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Cates L, Codreanu A, Ciobanu N, Fosburgh H, Allender CJ, Centner H, Engelthaler DM, Crudu V, Cohen T, Menzies NA. Budget impact of next-generation sequencing for diagnosis of TB drug resistance in Moldova. Int J Tuberc Lung Dis 2022; 26:963-969. [PMID: 36163669 DOI: 10.5588/ijtld.22.0104] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Diagnosing drug resistance is critical for choosing effective TB treatment regimens. Next-generation sequencing (NGS) represents an alternative approach to conventional phenotypic drug susceptibility testing (pDST) for diagnosing TB drug resistance.METHODS We undertook a budget impact analysis estimating the costs of introduction and routine use of NGS in the Moldovan National TB Programme. We conducted an empirical costing study and collated price and operating characteristics for NGS platforms. We examined multiple NGS scenarios in comparison to the current approach (pDST) for pre-treatment drug resistance testing over 2021-2025.RESULTS Annual testing volume ranged from 912 to 1,926 patients. For the pDST scenario, we estimated total costs of US$362,000 (2021 USD) over the 5-year study period. Total costs for NGS scenarios ranged from US$475,000 to US$1,486,000. Lowest cost NGS options involved targeted sequencing as a replacement for pDST, and excluded individuals diagnosed as RIF-susceptible on Xpert® MTB/RIF. For all NGS scenarios, the majority (55-80%) of costs were devoted to reagent kits. Start-up costs of NGS were small relative to routine costs borne each year.CONCLUSION NGS adoption will require expanded resources compared to conventional pDST. Further work is required to better understand the feasibility of NGS in settings such as Moldova.
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Affiliation(s)
- L Cates
- Department of Global Health and Population Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - A Codreanu
- Institute of Phthisiopneumology, Chisinau, Moldova
| | - N Ciobanu
- Institute of Phthisiopneumology, Chisinau, Moldova
| | - H Fosburgh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - C J Allender
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - H Centner
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - D M Engelthaler
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - V Crudu
- Institute of Phthisiopneumology, Chisinau, Moldova
| | - T Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - N A Menzies
- Department of Global Health and Population Harvard T. H. Chan School of Public Health, Boston, MA, USA
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Yang C, Sobkowiak B, Naidu V, Codreanu A, Ciobanu N, Gunasekera KS, Chitwood MH, Alexandru S, Bivol S, Russi M, Havumaki J, Cudahy P, Fosburgh H, Allender CJ, Centner H, Engelthaler DM, Menzies NA, Warren JL, Crudu V, Colijn C, Cohen T. Phylogeography and transmission of M. tuberculosis in Moldova: A prospective genomic analysis. PLoS Med 2022; 19:e1003933. [PMID: 35192619 PMCID: PMC8903246 DOI: 10.1371/journal.pmed.1003933] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 03/08/2022] [Accepted: 01/31/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The incidence of multidrug-resistant tuberculosis (MDR-TB) remains critically high in countries of the former Soviet Union, where >20% of new cases and >50% of previously treated cases have resistance to rifampin and isoniazid. Transmission of resistant strains, as opposed to resistance selected through inadequate treatment of drug-susceptible tuberculosis (TB), is the main driver of incident MDR-TB in these countries. METHODS AND FINDINGS We conducted a prospective, genomic analysis of all culture-positive TB cases diagnosed in 2018 and 2019 in the Republic of Moldova. We used phylogenetic methods to identify putative transmission clusters; spatial and demographic data were analyzed to further describe local transmission of Mycobacterium tuberculosis. Of 2,236 participants, 779 (36%) had MDR-TB, of whom 386 (50%) had never been treated previously for TB. Moreover, 92% of multidrug-resistant M. tuberculosis strains belonged to putative transmission clusters. Phylogenetic reconstruction identified 3 large clades that were comprised nearly uniformly of MDR-TB: 2 of these clades were of Beijing lineage, and 1 of Ural lineage, and each had additional distinct clade-specific second-line drug resistance mutations and geographic distributions. Spatial and temporal proximity between pairs of cases within a cluster was associated with greater genomic similarity. Our study lasted for only 2 years, a relatively short duration compared with the natural history of TB, and, thus, the ability to infer the full extent of transmission is limited. CONCLUSIONS The MDR-TB epidemic in Moldova is associated with the local transmission of multiple M. tuberculosis strains, including distinct clades of highly drug-resistant M. tuberculosis with varying geographic distributions and drug resistance profiles. This study demonstrates the role of comprehensive genomic surveillance for understanding the transmission of M. tuberculosis and highlights the urgency of interventions to interrupt transmission of highly drug-resistant M. tuberculosis.
