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Al-mashhadani MK, Wilkinson SJ, Zimmerman WB. Carbon dioxide rich microbubble acceleration of biogas production in anaerobic digestion. Chem Eng Sci 2016. [DOI: 10.1016/j.ces.2016.09.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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2
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Kilner J, Corfe BM, McAuley MT, Wilkinson SJ. A deterministic oscillatory model of microtubule growth and shrinkage for differential actions of short chain fatty acids. Mol BioSyst 2016; 12:93-101. [DOI: 10.1039/c5mb00211g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Short-chain fatty acids have distinct effects on cytoskeletal proteins at the level of expression and organisation. We report a new oscillatory, deterministic model which accounts for different actions and predicts response according to fatty acid chain length.
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Affiliation(s)
- Josephine Kilner
- Biological and Systems Engineering Group
- ChELSI Institute
- Department of Chemical and Biological Engineering
- University of Sheffield S1 3JD
- UK
| | - Bernard M. Corfe
- Molecular Gastroenterology Research Group
- Academic Unit of Surgical Oncology
- Department of Oncology
- University of Sheffield
- The Medical School
| | | | - Stephen J. Wilkinson
- Biological and Systems Engineering Group
- ChELSI Institute
- Department of Chemical and Biological Engineering
- University of Sheffield S1 3JD
- UK
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Auley MTM, Mooney KM, Angell PJ, Wilkinson SJ. Mathematical modelling of metabolic regulation in aging. Metabolites 2015; 5:232-51. [PMID: 25923415 PMCID: PMC4495371 DOI: 10.3390/metabo5020232] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 12/20/2022] Open
Abstract
The underlying cellular mechanisms that characterize aging are complex and multifaceted. However, it is emerging that aging could be regulated by two distinct metabolic hubs. These hubs are the pathway defined by the mammalian target of rapamycin (mTOR) and that defined by the NAD+-dependent deacetylase enzyme, SIRT1. Recent experimental evidence suggests that there is crosstalk between these two important pathways; however, the mechanisms underpinning their interaction(s) remains poorly understood. In this review, we propose using computational modelling in tandem with experimentation to delineate the mechanism(s). We briefly discuss the main modelling frameworks that could be used to disentangle this relationship and present a reduced reaction pathway that could be modelled. We conclude by outlining the limitations of computational modelling and by discussing opportunities for future progress in this area.
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Affiliation(s)
- Mark T Mc Auley
- Faculty of Science & Engineering, University of Chester, Thornton Science Park, CH2 4NU, UK.
| | - Kathleen M Mooney
- Faculty of Health and Social Care, Edge Hill University, Ormskirk, Lancashire, L39 4QP, UK.
| | - Peter J Angell
- School of Health Sciences, Liverpool Hope University, Taggart Avenue, Liverpool, L16 9JD, UK.
| | - Stephen J Wilkinson
- Faculty of Science & Engineering, University of Chester, Thornton Science Park, CH2 4NU, UK.
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Hartcher KM, Tran KTN, Wilkinson SJ, Hemsworth PH, Thomson PC, Cronin GM. The effects of environmental enrichment and beak-trimming during the rearing period on subsequent feather damage due to feather-pecking in laying hens. Poult Sci 2015; 94:852-9. [PMID: 25717088 DOI: 10.3382/ps/pev061] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2015] [Indexed: 11/20/2022] Open
Abstract
This experiment investigated effects of environmental enrichment and beak-trimming during the rearing period on behavior in rearing and plumage damage later in life. Treatments were applied in a 2 × 2 factorial arrangement. Half of the birds were beak-trimmed at 1 d of age using an infra-red laser. A follow-up light-trim was performed at 11 wk of age with a hot blade. Environmental enrichment consisted of pecking strings, whole oats in the litter, and greater litter depth. Sixteen pens of 50 ISA Brown laying hens were used. Four pullets were selected from each pen as focal birds and observed in their home pens between 3 and 14 wk of age. Plumage damage was scored at the end of the experiment in wk 43. Beak-trimmed birds performed less ground-pecking (P = 0.003), less severe feather-pecking (P = 0.021) and more gentle feather-pecking (P = 0.018) than their non-trimmed counterparts during the rearing period. These birds also exhibited less feather damage in wk 43 (P < 0.001). The results indicate that gentle feather-pecking during rearing is not related to plumage damage when older. Additionally, higher rates of ground-pecking and severe feather-pecking during rearing may be predictive of plumage damage later in life. There was no effect of enrichment on plumage damage. It was concluded that while there was no effect on enrichment, beak-trimming appeared to be effective in reducing plumage damage in wk 43.
