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James ME, Allsopp RN, Groh JS, Kaur A, Wilkinson MJ, Ortiz-Barrientos D. Uncovering the genetic architecture of parallel evolution. Mol Ecol 2023; 32:5575-5589. [PMID: 37740681 DOI: 10.1111/mec.17134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 09/25/2023]
Abstract
Identifying the genetic architecture underlying adaptive traits is exceptionally challenging in natural populations. This is because associations between traits not only mask the targets of selection but also create correlated patterns of genomic divergence that hinder our ability to isolate causal genetic effects. Here, we examine the repeated evolution of components of the auxin pathway that have contributed to the replicated loss of gravitropism (i.e. the ability of a plant to bend in response to gravity) in multiple populations of the Senecio lautus species complex in Australia. We use a powerful approach which combines parallel population genomics with association mapping in a Multiparent Advanced Generation Inter-Cross (MAGIC) population to break down genetic and trait correlations to reveal how adaptive traits evolve during replicated evolution. We sequenced auxin and shoot gravitropism-related gene regions in 80 individuals from six natural populations (three parallel divergence events) and 133 individuals from a MAGIC population derived from two of the recently diverged natural populations. We show that artificial tail selection on gravitropism in the MAGIC population recreates patterns of parallel divergence in the auxin pathway in the natural populations. We reveal a set of 55 auxin gene regions that have evolved repeatedly during the evolution of the species, of which 50 are directly associated with gravitropism divergence in the MAGIC population. Our work creates a strong link between patterns of genomic divergence and trait variation contributing to replicated evolution by natural selection, paving the way to understand the origin and maintenance of adaptations in natural populations.
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Affiliation(s)
- Maddie E James
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Robin N Allsopp
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Jeffrey S Groh
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Avneet Kaur
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Melanie J Wilkinson
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
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2
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Wilkinson MJ, Yamashita R, James ME, Bally ISE, Dillon NL, Ali A, Hardner CM, Ortiz-Barrientos D. The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool. Sci Rep 2022; 12:20614. [PMID: 36450793 PMCID: PMC9712640 DOI: 10.1038/s41598-022-24800-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/21/2022] [Indexed: 12/11/2022] Open
Abstract
Genomic selection is a promising breeding technique for tree crops to accelerate the development of new cultivars. However, factors such as genetic structure can create spurious associations between genotype and phenotype due to the shared history between populations with different trait values. Genetic structure can therefore reduce the accuracy of the genotype to phenotype map, a fundamental requirement of genomic selection models. Here, we employed 272 single nucleotide polymorphisms from 208 Mangifera indica accessions to explore whether the genetic structure of the Australian mango gene pool explained variation in trunk circumference, fruit blush colour and intensity. Multiple population genetic analyses indicate the presence of four genetic clusters and show that the most genetically differentiated cluster contains accessions imported from Southeast Asia (mainly those from Thailand). We find that genetic structure was strongly associated with three traits: trunk circumference, fruit blush colour and intensity in M. indica. This suggests that the history of these accessions could drive spurious associations between loci and key mango phenotypes in the Australian mango gene pool. Incorporating such genetic structure in associations between genotype and phenotype can improve the accuracy of genomic selection, which can assist the future development of new cultivars.
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Affiliation(s)
- Melanie J Wilkinson
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Risa Yamashita
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Maddie E James
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ian S E Bally
- Queensland Department of Agriculture and Fisheries, Mareeba, QLD, 4880, Australia
| | - Natalie L Dillon
- Queensland Department of Agriculture and Fisheries, Mareeba, QLD, 4880, Australia
| | - Asjad Ali
- Queensland Department of Agriculture and Fisheries, Mareeba, QLD, 4880, Australia
| | - Craig M Hardner
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, 4072, Australia
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3
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James ME, Wilkinson MJ, Bernal DM, Liu H, North HL, Engelstädter J, Ortiz-Barrientos D. Phenotypic and genotypic parallel evolution in parapatric ecotypes of Senecio. Evolution 2021; 75:3115-3131. [PMID: 34687472 PMCID: PMC9299460 DOI: 10.1111/evo.14387] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 08/09/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022]
Abstract
The independent and repeated adaptation of populations to similar environments often results in the evolution of similar forms. This phenomenon creates a strong correlation between phenotype and environment and is referred to as parallel evolution. However, we are still largely unaware of the dynamics of parallel evolution, as well as the interplay between phenotype and genotype within natural systems. Here, we examined phenotypic and genotypic parallel evolution in multiple parapatric Dune‐Headland coastal ecotypes of an Australian wildflower, Senecio lautus. We observed a clear trait‐environment association in the system, with all replicate populations having evolved along the same phenotypic evolutionary trajectory. Similar phenotypes have arisen via mutational changes occurring in different genes, although many share the same biological functions. Our results shed light on how replicated adaptation manifests at the phenotypic and genotypic levels within populations, and highlight S. lautus as one of the most striking cases of phenotypic parallel evolution in nature.
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Affiliation(s)
- Maddie E James
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Melanie J Wilkinson
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Diana M Bernal
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Current Address: Biousos Neotropicales S.A.S, Bogotá, Colombia
| | - Huanle Liu
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Current Address: Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Henry L North
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Current Address: Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD, 4072, Australia
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4
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Vasudevan RS, Xu I, You H, Xu R, Taub PR, Wilkinson MJ. Lipid-lowering therapy is not intensified beyond 3-months if coronary angiography with fractional flow reserve (FFR) suggests non-obstructive coronary disease: a missed opportunity for prevention? Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.1253] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background/Introduction
Patients with non-obstructive CAD are at risk for future ASCVD events. Coronary angiography with FFR distinguishes obstructive from non-obstructive CAD, however, it is unknown how FFR assessment impacts subsequent lipid management in obstructive vs non-obstructive CAD.
Purpose
Examine patterns in intensification of lipid-lowering therapy after FFR assessment in those with obstructive vs non-obstructive CAD.
Methods
Records were reviewed from patients at a single institution who underwent FFR, instantaneous wave free ratio (iFR), or computed tomographic (CT)-FFR assessment between 2013–2020. Obstructive CAD was defined as presence of ≥1 lesion with FFR ≤0.8, iFR ≤0.89, or CT-FFR ≤0.8, or presence of obstructive CAD by visual assessment. The impact of obstructive vs non-obstructive CAD on the management of atherogenic lipids (LDL-C and non-HDL-C) after FFR was examined at 3, 6, and 12 months using Mann-Whitney U test.
Results
461 patients had obstructive CAD vs 338 with non-obstructive CAD. Most FFR, iFR, or CT-FFR assessments were performed for a non-ACS indication (n=628 (79%)). Mean (±SD) age was 66±11 yrs, with 248 (31%) women, and 658 (82%) white. Baseline LDL-C was similar in both groups: 2.2±1.1 mmol/L (obstructive CAD) and 2.1±0.9 mmol/L (non-obstructive CAD). Both groups had high baseline statin use (n=349 (76%) (obstructive CAD) vs n=241 (71%) (non-obstructive CAD)). At 3 months, mean LDL-C and non-HDL-C decreased in both those with obstructive (LDL-C −0.4 mmol/L, non-HDL-C −0.4 mmol/L) and non-obstructive CAD (LDL-C −0.3 mmol/L, non-HDL-C −0.4 mmol/L) (p>0.05), with a similar number of new statins initiated in each group. However, at 6 months, LDL-C and non-HDL-C increased in those with non-obstructive CAD (LDL-C +0.2 mmol/L, non-HDL-C +0.4 mmol/L), while atherogenic lipids further decreased in those with obstructive CAD (LDL-C −0.1 mmol/L (p=0.011), non-HDL-C −0.1 mmol/L (p=0.048)). Compared to non-obstructive CAD, there were more statins initiated by 6 months in those with obstructive CAD, although not statistically significant. At 12 months, LDL-C remained significantly lower in those with obstructive CAD compared to those with non-obstructive CAD (Figure, Table).
Conclusions
FFR assessment appears to prompt short-term intensification of lipid-lowering therapy in both those with obstructive and non-obstructive CAD (i.e. over 3 months), but this favorable effect on atherogenic lipids is lost in those with non-obstructive CAD by 6 and 12 months. Those with non-obstructive CAD are likely to benefit from long-term intensification of atherogenic lipid-lowering therapy to prevent ASCVD events, and therefore efforts should be made to maintain intensification of lipid-lowering therapy beyond 3 months in all patients undergoing FFR assessment.