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Affiliation(s)
- Chongguang Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | | | - Vijay Naidu
- Department of Mathematics, Simon Fraser University, Burnaby, Canada
| | | | - Nelly Ciobanu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Kenneth S. Gunasekera
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Melanie H. Chitwood
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | | | - Stela Bivol
- Center for Health Policies and Studies, Chisinau, Republic of Moldova
| | - Marcus Russi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Joshua Havumaki
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Patrick Cudahy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Heather Fosburgh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | | | - Heather Centner
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - David M. Engelthaler
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Nicolas A. Menzies
- Department of Global Health and Population, and Center for Health Decision Science, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Joshua L. Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Valeriu Crudu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, Canada
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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Allender CJ, Bowen JL, Celorrio V, Davies-Jones JA, Davies PR, Guan S, O’Reilly P, Sankar M. The Role of Growth Directors in Controlling the Morphology of Hematite Nanorods. Nanoscale Res Lett 2020; 15:161. [PMID: 32761390 PMCID: PMC7410940 DOI: 10.1186/s11671-020-03387-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
The control of the growth of hematite nanoparticles from iron chloride solutions under hydrothermal conditions in the presence of two different structure promoters has been studied using a range of both structural and spectroscopic techniques including the first report of photo induced force microscopy (PiFM) to map the topographic distribution of the structure-directing agents on the developing nanoparticles. We show that the shape of the nanoparticles can be controlled using the concentration of phosphate ions up to a limit determined to be ~6 × 10-3 mol. Akaganéite (β-FeOOH) is a major component of the nanoparticles formed in the absence of structure directors but only present in the very early stages (< 8 h) of particle growth when phosphate is present. The PiFM data suggest a correlation between the areas in which phosphate ions are adsorbed and areas where akaganéite persists on the surface. In contrast, goethite (α-FeOOH) is a directly observed precursor of the hematite nanorods when 1,2-diamino propane is present. The PiFM data shows goethite in the center of the developing particles consistent with a mechanism in which the iron hydroxide re-dissolves and precipitates at the nanorod ends as hematite.
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Affiliation(s)
| | - Jenna L. Bowen
- CMD Ltd, Green Meadow Springs, Cardiff, CF15 7AB UK
- Cardiff School of Pharmacy & Pharm. Sciences, Cardiff University, Cardiff, CF10 3NB UK
| | - Veronica Celorrio
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Oxfordshire, Didcot OX11 0DE UK
| | - Josh A. Davies-Jones
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff, CF10 3AT UK
| | - Philip R. Davies
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff, CF10 3AT UK
| | - Shaoliang Guan
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff, CF10 3AT UK
| | - Padraic O’Reilly
- Molecular Vista, 6840 Via Del Oro Suite 110, San Jose, CA 95119 USA
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Engelthaler DM, Streicher EM, Kelley EJ, Allender CJ, Wiggins K, Jimenez D, Lemmer D, Vittinghoff E, Theron G, Sirgel FA, Warren RM, Metcalfe JZ. Minority Mycobacterium tuberculosis Genotypic Populations as an Indicator of Subsequent Phenotypic Resistance. Am J Respir Cell Mol Biol 2020; 61:789-791. [PMID: 31774334 DOI: 10.1165/rcmb.2019-0178le] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
| | | | - Erin J Kelley
- Translational Genomics Research InstituteFlagstaff, Arizona
| | | | | | - Dulce Jimenez
- Translational Genomics Research InstituteFlagstaff, Arizona
| | - Darrin Lemmer
- Translational Genomics Research InstituteFlagstaff, Arizona
| | - Eric Vittinghoff
- University of California-San FranciscoSan Francisco, Californiaand
| | | | | | | | - John Z Metcalfe
- University of California, San FranciscoSan Francisco, California
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Neusser G, Eppler S, Bowen J, Allender CJ, Walther P, Mizaikoff B, Kranz C. FIB and MIP: understanding nanoscale porosity in molecularly imprinted polymers via 3D FIB/SEM tomography. Nanoscale 2017; 9:14327-14334. [PMID: 28948256 DOI: 10.1039/c7nr05725c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present combined focused ion beam/scanning electron beam (FIB/SEM) tomography as innovative method for differentiating and visualizing the distribution and connectivity of pores within molecularly imprinted polymers (MIPs) and non-imprinted control polymers (NIPs). FIB/SEM tomography is used in cell biology for elucidating three-dimensional structures such as organelles, but has not yet been extensively applied for visualizing the heterogeneity of nanoscopic pore networks, interconnectivity, and tortuosity in polymers. To our best knowledge, the present study is the first application of this strategy for analyzing the nanoscale porosity of MIPs. MIPs imprinted for propranolol - and the corresponding NIPs - were investigated establishing FIB/SEM tomography as a viable future strategy complementing conventional isotherm studies. For visualizing and understanding the properties of pore networks in detail, polymer particles were stained with osmium tetroxide (OsO4) vapor, and embedded in epoxy resin. Staining with OsO4 provides excellent contrast during high-resolution SEM imaging. After optimizing the threshold to discriminate between the stained polymer matrix, and pores filled with epoxy resin, a 3D model of the sampled volume may be established for deriving not only the pore volume and pore surface area, but also to visualize the interconnectivity and tortuosity of the pores within the sampled polymer volume. Detailed studies using different types of cross-linkers and the effect of hydrolysis on the resulting polymer properties have been investigated. In comparison of MIP and NIP, it could be unambiguously shown that the interconnectivity of the visualized pores in MIPs is significantly higher vs. the non-imprinted polymer, and that the pore volume and pore area is 34% and approx. 35% higher within the MIP matrix. This confirms that the templating process not only induces selective binding sites, but indeed also affects the physical properties of such polymers down to the nanoscale, and that additional chemical modification, e.g., via hydrolysis clearly affects that nature of the polymer.