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Affiliation(s)
- K M Hartcher
- Poultry Research Foundation, Faculty of Veterinary Science, The University of Sydney, Camden NSW 2570, Australia Poultry CRC, PO Box U242, University of New England, Armidale, NSW 2351, Australia
| | - K T N Tran
- Poultry Research Foundation, Faculty of Veterinary Science, The University of Sydney, Camden NSW 2570, Australia
| | - S J Wilkinson
- Poultry Research Foundation, Faculty of Veterinary Science, The University of Sydney, Camden NSW 2570, Australia
| | - P H Hemsworth
- Animal Welfare Science Centre, The University of Melbourne, Parkville, VIC 3010, Australia
| | - P C Thomson
- Poultry Research Foundation, Faculty of Veterinary Science, The University of Sydney, Camden NSW 2570, Australia
| | - G M Cronin
- Poultry Research Foundation, Faculty of Veterinary Science, The University of Sydney, Camden NSW 2570, Australia
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Prest JE, Treves Brown BJ, Fielden PR, Wilkinson SJ, Hawkes JJ. Scaling-up ultrasound standing wave enhanced sedimentation filters. Ultrasonics 2015; 56:260-270. [PMID: 25193111 DOI: 10.1016/j.ultras.2014.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 08/04/2014] [Accepted: 08/05/2014] [Indexed: 06/03/2023]
Abstract
Particle concentration and filtration is a key stage in a wide range of processing industries and also one that can be present challenges for high throughput, continuous operation. Here we demonstrate some features which increase the efficiency of ultrasound enhanced sedimentation and could enable the technology the potential to be scaled up. In this work, 20 mm piezoelectric plates were used to drive 100 mm high chambers formed from single structural elements. The coherent structural resonances were able to drive particles (yeast cells) in the water to nodes throughout the chamber. Ultrasound enhanced sedimentation was used to demonstrate the efficiency of the system (>99% particle clearance). Sub-wavelength pin protrusions were used for the contacts between the resonant chamber and other elements. The pins provided support and transferred power, replacing glue which is inefficient for power transfer. Filtration energies of ∼4 J/ml of suspension were measured. A calculation of thermal convection indicates that the circulation could disrupt cell alignment in ducts >35 mm high when a 1K temperature gradient is present; we predict higher efficiencies when this maximum height is observed. For the acoustic design, although modelling was minimal before construction, the very simple construction allowed us to form 3D models of the nodal patterns in the fluid and the duct structure. The models were compared with visual observations of particle movement, Chladni figures and scanning laser vibrometer mapping. This demonstrates that nodal planes in the fluid can be controlled by the position of clamping points and that the contacts could be positioned to increase the efficiency and reliability of particle manipulations in standing waves.
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Affiliation(s)
- Jeff E Prest
- Department of Chemistry Faraday Building, Lancaster University, Bailrigg, Lancaster LA1 4YB, UK
| | - Bernard J Treves Brown
- Manchester Institute of Biotechnology, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Peter R Fielden
- Department of Chemistry Faraday Building, Lancaster University, Bailrigg, Lancaster LA1 4YB, UK
| | - Stephen J Wilkinson
- University of Chester Faculty of Science and Engineering, Thornton Science Park, CH2 4NU, UK
| | - Jeremy J Hawkes
- Manchester Institute of Biotechnology, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.
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Li W, Angel R, Kim SW, Jiménez-Moreno E, Proszkowiec-Weglarz M, Iglesias BF, Wilkinson SJ, Cowieson AJ. Assessment of postcrumble addition of limestone and calcium-specific appetite in broilers during the starter phase. Poult Sci 2014; 93:2578-91. [PMID: 25085931 PMCID: PMC4988541 DOI: 10.3382/ps.2014-04081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A study was done to determine whether broilers can regulate Ca intake when limestone is provided separately or mixed with a crumbled feed of variable Ca and P content, and the influence of this on performance and apparent ileal digestibility (AID) of Ca and P (AIDP). Twelve crumbled diets were fed from 10 to 20 d of age (8 replicates, 8 broilers/replicate). Diets A to D contained 0.28% nonphytate P (nPP) and 0.27, 0.51, 0.77, and 1.02% Ca, respectively. Diets E to H contained 0.48% nPP and 0.41, 0.51, 0.77, and 1.02% Ca, respectively. A large particle size limestone was mixed manually to the crumbled diet on a daily basis to achieve 1.02% total Ca in diets A to H. Diets I to L had the same Ca and nPP as diets A to D, but limestone was provided in a separate feeder to assess spatial importance of limestone supply. Limestone consumption, provided in a separate feeder, decreased as Ca concentration increased in the crumble diet (P < 0.05). Calcium intake increased as Ca concentration in crumbled diets increased (P < 0.05). Increased tibia ash and decreased AIDP were observed as Ca intake increased (P < 0.05). When limestone was added to diets containing 0.28% nPP postcrumble, Ca intake (6.38 g/bird), tibia ash (717 mg/bone), and AIDP (39.78%) were not affected by crumbled diet Ca concentration or consumed Ca. Broilers fed diets containing 0.48% nPP and limestone mixed with the crumble, Ca intake changed (5.96, 6.93, 6.59, and 6.04 g/bird for crumble diet with 0.41, 0.51, 0.77, and 1.02% Ca, respectively). Increasing Ca concentration in the crumble from 0.41 to 1.02% resulted in greater tibia ash (875 mg/bone) but lower AIDP (P < 0.05), although Ca intake was similar. In conclusion, when large particle size limestone was provided ad libitum, the ability of broilers to select for Ca was not sufficient to meet their requirement when crumble Ca was less than 0.77%. The AIDP was highest in birds fed the 0.27% Ca concentration diet.