Funding Acknowledgement
Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): Amgen Investigator Initiated Study
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Affiliation(s)
- R S Vasudevan
- University of California San Diego, San Diego, United States of America
| | - I Xu
- University of California San Diego, San Diego, United States of America
| | - H You
- University of California San Diego, San Diego, United States of America
| | - R Xu
- University of California San Diego, San Diego, United States of America
| | - P R Taub
- University of California San Diego, San Diego, United States of America
| | - M J Wilkinson
- University of California San Diego, San Diego, United States of America
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5
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Wilkinson MJ, Snow H, Downey K, Thomas K, Riddell A, Francis N, Strauss DC, Hayes AJ, Smith MJF, Messiou C. CT diagnosis of ilioinguinal lymph node metastases in melanoma using radiological characteristics beyond size and asymmetry. BJS Open 2021; 5:6104886. [PMID: 33609385 PMCID: PMC7893466 DOI: 10.1093/bjsopen/zraa005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 08/27/2020] [Indexed: 11/23/2022] Open
Abstract
Background Diagnosis of lymph node (LN) metastasis in melanoma with non-invasive methods is challenging. The aim of this study was to evaluate the diagnostic accuracy of six LN characteristics on CT in detecting melanoma-positive ilioinguinal LN metastases, and to determine whether inguinal LN characteristics can predict pelvic LN involvement. Methods This was a single-centre retrospective study of patients with melanoma LN metastases at a tertiary cancer centre between 2008 and 2016. Patients who had preoperative contrast-enhanced CT assessment and ilioinguinal LN dissection were included. CT scans containing significant artefacts obscuring the pelvis were excluded. CT scans were reanalysed for six LN characteristics (extracapsular spread (ECS), minimum axis (MA), absence of fatty hilum (FH), asymmetrical cortical nodule (CAN), abnormal contrast enhancement (ACE) and rounded morphology (RM)) and compared with postoperative histopathological findings. Results A total of 90 patients were included. Median age was 58 (range 23–85) years. Eighty-eight patients (98 per cent) had pathology-positive inguinal disease and, of these, 45 (51 per cent) had concurrent pelvic disease. The most common CT characteristics found in pathology-positive inguinal LNs were MA greater than 10 mm (97 per cent), ACE (80 per cent), ECS (38 per cent) and absence of RM (38 per cent). In multivariable analysis, inguinal LN characteristics on CT indicative of pelvic disease were RM (odds ratio (OR) 3.3, 95 per cent c.i. 1.2 to 8.7) and ECS (OR 4.2, 1.6 to 11.3). Cloquet’s node is known to be a poor predictor of pelvic spread. Pelvic LN disease was present in 50 per cent patients, but only 7 per cent had a pathology-positive Cloquet’s node. Conclusion Additional CT radiological characteristics, especially ECS and RM, may improve diagnostic accuracy and aid clinical decisions regarding the need for inguinal or ilioinguinal dissection.
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Affiliation(s)
- M J Wilkinson
- Department of Academic Surgery, Sarcoma and Melanoma Unit, The Royal Marsden Hospital, London, UK
| | - H Snow
- Department of Academic Surgery, Sarcoma and Melanoma Unit, The Royal Marsden Hospital, London, UK
| | - K Downey
- Department of Radiology, The Royal Marsden Hospital, London, UK
| | - K Thomas
- Statistics Department, The Royal Marsden Hospital, London, UK
| | - A Riddell
- Department of Radiology, The Royal Marsden Hospital, London, UK
| | - N Francis
- Department of Pathology, The Royal Marsden Hospital (Honorary) and Charing Cross Hospital, London, UK
| | - D C Strauss
- Department of Academic Surgery, Sarcoma and Melanoma Unit, The Royal Marsden Hospital, London, UK
| | - A J Hayes
- Department of Academic Surgery, Sarcoma and Melanoma Unit, The Royal Marsden Hospital, London, UK.,Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - M J F Smith
- Department of Academic Surgery, Sarcoma and Melanoma Unit, The Royal Marsden Hospital, London, UK
| | - C Messiou
- Department of Radiology, The Royal Marsden Hospital, London, UK.,Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
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6
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Bott RK, Beckmann K, Zylstra J, Wilkinson MJ, Knight WRC, Baker CR, Kelly M, Maisey N, Qureshi A, Sevitt T, Van Hemelrijck M, Smyth EC, Allum WH, Lagergren J, Gossage JA, Cunningham D, Davies AR. Adjuvant therapy following oesophagectomy for adenocarcinoma in patients with a positive resection margin. Br J Surg 2020; 107:1801-1810. [PMID: 32990343 DOI: 10.1002/bjs.11864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/18/2020] [Accepted: 06/08/2020] [Indexed: 11/12/2022]
Abstract
BACKGROUND The role of adjuvant therapy in patients with oesophagogastric adenocarcinoma treated by neoadjuvant chemotherapy is contentious. In UK practice, surgical resection margin status is often used to classify patients for receiving adjuvant treatment. The aim of this study was to assess the survival benefit of adjuvant therapy in patients with positive (R1) resection margins. METHODS Two prospectively collected UK institutional databases were combined to identify eligible patients. Adjusted Cox regression analyses were used to compare overall and recurrence-free survival according to adjuvant treatment. Recurrence patterns were assessed as a secondary outcome. Propensity score-matched analysis was also performed. RESULTS Of 616 patients included in the combined database, 242 patients who had an R1 resection were included in the study. Of these, 112 patients (46·3 per cent) received adjuvant chemoradiotherapy, 46 (19·0 per cent) were treated with adjuvant chemotherapy and 84 (34·7 per cent) had no adjuvant treatment. In adjusted analysis, adjuvant chemoradiotherapy improved recurrence-free survival (hazard ratio (HR) 0·59, 95 per cent c.i. 0·38 to 0·94; P = 0·026), with a benefit in terms of both local (HR 0·48, 0·24 to 0·99; P = 0·047) and systemic (HR 0·56, 0·33 to 0·94; P = 0·027) recurrence. In analyses stratified by tumour response to neoadjuvant chemotherapy, non-responders (Mandard tumour regression grade 4-5) treated with adjuvant chemoradiotherapy had an overall survival benefit (HR 0·61, 0·38 to 0·97; P = 0·037). In propensity score-matched analysis, an overall survival benefit (HR 0·62, 0·39 to 0·98; P = 0·042) and recurrence-free survival benefit (HR 0·51, 0·30 to 0·87; P = 0·004) were observed for adjuvant chemoradiotherapy versus no adjuvant treatment. CONCLUSION Adjuvant therapy may improve overall survival and recurrence-free survival after margin-positive resection. This pattern seems most pronounced with adjuvant chemoradiotherapy in non-responders to neoadjuvant chemotherapy.
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Affiliation(s)
- R K Bott
- Department of Upper Gastrointestinal and General Surgery, St Thomas' Hospital.,School of Cancer and Pharmaceutical Sciences
| | - K Beckmann
- School of Cancer and Pharmaceutical Sciences, Translational Oncology and Urology Research, King's College London, London, UK.,University of South Australia Cancer Research Institute, University of South Australia, Adelaide, South Australia, Australia
| | - J Zylstra
- Department of Upper Gastrointestinal and General Surgery, St Thomas' Hospital
| | - M J Wilkinson
- Departments of Upper Gastrointestinal Surgery, London, UK
| | - W R C Knight
- Department of Upper Gastrointestinal and General Surgery, St Thomas' Hospital
| | - C R Baker
- Department of Upper Gastrointestinal and General Surgery, St Thomas' Hospital.,School of Cancer and Pharmaceutical Sciences
| | - M Kelly
- Department of Upper Gastrointestinal and General Surgery, St Thomas' Hospital.,School of Cancer and Pharmaceutical Sciences
| | - N Maisey
- Departments of Medical Oncology, London, UK
| | - A Qureshi
- Clinical Oncology, Guy's Hospital, London, UK
| | - T Sevitt
- Department of Medical Oncology, Maidstone Hospital, Maidstone, UK
| | - M Van Hemelrijck
- School of Cancer and Pharmaceutical Sciences, Translational Oncology and Urology Research, King's College London, London, UK
| | - E C Smyth
- Medical Oncology, Royal Marsden Hospital, London, UK
| | - W H Allum
- Departments of Upper Gastrointestinal Surgery, London, UK
| | - J Lagergren
- School of Cancer and Pharmaceutical Sciences.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - J A Gossage
- Department of Upper Gastrointestinal and General Surgery, St Thomas' Hospital.,School of Cancer and Pharmaceutical Sciences
| | - D Cunningham
- Medical Oncology, Royal Marsden Hospital, London, UK
| | - A R Davies
- Department of Upper Gastrointestinal and General Surgery, St Thomas' Hospital.,School of Cancer and Pharmaceutical Sciences
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7
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Walter GM, Richards TJ, Wilkinson MJ, Blows MW, Aguirre JD, Ortiz‐Barrientos D. Loss of ecologically important genetic variation in late generation hybrids reveals links between adaptation and speciation. Evol Lett 2020; 4:302-316. [PMID: 32774880 PMCID: PMC7403682 DOI: 10.1002/evl3.187] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 06/02/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
Adaptation to contrasting environments occurs when advantageous alleles accumulate in each population, but it remains largely unknown whether these same advantageous alleles create genetic incompatibilities that can cause intrinsic reproductive isolation leading to speciation. Identifying alleles that underlie both adaptation and reproductive isolation is further complicated by factors such as dominance and genetic interactions among loci, which can affect both processes differently and obscure potential links between adaptation and speciation. Here, we use a combination of field and glasshouse experiments to explore the connection between adaptation and speciation while accounting for dominance and genetic interactions. We created a hybrid population with equal contributions from four contrasting ecotypes of Senecio lautus (Asteraceae), which produced hybrid genomes both before (F1 hybrid generation) and after (F4 hybrid generation) recombination among the parental ecotypes. In the glasshouse, plants in the second generation (F2 hybrid generation) showed reduced fitness as a loss of fertility. However, fertility was recovered in subsequent generations, suggesting that genetic variation underlying the fitness reduction was lost in subsequent generations. To quantify the effects of losing genetic variation at the F2 generation on the fitness of later generation hybrids, we used a reciprocal transplant to test for fitness differences between parental ecotypes, and F1 and F4 hybrids in all four parental habitats. Compared to the parental ecotypes and F1 hybrids, variance in F4 hybrid fitness was lower, and lowest in habitats that showed stronger native-ecotype advantage, suggesting that stronger natural selection for the native ecotype reduced fitness variation in the F4 hybrids. Fitness trade-offs that were present in the parental ecotypes and F1 hybrids were absent in the F4 hybrid. Together, these results suggest that the genetic variation lost after the F2 generation was likely associated with both adaptation and intrinsic reproductive isolation among ecotypes from contrasting habitats.