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Affiliation(s)
- G Neusser
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
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Nualnoi T, Norris MH, Tuanyok A, Brett PJ, Burtnick MN, Keim PS, Settles EW, Allender CJ, AuCoin DP. Development of Immunoassays for Burkholderia pseudomallei Typical and Atypical Lipopolysaccharide Strain Typing. Am J Trop Med Hyg 2016; 96:358-367. [PMID: 27994103 PMCID: PMC5303037 DOI: 10.4269/ajtmh.16-0308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 04/18/2016] [Accepted: 10/27/2016] [Indexed: 01/31/2023] Open
Abstract
Burkholderia pseudomallei is the causative agent of melioidosis, a severe infection endemic to many tropical regions. Lipopolysaccharide (LPS) is recognized as an important virulence factor used by B. pseudomallei. Isolates of B. pseudomallei have been shown to express one of four different types of LPS (typical LPS, atypical LPS types B and B2, and rough LPS) and in vitro studies have demonstrated that LPS types may impact disease severity. The association between LPS types and clinical manifestations, however, is still unknown, in part because an effective method for LPS type identification is not available. Thus, we developed antigen capture immunoassays capable of distinguishing between the LPS types. Mice were injected with B or B2 LPS for atypical LPS–specific monoclonal antibody (mAb) isolation; only two mAbs (3A2 and 5B4) were isolated from mice immunized with B2 LPS. Immunoblot analysis and surface plasmon resonance demonstrated that 3A2 and 5B4 are reactive with both B2 and B LPS where 3A2 was shown to possess higher affinity. Assays were then developed using capsular polysaccharide–specific mAb 4C4 for bacterial capture and 4C7 (previously shown to bind typical LPS) or 3A2 mAbs for typical or atypical LPS strain detection, respectively. The evaluations performed with 197 strains of Burkholderia and non-Burkholderia species showed that the assays are reactive to B. pseudomallei and Burkholderia mallei strains and have an accuracy of 98.8% (zero false positives and two false negatives) for LPS typing. The results suggest that the assays are effective and applicable for B. pseudomallei LPS typing.
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Affiliation(s)
- Teerapat Nualnoi
- Department of Microbiology and Immunology, University of Nevada School of Medicine, Reno, Nevada
| | - Michael H Norris
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida
| | - Apichai Tuanyok
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida
| | - Paul J Brett
- Department of Microbiology and Immunology, University of South Alabama, Mobile, Alabama
| | - Mary N Burtnick
- Department of Microbiology and Immunology, University of South Alabama, Mobile, Alabama
| | - Paul S Keim
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona
| | - Erik W Settles
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona
| | | | - David P AuCoin
- Department of Microbiology and Immunology, University of Nevada School of Medicine, Reno, Nevada
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Baxani DK, Morgan AJL, Jamieson WD, Allender CJ, Barrow DA, Castell OK. Frontispiece: Bilayer Networks within a Hydrogel Shell: A Robust Chassis for Artificial Cells and a Platform for Membrane Studies. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/anie.201684661] [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] [Indexed: 11/09/2022]
Affiliation(s)
- Divesh K. Baxani
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences; Cardiff University; Redwood Building, King Edward VII Avenue CF10 3NB Cardiff UK
| | - Alex J. L. Morgan
- School of Engineering; Cardiff University; 14-17 The Parade CF4 3AA Cardiff UK
| | - William D. Jamieson
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences; Cardiff University; Redwood Building, King Edward VII Avenue CF10 3NB Cardiff UK
| | - Christopher J. Allender
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences; Cardiff University; Redwood Building, King Edward VII Avenue CF10 3NB Cardiff UK
| | - David A. Barrow
- School of Engineering; Cardiff University; 14-17 The Parade CF4 3AA Cardiff UK
| | - Oliver K. Castell
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences; Cardiff University; Redwood Building, King Edward VII Avenue CF10 3NB Cardiff UK
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Baxani DK, Morgan AJL, Jamieson WD, Allender CJ, Barrow DA, Castell OK. Frontispiz: Bilayer Networks within a Hydrogel Shell: A Robust Chassis for Artificial Cells and a Platform for Membrane Studies. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201684661] [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] [Indexed: 11/05/2022]
Affiliation(s)
- Divesh K. Baxani
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences; Cardiff University; Redwood Building, King Edward VII Avenue CF10 3NB Cardiff UK
| | - Alex J. L. Morgan
- School of Engineering; Cardiff University; 14-17 The Parade CF4 3AA Cardiff UK
| | - William D. Jamieson
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences; Cardiff University; Redwood Building, King Edward VII Avenue CF10 3NB Cardiff UK
| | - Christopher J. Allender
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences; Cardiff University; Redwood Building, King Edward VII Avenue CF10 3NB Cardiff UK
| | - David A. Barrow
- School of Engineering; Cardiff University; 14-17 The Parade CF4 3AA Cardiff UK
| | - Oliver K. Castell
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences; Cardiff University; Redwood Building, King Edward VII Avenue CF10 3NB Cardiff UK
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Baxani DK, Morgan AJL, Jamieson WD, Allender CJ, Barrow DA, Castell OK. Bilayer Networks within a Hydrogel Shell: A Robust Chassis for Artificial Cells and a Platform for Membrane Studies. Angew Chem Int Ed Engl 2016; 55:14240-14245. [PMID: 27726260 PMCID: PMC5129564 DOI: 10.1002/anie.201607571] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [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: 08/04/2016] [Indexed: 11/07/2022]
Abstract
The ability to make artificial lipid bilayers compatible with a wide range of environments, and with sufficient structural rigidity for manual handling, would open up a wealth of opportunities for their more routine use in real‐world applications. Although droplet interface bilayers (DIBs) have been demonstrated in a host of laboratory applications, from chemical logic to biosynthesis reaction vessels, their wider use is hampered by a lack of mechanical stability and the largely manual methods employed in their production. Multiphase microfluidics has enabled us to construct hierarchical triple emulsions with a semipermeable shell, in order to form robust, bilayer‐bound, droplet networks capable of communication with their external surroundings. These constructs are stable in air, water, and oil environments and overcome a critical obstacle of achieving structural rigidity without compromising environmental interaction. This paves the way for practical application of artificial membranes or droplet networks in diverse areas such as medical applications, drug testing, biophysical studies and their use as synthetic cells.