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Affiliation(s)
- W Li
- Department of Animal and Avian Sciences, University of Maryland, College Park 20740
| | - R Angel
- Department of Animal and Avian Sciences, University of Maryland, College Park 20740
| | - S-W Kim
- Department of Animal and Avian Sciences, University of Maryland, College Park 20740
| | - E Jiménez-Moreno
- Department of Animal and Avian Sciences, University of Maryland, College Park 20740
| | | | - B F Iglesias
- Instituto Nacional de Tecnología Agropecuaria, Pergamino, 1425, Argentina
| | - S J Wilkinson
- Poultry Research Foundation, Faculty of Veterinary Science, the University of Sydney, Sydney, 2006, Australia
| | - A J Cowieson
- Poultry Research Foundation, Faculty of Veterinary Science, the University of Sydney, Sydney, 2006, Australia
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Wilkinson SJ, Bradbury EJ, Thomson PC, Bedford MR, Cowieson AJ. Nutritional geometry of calcium and phosphorus nutrition in broiler chicks. The effect of different dietary calcium and phosphorus concentrations and ratios on nutrient digestibility. Animal 2014; 8:1080-8. [PMID: 24840343 DOI: 10.1017/s1751731114001049] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A total of 600 Ross 308-day-old male broiler chicks were used in a 28 day digestibility study to investigate the interaction between dietary calcium (Ca) and non-phytate phosphorus (nPP) on the digestibility of minerals and amino acids. Diets were formulated to be nutritionally adequate except for Ca and nPP. Fifteen mash diets based on corn and soya bean meal with varying concentrations of Ca (6.4 to 12.0 g/kg) and nPP (2.4 to 7.0 g/kg) were used. Diets were clustered around total densities of Ca and nPP of 12, 13.5 or 15.0 (g/kg) and within each density, a range of five Ca : nPP ratios (1.14 : 1, 1.5 : 1, 2.0 : 1, 2.75 : 1 and 4.0 : 1) were fed. Birds had free access to feed and water throughout the study. At day 28, birds were euthanised for the determination of apparent ileal mineral and amino acid digestibility. Data were modelled in R version 2.15 using a linear mixed-effects model and interrogation of the data was performed by fitting a low order polynomial function. At high Ca concentrations, increasing nPP led to an increase in the apparent digestibility of minerals. Apparent ileal digestibility of phosphorus (P) was enhanced with increasing dietary nPP up to 5.5 g/kg beyond which no improvements were found. Maximal Ca digestibility was found in diets with >8.0 g/kg Ca with concomitant low concentrations of nPP. Diets with a broader Ca : nPP ratio improved the digestibility of Ca but were deleterious to the digestibility of P. In this study, apparent digestibility of amino acids was broadly unaffected by dietary Ca and nPP concentrations. However, interactions between Ca and nPP were observed for the digestibility of glutamine, tyrosine and methionine (all P<0.001). Nitrogen digestibility showed discrete optima around 10.0 and 5.0 g/kg nPP and Na digestibility was maximised around 8 to 9.0 g/kg Ca and 4.5 to 5.4 g/kg nPP. These data show that the ratio of Ca : nPP is more influential to mineral digestibility than the absolute dietary concentration of each macro mineral.
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Affiliation(s)
- S J Wilkinson
- 1Poultry Research Foundation,The University of Sydney, Faculty of Veterinary Science,425 Werombi Road,Camden,NSW 2570,Australia
| | - E J Bradbury
- 1Poultry Research Foundation,The University of Sydney, Faculty of Veterinary Science,425 Werombi Road,Camden,NSW 2570,Australia
| | - P C Thomson
- 2Faculty of Veterinary Science,The University of Sydney,Camden,NSW 2570,Australia
| | - M R Bedford
- 3AB Vista Feed Ingredients,Marlborough,Wiltshire,SN84AN,UK
| | - A J Cowieson
- 1Poultry Research Foundation,The University of Sydney, Faculty of Veterinary Science,425 Werombi Road,Camden,NSW 2570,Australia
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Pybus LP, Dean G, West NR, Smith A, Daramola O, Field R, Wilkinson SJ, James DC. Model-directed engineering of “difficult-to-express” monoclonal antibody production by Chinese hamster ovary cells. Biotechnol Bioeng 2013; 111:372-85. [DOI: 10.1002/bit.25116] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 08/03/2013] [Accepted: 09/09/2013] [Indexed: 12/13/2022]
Affiliation(s)
- Leon P. Pybus
- ChELSI Institute; Department of Chemical and Biological Engineering; University of Sheffield; Mappin Street Sheffield S1 3JD UK
| | - Greg Dean
- Cell Sciences; BioPharmaceutical Development, MedImmune, Granta Park; Cambridge UK
| | - Nathan R. West
- ChELSI Institute; Department of Chemical and Biological Engineering; University of Sheffield; Mappin Street Sheffield S1 3JD UK
| | - Andrew Smith
- Cell Sciences; BioPharmaceutical Development, MedImmune, Granta Park; Cambridge UK
| | - Olalekan Daramola
- Cell Sciences; BioPharmaceutical Development, MedImmune, Granta Park; Cambridge UK
| | - Ray Field
