanced binding of cellular proteins. In addition, we also demonstrate that an MM derived cell line possesses an altered repertoire of RNA binding proteins. Our data suggest that the deregulated expression of c -myc in MM could result both from the effect of the mutation and the additional proteins which are present in these cell types.
- Published
- 1998
- Full Text
- View/download PDF
29. Microsatellite instability in ductal carcinoma in situ of the breast.
- Author
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Walsh T, Chappell SA, Shaw JA, and Walker RA
- Subjects
- Breast Neoplasms metabolism, Breast Neoplasms pathology, Carcinoma in Situ metabolism, Carcinoma in Situ pathology, Carcinoma, Ductal, Breast metabolism, Carcinoma, Ductal, Breast pathology, DNA Repair, Humans, Immunoenzyme Techniques, Loss of Heterozygosity, Mutation, Neoplasm Proteins metabolism, Receptor, ErbB-2 metabolism, Tumor Suppressor Protein p53 metabolism, Breast Neoplasms genetics, Carcinoma in Situ genetics, Carcinoma, Ductal, Breast genetics, Microsatellite Repeats
- Abstract
Microsatellite instability (MI+) is associated with defects in mismatch repair, resulting in a 'mutator' phenotype and the development and progression of cancer. MI+ has been documented in invasive breast carcinomas. This study was undertaken to determine whether MI+ is found in the early non-invasive form of breast cancer, ductal carcinoma in situ (DCIS). We examined microdissected ducts from 23 cases of DCIS with 11 markers comprising mono-, di-, and trinucleotide repeats from six chromosomal regions. Five tumours (22 per cent) displayed MI+ at two or more loci, in all ducts examined. A further seven (30 per cent) tumours showed alterations at a single locus (the DM-1 trinucleotide), and for two of these, heterogeneity between ducts was observed. Alterations at microsatellite repeat motifs in the coding regions of four cancer-associated genes (TGF beta RII, IGFIIR, BAX, and E2F-4) were not observed. Immunohistochemistry revealed that there was no loss of reactivity for the mismatch repair proteins, MLH1, MSH2, and PMS2, in the DCIS cases. In general, MI+ tumours and those with alterations at the DM-1 microsatellite were predominantly of higher nuclear grade and expressing c-erbB-2, suggesting that aberrations in DNA repair functions may lead to the acquisition of a more aggressive phenotype in breast cancer.
- Published
- 1998
- Full Text
- View/download PDF
30. C-Myc 5' untranslated region contains an internal ribosome entry segment.
- Author
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Stoneley M, Paulin FE, Le Quesne JP, Chappell SA, and Willis AE
- Subjects
- Base Sequence, Chromosome Mapping, HeLa Cells, Humans, Molecular Sequence Data, Nucleic Acid Conformation, Proto-Oncogene Mas, Proto-Oncogene Proteins c-myc metabolism, RNA, Messenger metabolism, Tumor Cells, Cultured, Protein Biosynthesis, Proto-Oncogene Proteins c-myc genetics, Ribosomes metabolism
- Abstract
Translation in eukaryotic cells is generally initiated by ribosome scanning from the 5' end of the capped mRNA. However, initiation of translation may also occur by a mechanism which is independent of the cap structure and in this case ribosomes are directed to the start codon by an internal ribosome entry segment (IRES). Picornaviruses represent the paradigm for this mechanism, but only a few examples exist which show that this mechanism is used by eukaryotic cells. In this report we show data which demonstrate that the 5' UTR of the proto-oncogene c-myc contains an IRES. When a dicistronic reporter vector, with c-myc 5' UTR inserted between the two cistrons, was transfected into both HepG2 and HeLa cells, the translation of the downstream cistron was increased by 50-fold, demonstrating that translational regulation of c-myc is mediated through cap-independent mechanisms. This is the first example of a proto-oncogene regulated in this manner and suggests that aberrant translational regulation of c-myc is likely to play a role in tumorigenesis.
- Published
- 1998
- Full Text
- View/download PDF
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