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Affiliation(s)
- Divesh K Baxani
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, CF10 3NB, Cardiff, UK
| | - Alex J L Morgan
- School of Engineering, Cardiff University, 14-17 The Parade, CF4 3AA, Cardiff, UK
| | - William D Jamieson
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, CF10 3NB, Cardiff, UK
| | - Christopher J Allender
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, CF10 3NB, Cardiff, UK
| | - David A Barrow
- School of Engineering, Cardiff University, 14-17 The Parade, CF4 3AA, Cardiff, UK
| | - Oliver K Castell
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, CF10 3NB, Cardiff, UK.
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Baxani DK, Morgan AJL, Jamieson WD, Allender CJ, Barrow DA, Castell OK. Bilayer Networks within a Hydrogel Shell: A Robust Chassis for Artificial Cells and a Platform for Membrane Studies. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607571] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Divesh K. Baxani
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences; Cardiff University; Redwood Building, King Edward VII Avenue CF10 3NB Cardiff UK
| | - Alex J. L. Morgan
- School of Engineering; Cardiff University; 14-17 The Parade CF4 3AA Cardiff UK
| | - William D. Jamieson
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences; Cardiff University; Redwood Building, King Edward VII Avenue CF10 3NB Cardiff UK
| | - Christopher J. Allender
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences; Cardiff University; Redwood Building, King Edward VII Avenue CF10 3NB Cardiff UK
| | - David A. Barrow
- School of Engineering; Cardiff University; 14-17 The Parade CF4 3AA Cardiff UK
| | - Oliver K. Castell
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences; Cardiff University; Redwood Building, King Edward VII Avenue CF10 3NB Cardiff UK
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Spring-Pearson SM, Stone JK, Doyle A, Allender CJ, Okinaka RT, Mayo M, Broomall SM, Hill JM, Karavis MA, Hubbard KS, Insalaco JM, McNew LA, Rosenzweig CN, Gibbons HS, Currie BJ, Wagner DM, Keim P, Tuanyok A. Pangenome Analysis of Burkholderia pseudomallei: Genome Evolution Preserves Gene Order despite High Recombination Rates. PLoS One 2015; 10:e0140274. [PMID: 26484663 PMCID: PMC4613141 DOI: 10.1371/journal.pone.0140274] [Citation(s) in RCA: 30] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/23/2015] [Indexed: 11/19/2022] Open
Abstract
The pangenomic diversity in Burkholderia pseudomallei is high, with approximately 5.8% of the genome consisting of genomic islands. Genomic islands are known hotspots for recombination driven primarily by site-specific recombination associated with tRNAs. However, recombination rates in other portions of the genome are also high, a feature we expected to disrupt gene order. We analyzed the pangenome of 37 isolates of B. pseudomallei and demonstrate that the pangenome is ‘open’, with approximately 136 new genes identified with each new genome sequenced, and that the global core genome consists of 4568±16 homologs. Genes associated with metabolism were statistically overrepresented in the core genome, and genes associated with mobile elements, disease, and motility were primarily associated with accessory portions of the pangenome. The frequency distribution of genes present in between 1 and 37 of the genomes analyzed matches well with a model of genome evolution in which 96% of the genome has very low recombination rates but 4% of the genome recombines readily. Using homologous genes among pairs of genomes, we found that gene order was highly conserved among strains, despite the high recombination rates previously observed. High rates of gene transfer and recombination are incompatible with retaining gene order unless these processes are either highly localized to specific sites within the genome, or are characterized by symmetrical gene gain and loss. Our results demonstrate that both processes occur: localized recombination introduces many new genes at relatively few sites, and recombination throughout the genome generates the novel multi-locus sequence types previously observed while preserving gene order.