- Cell Sciences; BioPharmaceutical Development, MedImmune, Granta Park; Cambridge UK
| | - Stephen J. Wilkinson
- ChELSI Institute; Department of Chemical and Biological Engineering; University of Sheffield; Mappin Street Sheffield S1 3JD UK
| | - David C. James
- ChELSI Institute; Department of Chemical and Biological Engineering; University of Sheffield; Mappin Street Sheffield S1 3JD UK
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Bratuskins PA, McGarry HA, Wilkinson SJ. Sexual harassment of Australian female general practitioners by patients. Med J Aust 2013; 199:454. [DOI: 10.5694/mja12.11855] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 08/15/2013] [Indexed: 11/17/2022]
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Davies SL, O'Callaghan PM, McLeod J, Pybus LP, Sung YH, Rance J, Wilkinson SJ, Racher AJ, Young RJ, James DC. Impact of gene vector design on the control of recombinant monoclonal antibody production by Chinese hamster ovary cells. Biotechnol Prog 2011; 27:1689-99. [PMID: 21882365 DOI: 10.1002/btpr.692] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 05/17/2011] [Indexed: 01/17/2023]
Abstract
In this study, we systematically compare two vector design strategies for recombinant monoclonal antibody (Mab) synthesis by Chinese hamster ovary (CHO) cells; a dual open reading frame (ORF) expression vector utilizing separate cytomegalovirus (CMV) promoters to drive heavy chain (HC) and light chain (LC) expression independently, and a single ORF vector design employing a single CMV promoter to drive HC and LC polypeptide expression joined by a foot and mouth disease virus F2A polypeptide self-cleaving linker sequence. Initial analysis of stable transfectants showed that transfectants utilizing the single ORF vector designs exhibited significantly reduced Mab production. We employed an empirical modeling strategy to quantitatively describe the cellular constraints on recombinant Mab synthesis in all stable transfectants. In all transfectants, an intracellular molar excess of LC polypeptide over HC polypeptide was observed. For CHO cells transfected with the single ORF vectors, model-predicted, and empirical intracellular intermediate levels could only be reconciled by inclusion of nascent HC polypeptide degradation. Whilst a local sensitivity analysis showed that qMab of all transfectants was primarily constrained by recombinant mRNA translation rate, our data indicated that all single ORF transfectants exhibited a reduced level of recombinant gene transcription and that Mab folding and assembly reactions generically exerted greater control over qMab. We infer that the productivity of single ORF transfectants is limited by ER processing/degradation "capacity" which sets a limit on transcriptional input. We conclude that gene vector design for oligomeric recombinant proteins should be based on an understanding of protein-specific synthetic kinetics rather than polypeptide stoichiometry.
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Affiliation(s)
- Sarah L Davies
- Dept. of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, U.K
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McLeod J, O'Callaghan PM, Pybus LP, Wilkinson SJ, Root T, Racher AJ, James DC. An empirical modeling platform to evaluate the relative control discrete CHO cell synthetic processes exert over recombinant monoclonal antibody production process titer. Biotechnol Bioeng 2011; 108:2193-204. [PMID: 21445882 DOI: 10.1002/bit.23146] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 01/31/2011] [Accepted: 03/14/2011] [Indexed: 12/16/2022]
Abstract
In this study we have combined empirically derived mathematical models of intracellular Mab synthesis to quantitatively compare the degree to which individual cellular processes limit recombinant IgG(4) monoclonal antibody production by GS-CHO cells throughout a state-of-the-art industrial fed-batch culture process. Based on the calculation of a production process control coefficient for each stage of the intracellular Mab synthesis and secretion pathway, we identified the major cellular restrictions on Mab production throughout the entire culture process to be recombinant heavy chain gene transcription and heavy chain mRNA translation. Surprisingly, despite a substantial decline in the rate of cellular biomass synthesis during culture, with a concomitant decline in the calculated rate constants for energy-intensive Mab synthetic processes (Mab folding/assembly and secretion), these did not exert significant control of Mab synthesis at any stage of production. Instead, cell-specific Mab production was maintained by increased Mab gene transcription which offset the decline in cellular biosynthetic rates. Importantly, this study shows that application of this whole-process predictive modeling strategy should rationally precede and inform cell engineering approaches to increase production of a recombinant protein by a mammalian host cell--where control of productivity is inherently protein product and cell line specific.