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Affiliation(s)
- Greg M. Walter
- School of Biological SciencesUniversity of QueenslandBrisbane4072Australia
- Current address: School of Biological SciencesMonash UniversityMelbourne3800Australia
| | - Thomas J. Richards
- Department of Ecology and GeneticsUppsala UniversityUppsalaSE‐752 36Sweden
| | | | - Mark W. Blows
- School of Biological SciencesUniversity of QueenslandBrisbane4072Australia
| | - J. David Aguirre
- School of Natural and Computational SciencesMassey UniversityAuckland0745New Zealand
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8
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Wilkinson MJ, Gyorki DE. Extent of ulceration in cutaneous melanoma: is this biomarker ready for primetime? Br J Dermatol 2020; 184:192-193. [PMID: 32729117 DOI: 10.1111/bjd.19386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2020] [Indexed: 11/30/2022]
Affiliation(s)
- M J Wilkinson
- Division of Cancer Surgery, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - D E Gyorki
- Division of Cancer Surgery, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
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9
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Downs JS, Wilkinson MJ, Gyorki DE, Speakman D. Providing cancer surgery in the COVID-19 crisis. Br J Surg 2020; 107:e248. [PMID: 32406931 PMCID: PMC7929328 DOI: 10.1002/bjs.11693] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 11/23/2022]
Affiliation(s)
- J S Downs
- Division of Cancer Surgery Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - M J Wilkinson
- Division of Cancer Surgery Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - D E Gyorki
- Division of Cancer Surgery Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - D Speakman
- Division of Cancer Surgery Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
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10
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Walter GM, Wilkinson MJ, Aguirre JD, Blows MW, Ortiz-Barrientos D. Environmentally induced development costs underlie fitness tradeoffs. Ecology 2018; 99:1391-1401. [PMID: 29856491 DOI: 10.1002/ecy.2234] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 02/05/2018] [Accepted: 03/19/2018] [Indexed: 11/07/2022]
Abstract
Local adaptation can lead to genotype-by-environment interactions, which can create fitness tradeoffs in alternative environments, and govern the distribution of biodiversity across geographic landscapes. Exploring the ecological circumstances that promote the evolution of fitness tradeoffs requires identifying how natural selection operates and during which ontogenetic stages natural selection is strongest. When organisms disperse to areas outside their natural range, tradeoffs might emerge when organisms struggle to reach key life history stages, or alternatively, die shortly after reaching life history stages if there are greater risks of mortality associated with costs to developing in novel environments. We used multiple populations from four ecotypes of an Australian native wildflower (Senecio pinnatifolius) in reciprocal transplants to explore how fitness tradeoffs arise across ontogeny. We then assessed whether the survival probability for plants from native and foreign populations was contingent on reaching key developmental stages. We found that fitness tradeoffs emerged as ontogeny progressed when native plants were more successful than foreign plants at reaching seedling establishment and maturity. Native and foreign plants that failed to reach seedling establishment died at the same rate, but plants from foreign populations died quicker than native plants after reaching seedling establishment, and died quicker regardless of whether they reached sexual maturity or not. Development rates were similar for native and foreign populations, but changed depending on the environment. Together, our results suggest that natural selection for environment-specific traits early in life history created tradeoffs between contrasting environments. Plants from foreign populations were either unable to develop to seedling establishment, or they suffered increased mortality as a consequence of reaching seedling establishment. The observation of tradeoffs together with environmentally dependent changes in development rate suggest that foreign environments induce organisms to develop at a rate different from their native habitat, incurring consequences for lifetime fitness and population divergence.
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Affiliation(s)
- Greg M Walter
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Melanie J Wilkinson
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - J David Aguirre
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland, 4072, Australia.,Institute of Natural and Mathematical Sciences, Massey University, Auckland, 0745, New Zealand
| | - Mark W Blows
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland, 4072, Australia
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11
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Floris SD, Talbot JJ, Wilkinson MJ, Herr JD, Steele RP. Quantum molecular motion in the mixed ion-radical complex, [(H 2O)(H 2S)] . Phys Chem Chem Phys 2016; 18:27450-27459. [PMID: 27711703 DOI: 10.1039/c6cp05299a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The cation dimer of water and hydrogen sulfide, [(H2O)(H2S)]+, serves as a fundamental model for the oxidation chemistry of H2S. The known oxidative metabolism of H2S by biological species in sulfur-rich environments has motivated the study of the inherent properties of this benchmark complex, with possible mechanistic implications for modern water oxidation chemistry. The low-energy isomer of this open-shell ion is a proton-transferred (PT) structure, H3O+SH˙. An alternative PT structure, H3S+OH˙, and a hemibonded (HB) isomer, [H2O·SH2]+, are also stable isomers, placing this complex intermediate to known (H2O)2+ (PT) and (H2S)2+ (HB) limiting regimes. This intermediate character suggested the possibility of unique molecular motion, even in the vibrational ground state. Path integral molecular dynamics and anharmonic vibrational spectroscopy simulations have been performed in this study, in order to understand the inherent quantum molecular motion of this complex. The resulting structural distributions were found to deviate significantly from both classical and harmonic analyses, including the observation of large-amplitude anharmonic motion of the central proton and nearly free rotation of the terminal hydrogens. The predicted vibrational spectra are particularly unique and suggest characteristic signatures of the strong electronic interactions and anharmonic vibrational mode couplings in this radical cation.
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Affiliation(s)
- S D Floris
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, UT, USA.
| | - J J Talbot
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, UT, USA.
| | - M J Wilkinson
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, UT, USA.
| | - J D Herr
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, UT, USA.
| | - R P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, UT, USA.
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Walter GM, Wilkinson MJ, James ME, Richards TJ, Aguirre JD, Ortiz‐Barrientos D. Diversification across a heterogeneous landscape. Evolution 2016; 70:1979-92. [DOI: 10.1111/evo.13009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 07/05/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Greg M. Walter
- School of Biological Sciences University of Queensland St. Lucia QLD 4072 Australia
| | - Melanie J. Wilkinson
- School of Biological Sciences University of Queensland St. Lucia QLD 4072 Australia
| | - Maddie E. James
- School of Biological Sciences University of Queensland St. Lucia QLD 4072 Australia
| | - Thomas J. Richards
- School of Biological Sciences University of Queensland St. Lucia QLD 4072 Australia
| | - J. David Aguirre
- School of Biological Sciences University of Queensland St. Lucia QLD 4072 Australia
- Institute of Natural and Mathematical Sciences Massey University Auckland 0745 New Zealand
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13
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Wilkinson MJ, Fitzgerald JEF, Strauss DC, Hayes AJ, Thomas JM, Messiou C, Fisher C, Benson C, Tekkis PP, Judson I. Surgical treatment of gastrointestinal stromal tumour of the rectum in the era of imatinib. Br J Surg 2015; 102:965-71. [PMID: 25970743 DOI: 10.1002/bjs.9818] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/01/2015] [Accepted: 03/03/2015] [Indexed: 11/10/2022]
Abstract
BACKGROUND Gastrointestinal stromal tumours (GISTs) of the rectum often require radical surgery to achieve complete resection. This study investigated the management and outcome of surgery for rectal GISTs and the role of imatinib. METHODS A cohort study was undertaken of patients identified from a database at one tertiary sarcoma referral centre over a continuous period, from January 2001 to January 2013. RESULTS Over 12 years, 19 patients presented with a primary rectal GIST. Median age was 57 (range 30-77) years. Neoadjuvant imatinib was used in 15 patients, significantly reducing mean tumour size from 7·6 (95 per cent c.i. 6·1 to 9·0) to 4·1 (2·8 to 5·3) cm (P < 0·001). Nine of these patients underwent surgical resection. Imatinib therapy enabled sphincter-preserving surgery to be undertaken in seven patients who would otherwise have required abdominoperineal resection or pelvic exenteration for tumour clearance. Neoadjuvant imatinib treatment also led to a significant reduction in mean(s.d.) tumour mitotic count from 16(16) to 4(9) per 50 high-power fields (P = 0·015). Imatinib was used only as adjuvant treatment in two patients. There were three deaths, all from unrelated causes. Eleven of the 13 patients who underwent resection were alive without evidence of recurrence at latest follow-up, with a median disease-free survival of 38 (range 20-129) months and overall survival of 62 (39-162) months. CONCLUSION The use of neoadjuvant imatinib for rectal GISTs significantly decreased both tumour size and mitotic activity, which permitted less radical sphincter-preserving surgery.