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Affiliation(s)
- Senanu M. Spring-Pearson
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
| | - Joshua K. Stone
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
| | - Adina Doyle
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
| | - Christopher J. Allender
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
| | - Richard T. Okinaka
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
| | - Mark Mayo
- Menzies School of Health Research and Infectious Disease Department, Royal Darwin Hospital. Darwin, Northern Territory, Australia
| | - Stacey M. Broomall
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - Jessica M. Hill
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - Mark A. Karavis
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - Kyle S. Hubbard
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - Joseph M. Insalaco
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - Lauren A. McNew
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - C. Nicole Rosenzweig
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - Henry S. Gibbons
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - Bart J. Currie
- Menzies School of Health Research and Infectious Disease Department, Royal Darwin Hospital. Darwin, Northern Territory, Australia
| | - David M. Wagner
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
| | - Paul Keim
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
- * E-mail:
| | - Apichai Tuanyok
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, FL, United States of America
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Sahl JW, Allender CJ, Colman RE, Califf KJ, Schupp JM, Currie BJ, Van Zandt KE, Gelhaus HC, Keim P, Tuanyok A. Genomic characterization of Burkholderia pseudomallei isolates selected for medical countermeasures testing: comparative genomics associated with differential virulence. PLoS One 2015; 10:e0121052. [PMID: 25803742 PMCID: PMC4372212 DOI: 10.1371/journal.pone.0121052] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/27/2015] [Indexed: 01/06/2023] Open
Abstract
Burkholderia pseudomallei is the causative agent of melioidosis and a potential bioterrorism agent. In the development of medical countermeasures against B. pseudomallei infection, the US Food and Drug Administration (FDA) animal Rule recommends using well-characterized strains in animal challenge studies. In this study, whole genome sequence data were generated for 6 B. pseudomallei isolates previously identified as candidates for animal challenge studies; an additional 5 isolates were sequenced that were associated with human inhalational melioidosis. A core genome single nucleotide polymorphism (SNP) phylogeny inferred from a concatenated SNP alignment from the 11 isolates sequenced in this study and a diverse global collection of isolates demonstrated the diversity of the proposed Animal Rule isolates. To understand the genomic composition of each isolate, a large-scale blast score ratio (LS-BSR) analysis was performed on the entire pan-genome; this demonstrated the variable composition of genes across the panel and also helped to identify genes unique to individual isolates. In addition, a set of ~550 genes associated with pathogenesis in B. pseudomallei were screened against the 11 sequenced genomes with LS-BSR. Differential gene distribution for 54 virulence-associated genes was observed between genomes and three of these genes were correlated with differential virulence observed in animal challenge studies using BALB/c mice. Differentially conserved genes and SNPs associated with disease severity were identified and could be the basis for future studies investigating the pathogenesis of B. pseudomallei. Overall, the genetic characterization of the 11 proposed Animal Rule isolates provides context for future studies involving B. pseudomallei pathogenesis, differential virulence, and efficacy to therapeutics.
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Affiliation(s)
- Jason W. Sahl
- Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Christopher J. Allender
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Rebecca E. Colman
- Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Katy J. Califf
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - James M. Schupp
- Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Bart J. Currie
- Department of Tropical and Emerging Infectious Diseases, Menzies School of Health Research, Casuarina NT, Australia
| | | | - H. Carl Gelhaus
- Battelle Biomedical Research Center (BBRC), Columbus, Ohio, United States of America
| | - Paul Keim
- Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Apichai Tuanyok
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, and Pacific Center for Emerging Infections Diseases Research, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
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Abstract
Burkholderia pseudomallei isolates from the Western Hemisphere are difficult to differentiate from those from regions in which melioidosis is traditionally endemic. We used internal transcribed spacer typing to determine that B. pseudomallei isolates from the Western Hemisphere are consistently type G. Knowledge of this relationship might be useful for epidemiologic investigations.
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Stone JK, Mayo M, Grasso SA, Ginther JL, Warrington SD, Allender CJ, Doyle A, Georgia S, Kaestli M, Broomall SM, Karavis MA, Insalaco JM, Hubbard KS, McNew LA, Gibbons HS, Currie BJ, Keim P, Tuanyok A. Detection of Burkholderia pseudomallei O-antigen serotypes in near-neighbor species. BMC Microbiol 2012; 12:250. [PMID: 23126230 PMCID: PMC3541218 DOI: 10.1186/1471-2180-12-250] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [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: 07/28/2012] [Accepted: 10/31/2012] [Indexed: 11/15/2022] Open
Abstract
Background Burkholderia pseudomallei is the etiological agent of melioidosis and a CDC category B select agent with no available effective vaccine. Previous immunizations in mice have utilized the lipopolysaccharide (LPS) as a potential vaccine target because it is known as one of the most important antigenic epitopes in B. pseudomallei. Complicating this strategy are the four different B. pseudomallei LPS O-antigen types: A, B, B2, and rough. Sero-crossreactivity is common among O-antigens of Burkholderia species. Here, we identified the presence of multiple B. pseudomallei O-antigen types and sero-crossreactivity in its near-neighbor species. Results PCR screening of O-antigen biosynthesis genes, phenotypic characterization using SDS-PAGE, and immunoblot analysis showed that majority of B. mallei and B. thailandensis strains contained the typical O-antigen type A. In contrast, most of B. ubonensis and B. thailandensis-like strains expressed the atypical O-antigen types B and B2, respectively. Most B. oklahomensis strains expressed a distinct and non-seroreactive O-antigen type, except strain E0147 which expressed O-antigen type A. O-antigen type B2 was also detected in B. thailandensis 82172, B. ubonensis MSMB108, and Burkholderia sp. MSMB175. Interestingly, B. thailandensis-like MSMB43 contained a novel serotype B positive O-antigen. Conclusions This study expands the number of species which express B. pseudomallei O-antigen types. Further work is required to elucidate the full structures and how closely these are to the B. pseudomallei O-antigens, which will ultimately determine the efficacy of the near-neighbor B serotypes for vaccine development.