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Affiliation(s)
- Jane McLeod
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield S1 3JD, UK
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Kilner J, Corfe BM, Wilkinson SJ. Modelling the microtubule: towards a better understanding of short-chain fatty acid molecular pharmacology. Mol BioSyst 2011; 7:975-83. [DOI: 10.1039/c0mb00281j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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O'Callaghan PM, McLeod J, Pybus LP, Lovelady CS, Wilkinson SJ, Racher AJ, Porter A, James DC. Cell line-specific control of recombinant monoclonal antibody production by CHO cells. Biotechnol Bioeng 2010; 106:938-51. [DOI: 10.1002/bit.22769] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sheach LA, Adeney EM, Kucukmetin A, Wilkinson SJ, Fisher AD, Elattar A, Robson CN, Edmondson RJ. Androgen-related expression of G-proteins in ovarian cancer. Br J Cancer 2009; 101:498-503. [PMID: 19623182 PMCID: PMC2720237 DOI: 10.1038/sj.bjc.6605153] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Epidemiological and in vitro data implicate androgens in the aetiology of ovarian cancer, but the mechanisms by which this is mediated are unclear. In this study, we wished to examine the effects of androgens on gene expression in ovarian cancer. METHODS The expression of androgen receptor (AR) in OVCAR3 and OSEC2 cells was confirmed using immunoblotting and response to androgens was measured using flow cytometric assessment of S-phase fraction. The differential gene expression between androgen stimulated and unstimulated OVCAR3 ovarian cancer cells was examined with a cDNA microarray. The upregulation of a subset of these genes was then confirmed with reverse transcriptase PCR in both OVCAR3 and OSEC2, an ovarian epithelial cell line. Finally, the clinical significance of this upregulation was investigated by examining the expression of Rab25 and Rab35, two G-protein-related molecules in an ovarian cancer tissue microarray (TMA). RESULTS OVCAR3 and OSEC2 cells were shown to express the AR and showed an increase in S-phase fraction in response to androgen treatment. Treatment of OVCAR3 cells with androgen resulted in a significant upregulation of 121 genes. These findings were confirmed for a subset of seven monomeric G-protein-related genes in both OVCAR3 and OSEC2 cells. After staining for Rab25 and Rab35, the majority of TMA sections examined showed expression for Rab25 (92%) and Rab35 (95%). The expression of Rab25 correlated with histological grade, and expression was higher in endometrioid (median histoscore 10.5) than serous (7.5) or mucinous (5.3) tumours. The expression of Rab25 correlated positively with AR expression supporting its role as an androgen responsive gene in ovarian cancer. CONCLUSIONS These results suggest that androgens can effect expression of the oncogenic GTPases in ovarian cancer. We propose that the androgen responsive Rab35 may have clinical importance as a biomarker of AR function.
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Affiliation(s)
- L A Sheach
- Northern Institute for Cancer Research, Newcastle University, Newcastle, UK
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Abstract
We have built a detailed kinetic model of translation initiation in yeast and have used a novel approach to determine the flux controlling steps based on limited experimental data. An efficient parameter estimation method was adapted in order to fit the most uncertain parameters (rate constants) to in vivo measurements in yeast. However, it was found that there were many other sets of plausible parameter values that also gave a good fit of the model to the data. We therefore used random sampling of this uncertain parameter space to generate a large number of diverse fitted parameter sets. A compact characterization of these parameter sets was provided by considering flux control. In particular, we suggest that the rate of translation initiation is most strongly influenced by one of two reactions: either the guanine nucleotide exchange reaction involving initiation factors eIF2 and eIF2B or the assembly of the multifactor complex from its constituent protein/tRNA containing complexes. It is hoped that the approach presented in this paper will add to our understanding of translation initiation pathway and can be used to identify key system-level properties of other biochemical processes.
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Affiliation(s)
- Richard J Dimelow
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M1 7DN, UK.
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Wilkinson SJ, Kucukmetin A, Cross P, Darby S, Gnanapragasam VJ, Calvert AH, Robson CN, Edmondson RJ. Expression of gonadotrophin releasing hormone receptor I is a favorable prognostic factor in epithelial ovarian cancer. Hum Pathol 2008; 39:1197-204. [PMID: 18495208 DOI: 10.1016/j.humpath.2007.12.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2007] [Revised: 12/10/2007] [Accepted: 12/20/2007] [Indexed: 10/22/2022]
Abstract
The majority of epithelial ovarian cancers originate in the ovarian surface epithelium. The ovarian surface epithelium is a hormonally responsive tissue, and hormones are thought to play a key role in the development of this type of cancer. Gonadotrophin releasing hormone II is one of 2 isoforms which are thought to act through gonadotrophin releasing hormone receptor I, and gonadotrophin releasing hormone II has been shown to cause growth inhibition of cultured ovarian surface epithelium. The aim of this study was to investigate the expression levels and prognostic significance of gonadotrophin releasing hormone II and the gonadotrophin releasing hormone receptor I in epithelial ovarian cancer. Gonadotrophin releasing hormone II and gonadotrophin releasing hormone receptor I messenger RNA expression was examined in 23 cancers and 7 normal ovarian surface epithelium samples by quantitative real time polymerase chain reaction. An ovarian cancer tissue microarray containing 139 cases was constructed and immunohistochemical analysis of gonadotrophin releasing hormone II and gonadotrophin releasing hormone receptor I protein expression was performed and correlated with clinical outcome data. Gonadotrophin releasing hormone II messenger RNA expression was lower in cancer samples compared to normal ovarian surface epithelium samples (P < .05). Gonadotrophin releasing hormone II protein expression correlated with histologic subtype (25% serous versus 45% nonserous, P < .05) but not with overall survival. Gonadotrophin releasing hormone receptor I messenger RNA expression was highest in serous tumors when compared to non serous (P < .05) and normal tissue (P < .001). Expression of the gonadotrophin releasing hormone receptor I protein was also found to correlate with patient survival (P < .05). We have demonstrated gonadotrophin releasing hormone II and its receptor, gonadotrophin releasing hormone receptor I, are present in clinical ovarian samples, and that gonadotrophin releasing hormone receptor I protein expression is a favorable prognostic factor, suggesting these proteins play an important role in the development of epithelial ovarian cancer.
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Affiliation(s)
- S J Wilkinson
- Northern Institute for Cancer Research, Newcastle University, NE2 4HH Newcastle, UK.