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Affiliation(s)
- M J Wilkinson
- Sarcoma and Melanoma Unit, Department of Academic Surgery, Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - J E F Fitzgerald
- Colorectal Surgery Unit, Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - D C Strauss
- Sarcoma and Melanoma Unit, Department of Academic Surgery, Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - A J Hayes
- Sarcoma and Melanoma Unit, Department of Academic Surgery, Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - J M Thomas
- Sarcoma and Melanoma Unit, Department of Academic Surgery, Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - C Messiou
- Sarcoma and Melanoma Unit, Department of Academic Surgery, Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - C Fisher
- Sarcoma and Melanoma Unit, Department of Academic Surgery, Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - C Benson
- Sarcoma and Melanoma Unit, Department of Academic Surgery, Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - P P Tekkis
- Colorectal Surgery Unit, Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - I Judson
- Sarcoma and Melanoma Unit, Department of Academic Surgery, Royal Marsden Hospital NHS Foundation Trust, London, UK
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14
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Glover AR, Allan CP, Wilkinson MJ, Strauss DC, Thomas JM, Hayes AJ. Outcomes of routine ilioinguinal lymph node dissection for palpable inguinal melanoma nodal metastasis. Br J Surg 2014; 101:811-9. [PMID: 24752717 DOI: 10.1002/bjs.9502] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2014] [Indexed: 11/07/2022]
Abstract
BACKGROUND Patients who present with palpable inguinal melanoma nodal metastasis have two surgical options: inguinal or ilioinguinal lymph node dissection. Indications for either operation remain controversial. This study examined survival and recurrence outcomes following ilioinguinal dissection for patients with palpable inguinal nodal metastasis, and assessed the incidence and preoperative predictors of pelvic nodal metastasis. METHODS This was a retrospective clinicopathological analysis of consecutive surgical patients with stage III malignant melanoma. All patients underwent a standardized ilioinguinal dissection at a specialist tertiary oncology hospital over a 12-year period (1998-2010). RESULTS Some 38.9 per cent of 113 patients had metastatic pelvic nodes. Over a median follow-up of 31 months, the 5-year overall survival rate was 28 per cent for patients with metastatic inguinal and pelvic nodes, and 51 per cent for those with inguinal nodal metastasis only (P = 0.002). The nodal basin control rate was 88.5 per cent. Despite no evidence of pelvic node involvement on preoperative computed tomography (CT), six patients (5.3 per cent) with a single metastatic inguinal lymph node had metastatic pelvic lymph nodes. Logistic regression analysis showed that the number of metastatic inguinal nodes (odds ratio 1.56; P = 0.021) and suspicious CT findings (odds ratio 9.89; P = 0.001) were both significantly associated with metastatic pelvic nodes. The specificity of CT was good (89.2 per cent) in detecting metastatic pelvic nodes, but the sensitivity was limited (57.9 per cent). CONCLUSION Metastatic pelvic nodes are common when palpable metastatic inguinal nodes are present. Long-term survival can be achieved following their resection by ilioinguinal dissection. As metastatic pelvic nodes cannot be diagnosed reliably by preoperative CT, patients presenting with palpable inguinal nodal metastasis should be considered for ilioinguinal dissection.
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Affiliation(s)
- A R Glover
- Kolling Institute of Medical Research, Royal North Shore Hospital and University of Sydney, Sydney, New South Wales
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15
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Roda F, Liu H, Wilkinson MJ, Walter GM, James ME, Bernal DM, Melo MC, Lowe A, Rieseberg LH, Prentis P, Ortiz-Barrientos D. CONVERGENCE AND DIVERGENCE DURING THE ADAPTATION TO SIMILAR ENVIRONMENTS BY AN AUSTRALIAN GROUNDSEL. Evolution 2013; 67:2515-29. [DOI: 10.1111/evo.12136] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 04/03/2013] [Indexed: 01/02/2023]
Affiliation(s)
- Federico Roda
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Huanle Liu
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Melanie J. Wilkinson
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Gregory M. Walter
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Maddie E. James
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Diana M. Bernal
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Maria C. Melo
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | | | | | - Peter Prentis
- Queensland Institute of Technology; Biogeosciences; Brisbane; QLD; 4001; Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
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16
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Wilkinson MJ, Fitzgerald JEF, Thomas JM, Hayes AJ, Strauss DC. Surgical resection for non-familial adenomatous polyposis-related intra-abdominal fibromatosis. Br J Surg 2012; 99:706-13. [PMID: 22359346 DOI: 10.1002/bjs.8703] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2012] [Indexed: 12/29/2022]
Abstract
BACKGROUND Intra-abdominal fibromatosis (IAF) in the context of familial adenomatosis polyposis (FAP) is associated with significant morbidity and high recurrence rates after surgical resection. Non-surgical treatments are therefore advocated. This study explored outcomes in patients with IAF not associated with FAP who underwent surgical resection. METHODS Data were analysed from a prospectively collected database at a sarcoma tertiary referral centre. RESULTS From 2001 to 2011, 15 patients without FAP underwent primary curative surgical resection of IAF. Their median (range) age was 42 (19-64) years. Median tumour size was 18 (8.5-25) cm and weight 1306 (236-2228) g. Complete macroscopic clearance was obtained in all patients. There were no deaths in hospital or within 30 days and only one patient developed a major complication. Median follow-up was 40 (6-119) months. During follow-up two patients developed a recurrence after a disease-free interval of 12 and 16 months. CONCLUSION In contrast to FAP-associated IAF, non-FAP-associated IAF has a very low recurrence rate after surgical resection. Surgical resection is therefore advocated as first-line treatment in patients with non-FAP-associated IAF when resection can be performed with low morbidity.
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Affiliation(s)
- M J Wilkinson
- Sarcoma and Melanoma Unit, Department of Academic Surgery, Royal Marsden Hospital NHS Foundation Trust, Fulham Road, London SW3 6JJ, UK.
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17
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Haider N, Wilkinson MJ. A set of plastid DNA-specific universal primers for flowering plants. Genetika 2011; 47:1204-1215. [PMID: 22117405] [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] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
MatKand rbcL are recommended as the official barcode loci for higher plants but there remains a need for additional universal markers. We generated a series of 84 new universal primers targeting 42 plastid loci that all yielded single amplicons when applied to DNA templates from 19 diverse higher plant families. Marker utility ultimately depends on sequence variability, with rapidly evolving loci being useful for barcoding or biogeographic applications and more conserved loci being better suited to deep phylogeny reconstruction. Whereas excessive size variation is undesirable for many applications, modest size variability caused by indels and the sequence variation frequently associated with indels are highly desirable. We therefore performed a quick screen of the markers for size and sequence variation using pooled DNA templates from 96 taxonomically diverse species. All markers produced little or no size variation (consistent with the presence of minor indels). The seven regions exhibiting most size variation in pooled (rpl23&rpl2.1, 16S, 23S, 4.5S&5S, petB&D, and rpl2, rpoCl and trnK introns) were then amplified for all species individually, confirming the pooled template results. When the most variable loci (introns of trnK and rpoC1) were sequenced for all 96 species, a high level of sequence variation (nucleotide substitutions and indels) was observed among congeneric species groups for both loci. Both markers therefore have potential as supplementary barcode markers.
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Affiliation(s)
- N Haider
- Department of Molecular Biology and Biotechnology, AECS, P.O. Box 6091, Damascus, Syria.
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Chiurugwi T, Beaumont MA, Wilkinson MJ, Battey NH. Adaptive divergence and speciation among sexual and pseudoviviparous populations of Festuca. Heredity (Edinb) 2011; 106:854-61. [PMID: 20959864 PMCID: PMC3186240 DOI: 10.1038/hdy.2010.128] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 07/26/2010] [Accepted: 09/06/2010] [Indexed: 11/09/2022] Open
Abstract
Pseudovivipary is an environmentally induced flowering abnormality in which vegetative shoots replace seminiferous (sexual) inflorescences. Pseudovivipary is usually retained in transplantation experiments, indicating that the trait is not solely induced by the growing environment. Pseudovivipary is the defining characteristic of Festuca vivipara, and arguably the only feature separating this species from its closest seminiferous relative, Festuca ovina. We performed phylogenetic and population genetic analysis on sympatric F. ovina and F. vivipara samples to establish whether pseudovivipary is an adaptive trait that accurately defines the separation of genetically distinct Festuca species. Chloroplast and nuclear marker-based analyses revealed that variation at a geographical level can exceed that between F. vivipara and F. ovina. We deduced that F. vivipara is a recent species that frequently arises independently within F. ovina populations and has not accumulated significant genetic differentiation from its progenitor. We inferred local gene flow between the species. We identified one amplified fragment length polymorphism marker that may be linked to a pseudovivipary-related region of the genome, and several other markers provide evidence of regional local adaptation in Festuca populations. We conclude that F. vivipara can only be appropriately recognized as a morphologically and ecologically distinct species; it lacks genetic differentiation from its relatives. This is the first report of a 'failure in normal flowering development' that repeatedly appears to be adaptive, such that the trait responsible for species recognition constantly reappears on a local basis.
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Affiliation(s)
- T Chiurugwi
- School of Biological Sciences, University of Reading, Reading, UK.