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Affiliation(s)
- Joshua K Stone
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
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15
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Tuanyok A, Stone JK, Mayo M, Kaestli M, Gruendike J, Georgia S, Warrington S, Mullins T, Allender CJ, Wagner DM, Chantratita N, Peacock SJ, Currie BJ, Keim P. The genetic and molecular basis of O-antigenic diversity in Burkholderia pseudomallei lipopolysaccharide. PLoS Negl Trop Dis 2012; 6:e1453. [PMID: 22235357 PMCID: PMC3250505 DOI: 10.1371/journal.pntd.0001453] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 11/11/2011] [Indexed: 02/07/2023] Open
Abstract
Lipopolysaccharide (LPS) is one of the most important virulence and antigenic components of Burkholderia pseudomallei, the causative agent of melioidosis. LPS diversity in B. pseudomallei has been described as typical, atypical or rough, based upon banding patterns on SDS-PAGE. Here, we studied the genetic and molecular basis of these phenotypic differences. Bioinformatics was used to determine the diversity of genes known or predicted to be involved in biosynthesis of the O-antigenic moiety of LPS in B. pseudomallei and its near-relative species. Multiplex-PCR assays were developed to target diversity of the O-antigen biosynthesis gene patterns or LPS genotypes in B. pseudomallei populations. We found that the typical LPS genotype (LPS genotype A) was highly prevalent in strains from Thailand and other countries in Southeast Asia, whereas the atypical LPS genotype (LPS genotype B) was most often detected in Australian strains (~13.8%). In addition, we report a novel LPS ladder pattern, a derivative of the atypical LPS phenotype, associated with an uncommon O-antigen biosynthesis gene cluster that is found in only a small B. pseudomallei sub-population. This new LPS group was designated as genotype B2. We also report natural mutations in the O-antigen biosynthesis genes that potentially cause the rough LPS phenotype. We postulate that the diversity of LPS may correlate with differential immunopathogenicity and virulence among B. pseudomallei strains.
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Affiliation(s)
- Apichai Tuanyok
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA.
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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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18
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Castell OK, Allender CJ, Barrow DA. Liquid-liquid phase separation: characterisation of a novel device capable of separating particle carrying multiphase flows. Lab Chip 2009; 9:388-396. [PMID: 19156287 DOI: 10.1039/b806946h] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Capillary forces on the microscale are exploited to create a continuous flow liquid-liquid phase separator. Segmented flow regimes of immiscible fluids are generated and subsequently separated into their component phases through an array of high aspect ratio, laser machined, separation ducts (36 microm wide, 130 microm deep) in a planar, integrated, polytetrafluoroethylene (PTFE) microdevice. A controlled pressure differential across the phase separator architecture facilitates the selective passage of the wetting, organic, phase through the separator ducts, enabling separation of microfluidic multiphase flow streams. The reported device is demonstrated to separate water and chloroform segmented flow regimes at flow rates up to 0.4 ml min(-1). Separation efficiency is quantified over a range of flow rates and applied pressure differentials, characterising device behaviour and limits of operation. Experimental measurements and observations are supported by theoretical hydrodynamic and capillary pressure modelling. The influence of material properties and geometric design parameters on phase separation is quantified and optimisation strategies proposed. The novel ability of the membrane free device to separate an organic phase containing suspended microparticulates, from an aqueous phase, is also demonstrated.
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19
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Allender CJ, Castell OK, Davies PR, Fiddy S, Hedin-Dahlström J, Stockenhuber M. A glimpse of the inner workings of the templated site. Chem Commun (Camb) 2009:165-7. [DOI: 10.1039/b811578h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Abstract
Highly efficient molecular extractions in continuous flow microfluidic systems are demonstrated utilising the rapid mixing properties of biphasic segmented flow in conjunction with suspended micro-particulate adsorbents. A continuous flow technique providing potential for continual on-line sample enrichment, purification and clean-up in chemical synthesis, and sample preparation.
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Affiliation(s)
- Oliver K Castell
- Molecular Recognition Research Unit, Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff, UK.
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21
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Allender CJ, Clancy KM, Degomez TE, McMillin JD, Woolbright SA, Keim P, Wagner DM. Lack of genetic differentiation in aggressive and secondary bark beetles (Coleoptera: Curculionidae, Scolytinae) from Arizona. Environ Entomol 2008; 37:817-824. [PMID: 18559189 DOI: 10.1603/0046-225x(2008)37[817:logdia]2.0.co;2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Bark beetles (Coleoptera: Curculionidae, Scolytinae) play an important role as disturbance agents in ponderosa pine (Pinus ponderosa Douglas ex Lawson) forests of Arizona. However, from 2001 to 2003, elevated bark beetle activity caused unprecedented levels of ponderosa pine mortality. A better understanding of the population structure of these species will facilitate analysis of their dispersal patterns and improve management strategies. Here, we use fluorescently labeled amplified fragment length polymorphism (fAFLP) analysis to resolve genetic variation among and within sampling locations in northcentral Arizona of Ips pini (Say), Dendroctonus brevicomis LeConte, and D. frontalis Zimmermann. We generated genetic fingerprints for >500 beetle specimens and analyzed genetic diversity. For all species, gene flow estimates among sampling locations were high, and significant population subdivision was not discernible across a large portion of ponderosa pine forests in Arizona. However, a weak relationship was detected with I. pini population structure and elevation. Because of the lack of genetic differentiation detected throughout the large study area, our findings suggest these insects are capable of long distance dispersal and exhibit a high degree of gene flow across a broad region. We conclude that our results are consistent with strong dispersal patterns and large population sizes of all three species.