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Westerhoff HV, Kolodkin A, Conradie R, Wilkinson SJ, Bruggeman FJ, Krab K, van Schuppen JH, Hardin H, Bakker BM, Moné MJ, Rybakova KN, Eijken M, van Leeuwen HJP, Snoep JL. Systems biology towards life in silico: mathematics of the control of living cells. J Math Biol 2008; 58:7-34. [PMID: 18278498 DOI: 10.1007/s00285-008-0160-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Revised: 01/11/2008] [Indexed: 12/13/2022]
Abstract
Systems Biology is the science that aims to understand how biological function absent from macromolecules in isolation, arises when they are components of their system. Dedicated to the memory of Reinhart Heinrich, this paper discusses the origin and evolution of the new part of systems biology that relates to metabolic and signal-transduction pathways and extends mathematical biology so as to address postgenomic experimental reality. Various approaches to modeling the dynamics generated by metabolic and signal-transduction pathways are compared. The silicon cell approach aims to describe the intracellular network of interest precisely, by numerically integrating the precise rate equations that characterize the ways macromolecules' interact with each other. The non-equilibrium thermodynamic or 'lin-log' approach approximates the enzyme rate equations in terms of linear functions of the logarithms of the concentrations. Biochemical Systems Analysis approximates in terms of power laws. Importantly all these approaches link system behavior to molecular interaction properties. The latter two do this less precisely but enable analytical solutions. By limiting the questions asked, to optimal flux patterns, or to control of fluxes and concentrations around the (patho)physiological state, Flux Balance Analysis and Metabolic/Hierarchical Control Analysis again enable analytical solutions. Both the silicon cell approach and Metabolic/Hierarchical Control Analysis are able to highlight where and how system function derives from molecular interactions. The latter approach has also discovered a set of fundamental principles underlying the control of biological systems. The new law that relates concentration control to control by time is illustrated for an important signal transduction pathway, i.e. nuclear hormone receptor signaling such as relevant to bone formation. It is envisaged that there is much more Mathematical Biology to be discovered in the area between molecules and Life.
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Affiliation(s)
- Hans V Westerhoff
- Molecular Cell Physiology, Institute of Molecular Cell Biology, Netherlands Institute for Systems Biology, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
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Bevilacqua A, Wilkinson SJ, Dimelow R, Murabito E, Rehman S, Nardelli M, van Eunen K, Rossell S, Bruggeman FJ, Blüthgen N, De Vos D, Bouwman J, Bakker BM, Westerhoff HV. Vertical systems biology: from DNA to flux and back. SEB Exp Biol Ser 2008; 61:65-91. [PMID: 18709737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Annamaria Bevilacqua
- Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, UK
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Wilkinson SJ, Benson N, Kell DB. Proximate parameter tuning for biochemical networks with uncertain kinetic parameters. ACTA ACUST UNITED AC 2008; 4:74-97. [DOI: 10.1039/b707506e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ihekwaba AEC, Wilkinson SJ, Waithe D, Broomhead DS, Li P, Grimley RL, Benson N. Bridging the gap between in silico and cell-based analysis of the nuclear factor-kappaB signaling pathway by in vitro studies of IKK2. FEBS J 2007; 274:1678-90. [PMID: 17313484 DOI: 10.1111/j.1742-4658.2007.05713.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previously, we have shown by sensitivity analysis, that the oscillatory behavior of nuclear factor (NF-kappaB) is coupled to free IkappaB kinase-2 (IKK2) and IkappaBalpha(IkappaBalpha), and that the phosphorylation of IkappaBalpha by IKK influences the amplitude of NF-kappaB oscillations. We have performed further analyses of the behavior of NF-kappaB and its signal transduction network to understand the dynamics of this system. A time lapse study of NF-kappaB translocation in 10,000 cells showed discernible oscillations in levels of nuclear NF-kappaB amongst cells when stimulated with interleukin (IL-1alpha), which suggests a small degree of synchronization amongst the cell population. When the kinetics for the phosphorylation of IkappaBalpha by IKK were measured, we found that the values for the affinity and catalytic efficiency of IKK2 for IkappaBalpha were dependent on assay conditions. The application of these kinetic parameters in our computational model of the NF-kappaB pathway resulted in significant differences in the oscillatory patterns of NF-kappaB depending on the rate constant value used. Hence, interpretation of in silico models should be made in the context of this uncertainty.
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Abstract
In our research programme small angle x-ray scattering (SAXS) is used to provide information on the axial arrangement of collagen molecules as well as data about the state of other components of the extra cellular matrix (ECM) in human tissues. Derivation of parameters to describe and simplify the data is required for much of the SAXS patterns analysis. A method is presented here to achieve function fitting to collagen diffraction peaks along with a representation of the underlying diffuse scatter. A simple model was used which proved reliable in fitting a variety of 2D diffraction patterns. The logarithm of the scatter intensity over the area of the scatter image was taken to reduce the range and improve fitting accuracy. Our model was then used to fit the log data. The model consisted of a radial exponential diffuse scatter component added to a specified number of Gaussian peaks. In 2D the peak model is toroidal, each component being rotated about a common specified centre. Initial search parameters from a 1D averaged sector were supplied to the iterative 2D fitting routine. With the aid of data weighting and basic wavelet filtering, successful and reliable fitting of a specified 2D model to real data is achievable. The process is easily automated. Multiple SAXS patterns can be fitted without operator intervention. As described the model is simple enough to converge rapidly and yet allows image data to be parameterized to a form suitable for extracting the requisite information. The fitting method is flexible enough to be extended to achieve a more comprehensive and complex pattern fitting in two dimensions if this turns out to be necessary. It is our intention to implement orientation distribution functions in the near future by including an angular scaling factor.