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19
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Jepras RI, Carter J, Pearson SC, Paul FE, Wilkinson MJ. Development of a robust flow cytometric assay for determining numbers of viable bacteria. Appl Environ Microbiol 2010; 61:2696-701. [PMID: 16535078 PMCID: PMC1388496 DOI: 10.1128/aem.61.7.2696-2701.1995] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several fluorescent probes were evaluated as indicators of bacterial viability by flow cytometry. The probes monitor a number of biological factors that are altered during loss of viability. The factors include alterations in membrane permeability, monitored by using fluorogenic substrates and fluorescent intercalating dyes such as propidium iodide, and changes in membrane potential, monitored by using fluorescent cationic and anionic potential-sensitive probes. Of the fluorescent reagents examined, the fluorescent anionic membrane potential probe bis-(1,3-dibutylbarbituric acid)trimethine oxonol [DiBAC(inf4)(3)] proved the best candidate for use as a general robust viability marker and is a promising choice for use in high-throughput assays. With this probe, live and dead cells within a population can be identified and counted 10 min after sampling. There was a close correlation between viable counts determined by flow cytometry and by standard CFU assays for samples of untreated cells. The results indicate that flow cytometry is a sensitive analytical technique that can rapidly monitor physiological changes of individual microorganisms as a result of external perturbations. The membrane potential probe DiBAC(inf4)(3) provided a robust flow cytometric indicator for bacterial cell viability.
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Allainguillaume J, Harwood T, Ford CS, Cuccato G, Norris C, Allender CJ, Welters R, King GJ, Wilkinson MJ. Rapeseed cytoplasm gives advantage in wild relatives and complicates genetically modified crop biocontainment. New Phytol 2009; 183:1201-1211. [PMID: 19496946 DOI: 10.1111/j.1469-8137.2009.02877.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Biocontainment methods for genetically modified crops closest to commercial reality (chloroplast transformation, male sterility) would be compromised (in absolute terms) by seed-mediated gene flow leading to chloroplast capture. Even in these circumstances, however, it can be argued that biocontainment still represses transgene movement, with the efficacy depending on the relative frequency of seed- and pollen-mediated gene flow. In this study, we screened for crop-specific chloroplast markers from rapeseed (Brassica napus) amongst sympatric and allopatric populations of wild B. oleracea in natural cliff-top populations and B. rapa in riverside and weedy populations. We found only modest crop chloroplast presence in wild B. oleracea and in weedy B. rapa, but a surprisingly high incidence in sympatric (but not in allopatric) riverside B. rapa populations. Chloroplast inheritance models indicate that elevated crop chloroplast acquisition is best explained if crop cytoplasm confers selective advantage in riverside B. rapa populations. Our results therefore imply that chloroplast transformation may slow transgene recruitment in two settings, but actually accelerate transgene spread in a third. This finding suggests that the appropriateness of chloroplast transformation for biocontainment policy depends on both context and geographical location.
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Affiliation(s)
- J Allainguillaume
- School of Biological Sciences, The University of Reading, Reading, Berkshire RG6 6AS, UK
| | - T Harwood
- Centre for Environmental Policy, Imperial College London, London SL5 7PY, UK
| | - C S Ford
- School of Biological Sciences, The University of Reading, Reading, Berkshire RG6 6AS, UK
| | - G Cuccato
- School of Biological Sciences, The University of Reading, Reading, Berkshire RG6 6AS, UK
| | - C Norris
- National Institute of Agricultural Botany (NIAB), Cambridge, Cambridgeshire CB3 0LE, UK
| | - C J Allender
- Warwick HRI, Wellesbourne, Warwickshire CV35 9EF, UK
| | - R Welters
- Natural Environment Research Council, Swindon, Berkshire SN2 1EU, UK
| | - G J King
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - M J Wilkinson
- School of Biological Sciences, The University of Reading, Reading, Berkshire RG6 6AS, UK
- Present address: Institute of Biological, Environmental and Rural Sciences, Edward Llwyd Building, Aberystwyth University, Aberystwyth SY23 3DA, UK
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Phillips-Mora W, Wilkinson MJ. Frosty pod of cacao: a disease with a limited geographic range but unlimited potential for damage. Phytopathology 2007; 97:1644-7. [PMID: 18943726 DOI: 10.1094/phyto-97-12-1644] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
ABSTRACT Moniliophthora roreri, the cause of frosty pod rot (FP), is a specialized fungal pathogen (family Marasmiaceae) that invades only actively growing pods of cacao, Theobroma cacao, and related species of Theobroma and Herrania. FP damages pods and the commercially important seeds that some of these species produce. M. roreri was confined to northwestern South America until the 1950s. Its appearance in Panama in 1956 signaled a change in its geographic distribution. Now, it is found in 11 countries in tropical America. The fungus is currently in an active dispersal phase, possibly due to an increase in human-mediated spread. FP is more destructive than black pod (Phytophthora spp.) and more dangerous and difficult to control than witches' broom, caused by Moniliophthora (Crinipellis) perniciosa. The aggressiveness of M. roreri, its capacity to survive different environmental conditions, its rapid natural dispersal, its propensity for man-mediated dispersal, and the susceptibility of most commercial cacao genotypes, all indicate that FP presents a substantial threat to cacao cultivation worldwide.
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Shaw MW, Harwood TD, Wilkinson MJ, Elliott L. Assembling spatially explicit landscape models of pollen and spore dispersal by wind for risk assessment. Proc Biol Sci 2006; 273:1705-13. [PMID: 16769644 PMCID: PMC1634921 DOI: 10.1098/rspb.2006.3491] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 01/22/2006] [Indexed: 11/12/2022] Open
Abstract
Models of windblown pollen or spore movement are required to predict gene flow from genetically modified (GM) crops and the spread of fungal diseases. We suggest a simple form for a function describing the distance moved by a pollen grain or fungal spore, for use in generic models of dispersal. The function has power-law behaviour over sub-continental distances. We show that air-borne dispersal of rapeseed pollen in two experiments was inconsistent with an exponential model, but was fitted by power-law models, implying a large contribution from distant fields to the catches observed. After allowance for this 'background' by applying Fourier transforms to deconvolve the mixture of distant and local sources, the data were best fit by power-laws with exponents between 1.5 and 2. We also demonstrate that for a simple model of area sources, the median dispersal distance is a function of field radius and that measurement from the source edge can be misleading. Using an inverse-square dispersal distribution deduced from the experimental data and the distribution of rapeseed fields deduced by remote sensing, we successfully predict observed rapeseed pollen density in the city centres of Derby and Leicester (UK).
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Affiliation(s)
- M W Shaw
- School of Biological Sciences, The University of Reading, 2 Earley Gate, Whiteknights, Reading RG6 6AU, UK.
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23
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Allainguillaume J, Alexander M, Bullock JM, Saunders M, Allender CJ, King G, Ford CS, Wilkinson MJ. Fitness of hybrids between rapeseed (Brassica napus) and wild Brassica rapa in natural habitats. Mol Ecol 2006; 15:1175-84. [PMID: 16599976 DOI: 10.1111/j.1365-294x.2006.02856.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fitness of hybrids between genetically modified (GM) crops and wild relatives influences the likelihood of ecological harm. We measured fitness components in spontaneous (non-GM) rapeseed x Brassica rapa hybrids in natural populations. The F1 hybrids yielded 46.9% seed output of B. rapa, were 16.9% as effective as males on B. rapa and exhibited increased self-pollination. Assuming 100% GM rapeseed cultivation, we conservatively predict < 7000 second-generation transgenic hybrids annually in the United Kingdom (i.e. approximately 20% of F1 hybrids). Conversely, whilst reduced hybrid fitness improves feasibility of bio-containment, stage projection matrices suggests broad scope for some transgenes to offset this effect by enhancing fitness.
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Affiliation(s)
- J Allainguillaume
- School of Biological Sciences, Plant Science Laboratories, The University of Reading, Whiteknights, Reading RG6 6AS, UK
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Pardi F, Sibly RM, Wilkinson MJ, Whittaker JC. On the structural differences between markers and genomic AC microsatellites. J Mol Evol 2005; 60:688-93. [PMID: 15983876 DOI: 10.1007/s00239-004-0274-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2004] [Accepted: 09/07/2004] [Indexed: 10/25/2022]
Abstract
AC microsatellites have proved particularly useful as genetic markers. For some purposes, such as in population biology, the inferences drawn depend on the quantitative values of their mutation rates. This, together with intrinsic biological interest, has led to widespread study of microsatellite mutational mechanisms. Now, however, inconsistencies are appearing in the results of marker-based versus non-marker-based studies of mutational mechanisms. The reasons for this have not been investigated, but one possibility, pursued here, is that the differences result from structural differences between markers and genomic microsatellites. Here we report a comparison between the CEPH AC marker microsatellites and the global population of AC microsatellites in the human genome. AC marker microsatellites are longer than the global average. Controlling for length, marker microsatellites contain on average fewer interruptions, and have longer segments, than their genomic counterparts. Related to this, marker microsatellites show a greater tendency to concentrate the majority of their repeats into one segment. These differences plausibly result from scientists selecting markers for their high polymorphism. In addition to the structural differences, there are differences in the base composition of flanking sequences, marker flanking regions being richer in C and G and poorer in A and T. Our results indicate that there are profound differences between marker and genomic microsatellites that almost certainly affect their mutation rates. There is a need for a unified model of mutational mechanisms that accounts for both marker-derived and genomic observations. A suggestion is made as to how this might be done.