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Affiliation(s)
- Christopher J Allender
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011-5640, USA
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22
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Smith MW, Smith JW, Harris C, Brancale A, Allender CJ, Gumbleton M. Phage display identification of functional binding peptides against 4-acetamidophenol (Paracetamol): An exemplified approach to target low molecular weight organic molecules. Biochem Biophys Res Commun 2007; 358:285-91. [PMID: 17482566 DOI: 10.1016/j.bbrc.2007.04.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Accepted: 04/19/2007] [Indexed: 11/24/2022]
Abstract
Peptide-phage display has been widely used to explore protein-protein interactions, however, despite the potential range of applications the use of this technology to identify peptides that bind low molecular weight organic molecules has not been explored. In this current study, we identified a phage clone (PARA-061) displaying the cyclic 7-mer peptide sequence N' AC-NPNNLSH-CGGGS C' that binds the low molecular weight organic molecule 4-acetamidophenol (4-AAP; paracetamol). To avoid occupancy of key functional groups on the target 4-AAP molecule our panning strategy was directed against insoluble complexes of 4-AAP rather than against the target linked to a stationary support or bearing an affinity tag. To augment the panning procedure we deleted phage that also bound the 4-AAP isomers, 2-AAP and 3-AAP. The identified PARA-061 peptide-phage clone displayed functional binding properties against 4-AAP in solution, able in a peptide sequence-dependant manner to prevent the in vitro hepatotoxicity of 4-AAP and reduce ( approximately 20%) the permeability of 4-AAP across a semi-permeable membrane. Molecular dynamic simulations generated a stable binding conformation between the PARA-061 peptide sequence and 4-AAP. In conclusion, we show that a phage display library can be used to identify peptide sequence-specific clones able to modulate the functional binding of a low molecular weight organic molecule. Such peptides may be expected to find utility in the next generation of hybrid polymer-based biosensing devices.
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Affiliation(s)
- Mathew W Smith
- Biomaterials and Biological Interfaces, Welsh School of Pharmacy, Redwood Building, Cardiff University, Cardiff CF10 3XF, UK
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23
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Touchman JW, Wagner DM, Hao J, Mastrian SD, Shah MK, Vogler AJ, Allender CJ, Clark EA, Benitez DS, Youngkin DJ, Girard JM, Auerbach RK, Beckstrom-Sternberg SM, Keim P. A North American Yersinia pestis draft genome sequence: SNPs and phylogenetic analysis. PLoS One 2007; 2:e220. [PMID: 17311096 PMCID: PMC1794153 DOI: 10.1371/journal.pone.0000220] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2006] [Accepted: 01/26/2007] [Indexed: 11/29/2022] Open
Abstract
Background Yersinia pestis, the causative agent of plague, is responsible for some of the greatest epidemic scourges of mankind. It is widespread in the western United States, although it has only been present there for just over 100 years. As a result, there has been very little time for diversity to accumulate in this region. Much of the diversity that has been detected among North American isolates is at loci that mutate too quickly to accurately reconstruct large-scale phylogenetic patterns. Slowly-evolving but stable markers such as SNPs could be useful for this purpose, but are difficult to identify due to the monomorphic nature of North American isolates. Methodology/Principal Findings To identify SNPs that are polymorphic among North American populations of Y. pestis, a gapped genome sequence of Y. pestis strain FV-1 was generated. Sequence comparison of FV-1 with another North American strain, CO92, identified 19 new SNP loci that differ among North American isolates. Conclusions/Significance The 19 SNP loci identified in this study should facilitate additional studies of the genetic population structure of Y. pestis across North America.
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Affiliation(s)
- Jeffrey W Touchman
- The Translational Genomics Research Institute, Phoenix, Ariziona, United States of America.
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Allender CJ, Allainguillaume J, Lynn J, King GJ. Simple sequence repeats reveal uneven distribution of genetic diversity in chloroplast genomes of Brassica oleracea L. and (n = 9) wild relatives. Theor Appl Genet 2007; 114:609-18. [PMID: 17143649 DOI: 10.1007/s00122-006-0461-5] [Citation(s) in RCA: 11] [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] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 11/06/2006] [Indexed: 05/12/2023]
Abstract
Diversity in the chloroplast genome of 171 accessions representing the Brassica 'C' (n = 9) genome, including domesticated and wild B. oleracea and nine inter-fertile related wild species, was investigated using six chloroplast SSR (microsatellite) markers. The lack of diversity detected among 105 cultivated and wild accessions of B. oleracea contrasted starkly with that found within its wild relatives. The vast majority of B. oleracea accessions shared a single haplotype, whereas as many as six haplotypes were detected in two wild species, B. villosa Biv. and B. cretica Lam.. The SSRs proved to be highly polymorphic across haplotypes, with calculated genetic diversity values (H) of 0.23-0.87. In total, 23 different haplotypes were detected in C genome species, with an additional five haplotypes detected in B. rapa L. (A genome n = 10) and another in B. nigra L. (B genome, n = 8). The low chloroplast diversity of B. oleracea is not suggestive of multiple domestication events. The predominant B. oleracea haplotype was also common in B. incana Ten. and present in low frequencies in B. villosa, B. macrocarpa Guss, B. rupestris Raf. and B. cretica. The chloroplast SSRs reveal a wealth of diversity within wild Brassica species that will facilitate further evolutionary and phylogeographic studies of this important crop genus.
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Affiliation(s)
- C J Allender
- Warwick HRI, Wellesbourne, Warwick CV35 9EF, UK.