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Affiliation(s)
- S J Wilkinson
- Department of Materials and Medical Sciences, Cranfield University, Shrivenham, Swindon, Wiltshire SN6 8LA, UK
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Round AR, Wilkinson SJ, Hall CJ, Rogers KD, Glatter O, Wess T, Ellis IO. A preliminary study of breast cancer diagnosis using laboratory based small angle x-ray scattering. Phys Med Biol 2005; 50:4159-68. [PMID: 16177537 DOI: 10.1088/0031-9155/50/17/017] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Breast tissue collected from tumour samples and normal tissue from bi-lateral mastectomy procedures were examined using small angle x-ray scattering. Previous work has indicated that breast tissue disease diagnosis could be performed using small angle x-ray scattering (SAXS) from a synchrotron radiation source. The technique would be more useful to health services if it could be made to work using a conventional x-ray source. Consistent and reliable differences in x-ray scatter distributions were observed between samples from normal and tumour tissue samples using the laboratory based 'SAXSess' system. Albeit from a small number of samples, a sensitivity of 100% was obtained. This result encourages us to pursue the implementation of SAXS as a laboratory based diagnosis technique.
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Affiliation(s)
- A R Round
- Daresbury Laboratories, Warrington, WA4 4AD, UK.
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Abstract
This article discusses the challenges overcome during the development of a blend-sampling technique and the successful validation of the blending operation for a tablet dosage form containing 2% active ingredient. Content uniformity results are discussedfor three pilot-scale (15-kg) and seven commercial-scale (150-kg) batches of tablets. Blend and core content uniformity data from the pilot-scale batches were acceptable. For the initial commercial-scale batches, although the tablet core content uniformity data were acceptable, the blend uniformity results were poor. The blend data for these batches had very high mean values, but acceptable relative standard deviations (RSDs). This suggested that the drug was being preferentially sampled by the thief but in a consistent, reproducible manner. Extensive testing was performed on a commercial-scale development batch to identify potential causes of sampling error. The results of this testing helped define the blend-sampling technique and strategy used to validate the mixing operation.
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Affiliation(s)
- T P Garcia
- Pfizer, Incorporated, Eastern Point Road, Groton, CT 06340, USA
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Abstract
STUDY DESIGN Mechanical testing of cadaveric lumbar spines and dual energy radiograph absorptiometry scanning were performed. OBJECTIVES To devise a technique to measure the strength of lumbar spinous processes and to determine the bone mineral density of the vertebrae used. SUMMARY OF BACKGROUND DATA The spinous process has been identified as the weakest part of the anatomy to which a flexible fixation device can be attached. It was unknown if the spinous processes could withstand the forces applied by the device. METHODS A hook was fitted to the spinous process of 32 lumbar vertebrae. A custom-built rig was designed to secure a vertebra to a materials testing machine. A loop of cord was passed over a bar mounted on the crosshead of the machine and around the two bollards of the hook. As the crosshead was raised, a tension was applied to the cord. Each vertebra was tested to failure. The bone mineral density of each vertebra was then measured using dual energy radiograph absorptiometry. RESULTS Failure of the specimens occurred by failure of the spinous process, pedicles, or vertebral body. The logarithm (base 10) of the load (N) at which failure occurred was 2.53 +/- 0.3, which corresponded to a mean failure load of 339 N. The bone mineral density of each vertebral body varied between 0.263 and 0.997 g/cm2. A significant linear correlation was found between bone strength and bone mineral density (P < 0.0001). CONCLUSIONS Specimens with a bone mineral density in the range of 0.263-0.997 g/cm2 failed at a mean load of 339 N when the load was applied through the spinous process hook of a flexible fixation device.
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Affiliation(s)
- D E Shepherd
- Department of Biomedical Physics and Bioengineering, University of Aberdeen, United Kingdom.
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Burgess JR, Duffield A, Wilkinson SJ, Ware R, Greenaway TM, Percival J, Hoffman L. Two families with an autosomal dominant inheritance pattern for papillary carcinoma of the thyroid. J Clin Endocrinol Metab 1997; 82:345-8. [PMID: 9024215 DOI: 10.1210/jcem.82.2.3789] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Papillary carcinoma of the thyroid (PTC) is the most prevalent malignancy of the thyroid gland. Although the majority of lesions are sporadic tumors, an established relationship exists between familial adenomatous polyposis (FAP) and PTC. Moreover, some authors postulate the existence of familial PTC as a distinct entity. Evidence for this is limited, however, there being few well characterized descriptions of pedigrees with high prevalence of PTC. AIMS The objective of the present study was to examine an apparent heritable predisposition to PTC occurring in two Tasmanian families in which PTC occurs commonly. METHODS Pedigree charts were constructed for both families and the medical records of the members reviewed. RESULTS In Pedigree I, 7 of 25 members had PTC (6 of these had coexisting multinodular goiter (MNG), and 11 others had MNG. In Pedigree II, identical male twins and their daughters had PTC. CONCLUSIONS In both families there is evidence of autosomal dominant inheritance of PTC. The association of PTC with MNG suggests a possible role for MNG in tumor pathogenesis in hereditary PTC. The majority of the patients were diagnosed with PTC before commencement of prospective screening, indicating clinically relevant disease in the families described.