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Syed NH, Sureshsundar S, Wilkinson MJ, Bhau BS, Cavalcanti JJV, Flavell AJ. Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.). Theor Appl Genet 2005; 110:1195-202. [PMID: 15761718 DOI: 10.1007/s00122-005-1948-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2004] [Accepted: 02/01/2005] [Indexed: 05/03/2023]
Abstract
The most popular retrotransposon-based molecular marker system in use at the present time is the sequence-specific amplification polymorphism (SSAP) system . This system exploits the insertional polymorphism of long terminal repeat (LTR) retrotransposons around the genome. Because the LTR sequence is used to design primers for this method, its successful application requires sequence information from the terminal region of the mobile elements . In this study, two LTR sequences were isolated from the cashew genome and used successfully to develop SSAP marker systems. These were shown to have higher levels of polymorphism than amplified fragment length polymorphic markers for this species.
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Affiliation(s)
- N H Syed
- Plant Research Unit, University of Dundee at SCRI, Invergowrie, Dundee, DD2 5DA, UK.
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Sargent DJ, Geibel M, Hawkins JA, Wilkinson MJ, Battey NH, Simpson DW. Quantitative and qualitative differences in morphological traits revealed between diploid Fragaria species. Ann Bot 2004; 94:787-96. [PMID: 15469944 PMCID: PMC4242284 DOI: 10.1093/aob/mch217] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [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: 03/15/2004] [Revised: 08/11/2004] [Accepted: 09/03/2004] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS The aims of this investigation were to highlight the qualitative and quantitative diversity apparent between nine diploid Fragaria species and produce interspecific populations segregating for a large number of morphological characters suitable for quantitative trait loci analysis. METHODS A qualitative comparison of eight described diploid Fragaria species was performed and measurements were taken of 23 morphological traits from 19 accessions including eight described species and one previously undescribed species. A principal components analysis was performed on 14 mathematically unrelated traits from these accessions, which partitioned the species accessions into distinct morphological groups. Interspecific crosses were performed with accessions of species that displayed significant quantitative divergence and, from these, populations that should segregate for a range of quantitative traits were raised. KEY RESULTS Significant differences between species were observed for all 23 morphological traits quantified and three distinct groups of species accessions were observed after the principal components analysis. Interspecific crosses were performed between these groups, and F2 and backcross populations were raised that should segregate for a range of morphological characters. In addition, the study highlighted a number of distinctive morphological characters in many of the species studied. CONCLUSIONS Diploid Fragaria species are morphologically diverse, yet remain highly interfertile, making the group an ideal model for the study of the genetic basis of phenotypic differences between species through map-based investigation using quantitative trait loci. The segregating interspecific populations raised will be ideal for such investigations and could also provide insights into the nature and extent of genome evolution within this group.
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Affiliation(s)
- Daniel J Sargent
- East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK.
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Sargent DJ, Davis TM, Tobutt KR, Wilkinson MJ, Battey NH, Simpson DW. A genetic linkage map of microsatellite, gene-specific and morphological markers in diploid Fragaria. Theor Appl Genet 2004; 109:1385-1391. [PMID: 15290052 DOI: 10.1007/s00122-004-1767-9] [Citation(s) in RCA: 36] [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] [Subscribe] [Scholar Register] [Received: 05/06/2004] [Accepted: 07/02/2004] [Indexed: 05/24/2023]
Abstract
Diploid Fragaria provide a potential model for genomic studies in the Rosaceae. To develop a genetic linkage map of diploid Fragaria, we scored 78 markers (68 microsatellites, one sequence-characterised amplified region, six gene-specific markers and three morphological traits) in an interspecific F2 population of 94 plants generated from a cross of F.vesca f. semperflorens x F. nubicola. Co-segregation analysis arranged 76 markers into seven discrete linkage groups covering 448 cM, with linkage group sizes ranging from 100.3 cM to 22.9 cM. Marker coverage was generally good; however some clustering of markers was observed on six of the seven linkage groups. Segregation distortion was observed at a high proportion of loci (54%), which could reflect the interspecific nature of the progeny and, in some cases, the self-incompatibility of F. nubicola. Such distortion may also account for some of the marker clustering observed in the map. One of the morphological markers, pale-green leaf (pg) has not previously been mapped in Fragaria and was located to the mid-point of linkage group VI. The transferable nature of the markers used in this study means that the map will be ideal for use as a framework for additional marker incorporation aimed at enhancing and resolving map coverage of the diploid Fragaria genome. The map also provides a sound basis for linkage map transfer to the cultivated octoploid strawberry.
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Affiliation(s)
- D J Sargent
- East Malling Research, New Road, East Malling, West Malling, Kent ME19 6BJ, UK.
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Albani MC, Battey NH, Wilkinson MJ. The development of ISSR-derived SCAR markers around the SEASONAL FLOWERING LOCUS (SFL) in Fragaria vesca. Theor Appl Genet 2004; 109:571-9. [PMID: 15292991 DOI: 10.1007/s00122-004-1654-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2003] [Accepted: 02/27/2004] [Indexed: 05/23/2023]
Abstract
Fragaria vesca is a short-lived perennial with a seasonal-flowering habit. Seasonality of flowering is widespread in the Rosaceae and is also found in the majority of temperate polycarpic perennials. Genetic analysis has shown that seasonal flowering is controlled by a single gene in F. vesca, the SEASONAL FLOWERING LOCUS ( SFL). Here, we report progress towards the marker-assisted selection and positional cloning of SFL, in which three ISSR markers linked to SFL were converted to locus-specific sequence-characterized amplified region (SCAR1-SCAR3) markers to allow large-scale screening of mapping progenies. We believe this is the first study describing the development of SCAR markers from ISSR profiles. The work also provides useful insight into the nature of polymorphisms generated by the ISSR marker system. Our results indicate that the ISSR polymorphisms originally detected were probably caused by point mutations in the positions targeted by primer anchors (causing differential PCR failure), by indels within the amplicon (leading to variation in amplicon size) and by internal sequence differences (leading to variation in DNA folding and so in band mobility). The cause of the original ISSR polymorphism was important in the selection of appropriate strategies for SCAR-marker development. The SCAR markers produced were mapped using a F. vesca f. vesca x F. vesca f. semperflorens testcross population. Marker SCAR2 was inseparable from the SFL, whereas SCAR1 mapped 3.0 cM to the north of the gene and SCAR3 1.7 cM to its south.
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Affiliation(s)
- M C Albani
- School of Plant Sciences, The University of Reading, Whiteknights, PO Box 221, Reading, UK
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29
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Campbell LC, Wilkinson MJ, Manz A, Camilleri P, Humphreys CJ. Electrophoretic manipulation of single DNA molecules in nanofabricated capillaries. Lab Chip 2004; 4:225-9. [PMID: 15159783 DOI: 10.1039/b312592k] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We demonstrate the use of nanofabricated capillaries, integrated as part of a microfluidic structure, to study the electrophoretic behaviour of single, fluorescently-labelled, molecules of DNA as a function of capillary size. The nanocapillaries, fabricated using a focused ion beam, have cross-sections down to 150 x 180 nm. Control of single-molecule direction and velocity was achieved using voltage manipulation. DNA mobility was found to increase with decreasing cross-section, which we interpret in terms of reduced electro-osmotic counter-flow. Such nanofabricated capillaries as part of larger fluidic structures have great potential for biotechnology, particularly single molecule manipulation and analysis.
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Affiliation(s)
- L C Campbell
- University of Cambridge, Department of Materials Science and Metallurgy, Pembroke Street, Cambridge, UK CB2 3Q2.
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30
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Thompson C, Champness NR, Khlobystov AN, Roberts CJ, Schröder M, Tendler SJB, Wilkinson MJ. Using microscopic techniques to reveal the mechanism of anion exchange in crystalline co-ordination polymers. J Microsc 2004; 214:261-71. [PMID: 15157194 DOI: 10.1111/j.0022-2720.2004.01346.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Co-ordination polymers are currently attracting extensive interest due to their potential applications as supramolecular hosts, vessels, and frameworks for storage and separations. Many applications rely on the ion exchange capabilities of these compounds, and considerable debate surrounds the mechanism by which ion exchange occurs in co-ordination polymers. Here AFM and SEM were applied, for the first time, to investigate this class of materials. In situ AFM studies revealed the mechanism by which anion exchange and the subsequent structural transformations of the crystalline co-ordination polymers [[Ag(4,4'-bipy)]BF(4)](infinity) and [[Ag(4,4'-bipy)]NO(3)](infinity) occur. The process is initiated by the dissolution of the metastable crystalline polymer, followed by the subsequent crystallization of the new stable phase on the surface of the original crystal. The formation of deep clefts in the metastable polymer crystal during the transformation allows the solution to access the successive crystalline layers. Thus, the entire process can be viewed as a self-perpetuating cascade of dissolution and recrystallization throughout the macroscopic crystal. SEM data consolidate the findings of AFM. These techniques collectively illustrate that the anion exchange, and subsequent structural transformation, proceeds via a solvent-mediated mechanism, rather than a purely solid-state one.
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Affiliation(s)
- C Thompson
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, The University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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Abstract
OBJECTIVE To document the frequency of conversations about alternative medicine during primary care consultations for back pain in diverse settings. DESIGN "Exit interview" type patient survey. SETTINGS General practices in Seattle, Washington; rural Israel; and Birmingham, England. PATIENTS A convenience sample of 218 adults completing a doctor visit for back pain. MAIN OUTCOME MEASURES Frequencies of doctor-patient discussions of alternative medicine. RESULTS Alternative medicine was discussed in a minority of visits (US site 40%, Israel site 37%, UK site 14%, p < 0.05). At each site, patients initiated at least half of the discussions. Users were five to six times more likely to discuss alternative medicine with their doctor than non-users (p < 0.05 for comparison at each site). The percentage of patients who used alternative medicine but left the consultation without discussing it was similar at all sites (US site 17%, Israel site 23%, UK site 15%). CONCLUSIONS Discussions of alternative medicine occurred in a minority of consultations for back pain although the rate varied considerably by site. Discussions were initiated primarily by patients who use it.
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Affiliation(s)
- J O Neher
- Department of Family Medicine, University of Washington School of Medicine, Seattle, USA.
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32
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Wilkinson MJ, Bell S, McGoldrick J, Williams AE. Unexpected deaths in young New Zealand white rabbits (Oryctolagus cuniculus). Contemp Top Lab Anim Sci 2001; 40:49-51. [PMID: 11451397] [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] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Five weeks after the arrival of a batch of six New Zealand White rabbits for use in antisera production, four died unexpectedly within a 48-h period. Necropsy findings showed a consistent pattern of liver pathology in all animals, with multiple miliary abscesses in all liver lobes. Of the remaining two animals in the cohort, one showed weight loss, mild jaundice, and ascites, and the other rabbit had only weight loss. The differential diagnosis for these unexpected deaths included parasitic and bacterial infections. Histopathologic examination of the liver confirmed a diagnosis of hepatic coccidiosis. The possible origin of the coccidia responsible for this outbreak is discussed.
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Affiliation(s)
- M J Wilkinson
- Department of Biological Services, University of Glasgow, Glasgow G61 1QH, Scotland, United Kingdom
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Wilkinson MJ, Davenport IJ, Charters YM, Jones AE, Allainguillaume J, Butler HT, Mason DC, Raybould AF. A direct regional scale estimate of transgene movement from genetically modified oilseed rape to its wild progenitors. Mol Ecol 2000; 9:983-91. [PMID: 10886660 DOI: 10.1046/j.1365-294x.2000.00986.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [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: 11/20/2022]
Abstract
One of the major environmental concerns over genetically modified (GM) crops relates to transgene movement into wild relatives. The pattern of hybridization ultimately affects the scale and rapidity of ecological change and the feasibility of containment. A new procedure for quantifying hybrid formation over large areas is described. Remote sensing was used to identify possible sites of sympatry between Brassica napus and its progenitor species across 15 000 km2 of south-east England in 1998. Two sympatric populations with B. rapa and one with B. oleracea were found over the entire survey area. Every newly recruited plant in these populations in 1999 was screened for hybrid status using flow cytometry and molecular analyses. One hybrid was observed from the 505 plants screened in the B. rapa populations but none of the nine B. oleracea recruits were hybrids. Measures to minimize gene flow are suggested, and a procedure for the post-release evaluation and containment of GM cultivars is proposed.
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Affiliation(s)
- M J Wilkinson
- Department of Agricultural Botany, School of Plant Sciences, Whiteknights, The University of Reading, PO Box 221, Reading, RG6 6AS, UK.
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35
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Abstract
We report the use of atomic force microscopy to observe the initial stages of beta-amyloid fibrillization in situ. The growth of individual beta-amyloid protofibrils on a mica substrate was followed over several hours. The first in situ visualization of protofibril formation from single aggregate units of beta-amyloid is reported. The growth of these protofibrils through the subsequent addition of these aggregate units is also observed. Growth of the protofibrils is bi-directional and the outgrowth of protofibrils from a common amyloid/heterogeneous core is also observed. Elongation also occurred by the addition of protofibrils from solution. This data provides an exciting insight into the early stages of beta-amyloid fibrillization and can be used to enhance the understanding of the mechanism(s) by which beta-amyloid fibrillizes and may consequently enable inhibition of one or more stages of fibrillization as a potential therapeutic strategy.
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Affiliation(s)
- H K Blackley
- Laboratory of Biophysics and Surface Analysis, School of Pharmaceutical Sciences University of Nottingham, Nottingham, NG7 2RD, UK
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36
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Abstract
Prior to re-housing a colony of laboratory short-tail grey opossums, the animals were found to harbour salmonella. This paper describes an unsuccessful attempt to eradicate the infection from the colony by means of antibiotic treatment and hygienic measures. A pilot treatment of five animals which received enrofloxacin 10 mg/kg for 5 days appeared to be successful in that no salmonellae were recovered from faeces or organs sampled after treatment. The process was repeated on the whole colony prior to a change of accommodation but 2 animals were found to be still infected, 5 weeks after cessation of treatment.
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Affiliation(s)
- M J Wilkinson
- Department of Biological Services, Veterinary Research Facility, University of Glasgow, Scotland, UK
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37
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Wilkinson MJ, Thornton JG. When is a research gift an inducement? Bull Med Ethics 1999; No. 151:2. [PMID: 11657987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Abstract
The Alzheimer's disease-related peptide beta(1-40) amyloid self-associates to form fibrils exhibiting a morphology characteristic of amyloidogenic proteins. The mechanism of this fibrillization process has yet to be fully elucidated. In this study we have immobilized the beta(1-40) amyloid to flat gold surfaces using thiol-based self-assembled monolayers. Atomic force microscopy reveals the presence of spherical units of beta(1-40) amyloid immediately following the initiation of fibrillization. Short fibrillar structures, termed nascent fibrils, which appear to be formed by the association of these units are also present at this time point. At later time points extended, branching networks of fibrils are observed. Some fibrils exhibit a more beaded appearance and greater axial periodicity than others. No nascent fibrils are seen to be present. We believe that these data identify an early fibril structure which could act as an intermediate in beta-amyloid fibrillization. The oligomeric units of which these nascent fibrils are comprised are also determined.
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Affiliation(s)
- H K Blackley
- Laboratory of Biophysics and Surface Analysis, School of Pharmaceutical Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
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39
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Abstract
Pollen-mediated movement of transgenes from transplastomic oilseed rape (Brassica napus) into wild relatives will be avoided if chloroplasts are maternally transmitted. We assess the probability of chloroplast exchange between conventional oilseed rape and wild Brassica rapa to model the future behavior of transplastomic cultivars. Primers specific to cpDNA were used to demonstrate maternal inheritance of chloroplasts in 47 natural hybrids between cultivated B. napus and wild B. rapa. We conclude that there will be no or negligible pollen-mediated chloroplast dispersal from oilseed rape. Transgene introgression could still occur in mixed populations, however, if B. napus acted as the recurrent female parent. Rate of transfer would then depend on the abundance of mixed populations, their persistence as mixtures, and hybridization frequency within stands. A low incidence of sympatry (0.6-0.7%) between wild B. rapa and cultivated B. napus along the river Thames, UK, in 1997 and 1998, suggests mixed stands will form only rarely. Eighteen feral populations of B. napus also showed a strong tendency toward rapid decline in plant number, seed return, and ultimately, extinction within 3 years. Conversely, hybrid production is significant in mixed stands, and the absence of control practices means that oilseed rape will have slightly greater persistence. We infer that some introgression from transplastomic B. napus into B. rapa is inevitable in mixed populations even though such populations will occur infrequently and will tend to lose B. napus plants relatively quickly. Chloroplast exchange will be extremely rare and scattered.
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Affiliation(s)
- S E Scott
- Department of Agricultural Botany, School of Plant Sciences, University of Reading, UK
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40
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Wilkinson MJ. Counselling. Br J Gen Pract 1998; 48:1271. [PMID: 9692300 PMCID: PMC1410180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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41
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Jepras RI, Paul FE, Pearson SC, Wilkinson MJ. Rapid assessment of antibiotic effects on Escherichia coli by bis-(1,3-dibutylbarbituric acid) trimethine oxonol and flow cytometry. Antimicrob Agents Chemother 1997; 41:2001-5. [PMID: 9303401 PMCID: PMC164052 DOI: 10.1128/aac.41.9.2001] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.2] [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: 02/05/2023] Open
Abstract
The effects of selected antibiotics on Escherichia coli were studied by flow cytometry with the fluorescent anionic membrane potential probe bis-(1,3-dibutylbarbituric acid) trimethine oxonol [DiBAC4(3)]. The actions of azithromycin, cefuroxime, and ciprofloxacin at five times the MIC on E. coli were compared by the traditional CFU assay and flow cytometry. Changes in viable counts of bacteria determined with DiBAC4(3) and by flow cytometry following treatment with the antibiotics showed trends similar to those found by the CFU assays. However, viable counts determined by flow cytometry following antibiotic treatment were 1 to 2 logs higher than those determined by the corresponding CFU assays. All the results obtained by flow cytometry were provided within 10 min after sampling, whereas the conventional CFU assay results took at least 18 h. The results indicated that flow cytometry is a sensitive analytical technique that can rapidly monitor the physiological changes of individual microorganisms following antibiotic action and can provide information on the mode of action of a drug. The membrane potential probe DiBAC4(3) provides a robust flow cytometric indicator for bacterial cell viability.