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Affiliation(s)
- J R Burgess
- Department of Diabetes and Endocrine Services, Royal Hobart Hospital, Tasmania, Australia
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Ramage AG, Wilkinson SJ. Evidence that different regional sympathetic outflows vary in their sensitivity to the sympathoinhibitory actions of putative 5-HT1A and alpha 2-adrenoceptor agonists in anaesthetized cats. Br J Pharmacol 1989; 98:1157-64. [PMID: 2575414 PMCID: PMC1854839 DOI: 10.1111/j.1476-5381.1989.tb12660.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
1. An investigation was carried out to determine whether the centrally acting hypotensive drugs whose mechanisms of action are due either to activation of 5-HT1A receptors (flesinoxan, 8-hydroxy-2-(di-n-propylamino)tetralin (8-OH-DPAT) and urapidil--also an alpha 1-adrenoceptor antagonist) or to activation of alpha 2-adrenoceptors (clonidine and moxonidine) cause differential sympathoinhibition. 2. Cats were anaesthetized with alpha-chloralose and simultaneous recordings were made of whole cardiac, splanchnic and renal nerve activity, blood pressure and heart rate. Cumulative dose-response (i.v.) curves were constructed in separate experiments for the above hypotensive agents on these parameters. 3. Renal nerve activity was found to be more sensitive to the sympathoinhibitory action of flesinoxan and 8-OH-DPAT when compared with cardiac nerve activity, whereas the reverse was observed for clonidine and moxonidine, cardiac being more sensitive than renal nerve activity. Splanchnic nerve activity was similarly affected by all drugs. Furthermore at the highest dose, all drugs tended to cause complete inhibition in all regional sympathetic nerve outflows. 4. Urapidil differed from all the above hypotensive drugs in that it caused a similar degree of sympathoinhibition in all sympathetic outflows at all doses. It is suggested that this may be due to the ability of urapidil to block central alpha 1-adrenoceptors in addition to stimulation of 5-HT1A receptors.
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Affiliation(s)
- A G Ramage
- Academic Department of Pharmacology, Royal Free Hospital School of Medicine, London
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Beard TC, Wilkinson SJ, Vial JH. Hazards of urinary alkalizing agents. Med J Aust 1988; 149:723. [PMID: 3200215 DOI: 10.5694/j.1326-5377.1988.tb120856.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Davies AD, Wilkinson SJ, Downes JJ, James O, Newton JT, Davies MG. Global ratings of stress in the elderly. Br J Clin Psychol 1988; 27:179-80. [PMID: 3395743 DOI: 10.1111/j.2044-8260.1988.tb00769.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The properties of four global ratings of life stress were investigated using data from 237 elderly subjects interviewed using the Brown & Harris life event and difficulties schedule. The global ratings had high one-year test-retest reliability and inter-rater reliability agreement. A summary measure of Adversity (based on contextual rating of all events and difficulties) may be reliably derived when a single index of life stress is desired. In the elderly sample Adversity was more closely related to chronic difficulties than to life-events.
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Affiliation(s)
- A D Davies
- Department of Psychology, University of Liverpool
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Corder R, Lowry PJ, Wilkinson SJ, Ramage AG. Comparison of the haemodynamic actions of neuropeptide Y, angiotensin II and noradrenaline in anaesthetised cats. Eur J Pharmacol 1986; 121:25-30. [PMID: 3754217 DOI: 10.1016/0014-2999(86)90388-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Blood pressure, heart rate, cardiac output, renal flow and femoral flow were recorded in open-chested anaesthetised cats. Dose-response curves were constructed for neuropeptide Y, angiotensin II and noradrenaline after pretreatment with atropine sulphate. Neuropeptide Y, on a molar basis, was 7 and 120 times less potent than noradrenaline and angiotensin, respectively, in producing a 50 mm Hg rise in mean arterial blood pressure. The pressor effect of neuropeptide Y was characterised by dose-dependent increases in total peripheral, renal and femoral resistance with little change in cardiac output. Neuropeptide Y had a similar potency to noradrenaline in causing these resistance changes. However, the pressor response to noradrenaline was associated with a dose-dependent increase in cardiac output. The pressor action of neuropeptide Y was not attenuated by adrenoceptor blockade by phenoxybenzamine (5 mg kg-1) and propranolol (1 mg kg-1).
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Abstract
The inter-rater reliability of Brown's measure of ongoing difficulties ('severity') is shown to be comparable with that of the measure of life events ('long-term threat') when using data from an elderly subject pool. Test-retest reliabilities for both the life event and difficulty measures are shown to be adequate if based on 'consensus' ratings. The question is raised of generalizability of the concepts of 'threat' and 'severity' across the lifespan.
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