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Affiliation(s)
- R I Jepras
- SmithKline Beecham Pharmaceuticals, New Frontiers Science Park, Harlow, Essex, United Kingdom
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42
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Wilkinson MJ. Questionnaire response rates. Br J Gen Pract 1997; 47:595. [PMID: 9406507 PMCID: PMC1313122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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Wilkinson MJ, Rapley DM, Gadsby R, Cohen MA. Does the BJGP need more fizz and pop?--A Midland Faculty readership survey. Br J Gen Pract 1997; 47:145-9. [PMID: 9167317 PMCID: PMC1312920] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The British Journal of General Practice (BJGP) is the leading primary care journal in the world. By impact factor, it ranks 24th of all medical journals. However, despite major changes in the journal since its inception in 1954, there have been no published readership surveys since a limited report in 1969. AIM To canvass members of the Midland Faculty and to add to the debate about the future of the BJGP. METHOD A postal questionnaire was sent to a random sample of 299 members, fellows and associates of the Midland Faculty asking for their views about the BJGP. RESULTS Two hundred replies were received (a response rate of 67%). The median year of qualification of responders was 1981, and 32 (16%) held academic posts. Ninety-nine (49%) disagreed with the present format of the BJGP, which compared poorly with the British Medical Journal (BMJ) in simple rank order of importance. Readership was equal to that of the BMJ (93% reading it within 28 days of arrival), but fewer people read it within a week of receiving it. The most popular sections were the editorials, original articles and letters; least popular were the book reviews and the pull-out magazine, Connection. All sections were rated excellent to average. Readers wished for an expansion of the BJGP to include clinical reviews, medical politics and humorous pieces. Most responders felt that Connection should remain separate. There was dissatisfaction with the delay between submission and publication of original articles, particularly among the academic general practitioners (GPs). Academics and fundholders did not differ from other readers in their views of the content or style of the BJGP. Half of the responders stated that the BJGP should be self-financing and should be open to more advertising. Responders' free comments largely related to improving the style of articles and expanding the BJGP. CONCLUSION There is a view that the present BJGP is not relevant to the non-academic GP. This is probably due to style rather than content. Simple comparisons with a weekly multi-disciplinary journal may not be valid. The style could be updated to improve retention of information and to highlight areas of particular relevance. Readers are satisfied with the core content of the BJGP but want it to expand to include humour, clinical reviews and medical politics, for example. There is no evidence that the BJGP is more appealing to the academic GP. This study supports an expanded BJGP with an improved style.
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Affiliation(s)
- M J Wilkinson
- Department of General Practice, University of Birmingham
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44
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Timmons AM, Charters YM, Crawford JW, Burn D, Scott SE, Dubbels SJ, Wilson NJ, Robertson A, O'Brien ET, Squire GR, Wilkinson MJ. Risks from transgenic crops. Nature 1996; 380:487. [PMID: 8606764 DOI: 10.1038/380487a0] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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45
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Charters YM, Robertson A, Wilkinson MJ, Ramsay G. PCR analysis of oilseed rape cultivars (Brassica napus L. ssp. oleifera) using 5' -anchored simple sequence repeat (SSR) primers. Theor Appl Genet 1996; 92:442-447. [PMID: 24166269 DOI: 10.1007/bf00223691] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/1995] [Accepted: 11/03/1995] [Indexed: 06/02/2023]
Abstract
Primers complementary to simple sequence repeats (SSRs) and with variable three-base 'anchors' at their 5' end, were used in PCR analyses to compare pooled DNA samples from various Brassica napus and B. rapa cultivars. Amplification products were resolved on polyacrylamide gels and detected by silver-nitrate staining. The resulting banding patterns were highly repeatable between replicate PCRs. Two of the primers produced polymorphisms at 33 and 23 band positions, respectively, and could each discriminate 16 of the 20 cultivars studied. Combined use of both primers allowed all 20 cultivars to be distinguished. The UPGMA dendrogram, based on the cultivar banding profiles, demonstrated clustering on the basis of winter/spring growth habit, high/low glucosinolate content, and cultivar origin (i.e. the breeder involved). Intracultivar polymorphism was investigated using a minimum of ten individuals for each cultivar and was found to vary considerably between cultivars. It is concluded that anchored SSR-PCR analysis is a highly informative and reproducible method for fingerprinting oilseed rape populations, but that intra-cultivar variation should be investigated before using banding profiles from pooled samples for the identification of individuals.
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Affiliation(s)
- Y M Charters
- Crop Genetics Department, Scottish Crop Research Institute (SCRI), DD2 5DA, Invergowrie, Dundee, Scotland
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46
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Abstract
A method was developed to prepare plant structures for confocal laser scanning microscopy by combining Feulgen staining with pararosaniline and embedding in LR White(TM). This procedure preserves intact, delicate structures for three-dimensional imaging without loss from sectioning or squashing, and the slides can be viewed several times without serious photo-bleaching.
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Affiliation(s)
- J P Braselton
- Department of Environmental and Plant Biology, Ohio University, Athens, 45701-2979, USA
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47
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Barr SN, Payne LA, Dale MF, Wilkinson MJ. Predictive correlates of shoot regeneration from potato protoplast culture. Plant Cell Rep 1996; 15:350-354. [PMID: 24178356 DOI: 10.1007/bf00232370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/1995] [Revised: 06/12/1995] [Indexed: 06/02/2023]
Abstract
Adaptation of protoplast regeneration systems for use on untested or recalcitrant potato genotypes can be a time-consuming exercise. Callus growth and xylogenesis were evaluated as early correlates of shooting potential to shorten this process. Callus growth was of limited value for predicting organogenesis but a linear relationship was observed between xylogenesis and shooting frequency. Increases in xylem content above a minimum threshold corresponded with increases in shooting frequency. The predictive value of the relationship was tested using a simple protocol modification (the culture of calli on a filter paper base). Calli on filter paper produced more xylem elements and shoots than those plated directly on medium. The potential of xylem content as a predictive test of shooting frequency is discussed.
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Affiliation(s)
- S N Barr
- Scottish Crop Research Institute, DD2 5DA, Invergowrie, Dundee, UK
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48
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Wilkinson MJ. Does 48 hours' bed rest influence the outcome of acute low back pain? Br J Gen Pract 1995; 45:481-4. [PMID: 7546872 PMCID: PMC1239372] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Bed rest is a traditional treatment for back pain, yet only in recent years has the therapeutic benefit of this been questioned. AIM The aim of this pilot study was to ascertain whether or not 48 hours' bed rest had an effect on the outcome of acute low back pain. METHOD The study was conducted as a randomized controlled trial to compare a prescription of 48 hours' strict bed rest with controls; the control subjects were encouraged to remain mobile and to have no daytime rest. Nine general practitioners from practices in the West Midlands recruited patients in the age range 16-60 years who presented with low back pain of less than seven days' duration, with or without pain radiation. The outcome measures assessed were: change in straight leg raise and lumbar flexion after seven days, Oswestry and Roland-Morris disability scores after seven days and 28 days, and time taken from work. RESULTS Forty two patients were recruited: 20 were allocated to bed rest and 22 as controls. Compared with the bed rest group the control group had statistically better Roland-Morris scores at day seven (P < 0.05) but not at day 28. At day seven, there were no statistically significant differences between groups in straight leg raise or lumbar flexion measurements although the control group had a better mean lumbar flexion than the bed rest group. The improvement in disability scores at day seven compared with day one was similar for the two groups but more of the control group had fully recovered (defined as scores of one or zero on the Roland-Morris disability scale and five or less on the Oswestry disability scale) by day seven. Remaining mobile did not appear to cause any adverse effects. The number of days lost from work in both groups was equal. A large number of self-remedies and physical therapies were recorded by subjects from both groups. CONCLUSION The results of this pilot study did not indicate whether bed rest or remaining mobile was superior for the treatment of acute low back pain; however, the study sample was small. Subjects in the control group possibly fared better as they appeared to have better lumbar flexion at day seven. It appears that 48 hours' bed rest cannot be recommended for the treatment of acute low back pain on the basis of this small study. Large-scale definitive trials are required to detect clinically significant differences.
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Affiliation(s)
- M J Wilkinson
- Department of General Practice, University of Birmingham
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Shivji AP, Brown F, Davies MC, Jennings KH, Roberts CJ, Wilkinson MJ, Williams PM. Scanning tunnelling microscopy studies of beta-amyloid fibril structure and assembly. FEBS Lett 1995; 371:25-8. [PMID: 7664877 DOI: 10.1016/0014-5793(95)00858-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [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: 01/26/2023]
Abstract
Alzheimer's disease is in part characterised by the deposit of beta-amyloid peptide in the form of fibrils in the brain. In this study, the scanning tunnelling microscope (STM) has been used to provide high resolution images of synthetic fibril structure and formation as a function of time. Short fibrils are observed following brief peptide incubation times. At longer incubation periods ribbon like filaments were observed. These results suggest that beta-amyloid self-assembly is an ordered process, with a correlation between time of incubation and length of beta-amyloid filament growth.
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Affiliation(s)
- A P Shivji
- Department of Pharmaceutical Sciences, University of Nottingham, UK
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Wilkinson MJ. Treatment of acute low back pain. N Engl J Med 1995; 332:1786; author reply 1787. [PMID: 7760900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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