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25
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Abstract
Molecular imprinting is a generic technology that allows for the introduction of sites of specific molecular affinity into otherwise homogeneous polymeric matrices. Commonly this technique has been shown to be effective when targeting small molecules of molecular weight <1500, while extending the technique to larger molecules such as proteins has proven difficult. A number of key inherent problems in protein imprinting have been identified, including permanent entrapment, poor mass transfer, denaturation, and heterogeneity in binding pocket affinity, which have been addressed using a variety of approaches. This review focuses on protein imprinting in its various forms, ranging from conventional bulk techniques to novel thin film and monolayer surface imprinting approaches.
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Affiliation(s)
- Nicholas W. Turner
- Cranfield Health, Cranfield University at Silsoe, Silsoe MK45 4DT, UK
- Department of Bioengineering, University of Utah, Salt Lake City, Utah 84112
| | - Christopher W. Jeans
- Welsh School of Pharmacy, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff CF1 3XF, UK
| | - Keith R. Brain
- Welsh School of Pharmacy, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff CF1 3XF, UK
| | - Christopher J. Allender
- Welsh School of Pharmacy, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff CF1 3XF, UK
| | - Vladimir Hlady
- Department of Bioengineering, University of Utah, Salt Lake City, Utah 84112
| | - David W. Britt
- Department of Bioengineering, University of Utah, Salt Lake City, Utah 84112
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, Utah 84322
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Castell OK, Allender CJ, Barrow DA. Novel biphasic separations utilising highly selective molecularly imprinted polymers as biorecognition solvent extraction agents. Biosens Bioelectron 2006; 22:526-33. [PMID: 16938448 DOI: 10.1016/j.bios.2006.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Revised: 07/13/2006] [Accepted: 07/13/2006] [Indexed: 10/24/2022]
Abstract
Molecularly imprinted polymers (MIPs) represent a class of artificial receptors that promise an environmentally robust alternative to naturally occurring biorecognition elements of biosensing devices and systems. However, in general, the performance of conventional MIPs in aqueous environments is poor. In the study reported here, this limitation has been addressed by the novel application of MIPs as a solvent extraction solid phase in a biphasic solvent system. This paper describes a previously unreported use of MIPs as solvent extraction reagents, their successful application to aqueous sample media and the opportunities for utilisation of this unique system in novel biosensing and separation procedures. This study demonstrates the development of a novel biphasic solvent system utilising MIP in the extracting phase to enhance both efficiency and selectivity of a simple two phase liquid extraction. Monodisperse propranolol imprinted polymer microspheres [p(divinylbenzene-co-methacrylic acid)] were prepared by precipitation polymerisation. Initially, the affinity of the polymers for (R,S)-propranolol was assessed by established techniques whereby the MIP demonstrated greater affinity for the template than did the non-imprinted control polymer (NIP). Importantly, MIP performance was also assessed using the novel dual solvent system. The depletion of (R,S)-propranolol from the aqueous phase into the polymer containing organic phase was determined. When compared to control extractions containing no polymer the presence of MIP in the extracting solvent phase resulted in an increased extraction of (R,S)-propranolol from the aqueous phase. Importantly, this extraction was significantly greater in the presence of MIP when compared to NIP. This unique principle generates opportunities for MIP based extractions and chemical enrichments in industrial applications, offering commercial, ecological and practical advantages to traditional solvent extraction techniques. The technique is readily transferable to analytical microsystems utilising MIP recognition elements generating promising opportunities for MIP based sensing of aqueous sample media.
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Affiliation(s)
- Oliver K Castell
- Molecular Recognition Research Unit, Welsh School of Pharmacy, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff CF10 3XF, United Kingdom
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Lavignac N, Brain KR, Allender CJ. Concentration dependent atrazine–atrazine complex formation promotes selectivity in atrazine imprinted polymers. Biosens Bioelectron 2006; 22:138-44. [PMID: 16690310 DOI: 10.1016/j.bios.2006.03.017] [Citation(s) in RCA: 24] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Revised: 02/10/2006] [Accepted: 03/22/2006] [Indexed: 11/15/2022]
Abstract
An atrazine (ATR) molecularly imprinted polymer (MIP) was prepared using a non-covalent strategy. The affinity and selectivity of the polymer was initially evaluated under non-equilibrium conditions and the polymer was shown to possess good template selectivity. The selectivity of the polymer was further investigated under equilibrium conditions and over a range of concentrations using Scatchard plots and Hill plots and by assessing distribution coefficients and normalised selectivity values. It was observed that both selectivity and affinity were dependent on the concentration of the ligand and that unusually selectivity and affinity were better at higher atrazine concentrations. It was concluded that this phenomenon resulted from the formation of atrazine-atrazine complexes during the pre-polymerisation stage and during rebinding and that the polymer demonstrated improved atrazine affinity when the conditions favoured complex formation.
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Affiliation(s)
- Nathalie Lavignac
- Molecular Recognition Research Unit, Welsh School of Pharmacy, Cardiff University, The Redwood Building, Cathays Park, Cardiff CF10 3XF, UK
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28
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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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Turner NW, Jeans CW, Brain KR, Allender CJ, Hlady V, Britt DW. From 3D to 2D: A Review of the Molecular Imprinting of Proteins. Biotechnol Prog 2006. [DOI: 10.1002/bp060122g] [Citation(s) in RCA: 302] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Hillberg AL, Brain KR, Allender CJ. Molecular imprinted polymer sensors: implications for therapeutics. Adv Drug Deliv Rev 2005; 57:1875-89. [PMID: 16257082 DOI: 10.1016/j.addr.2005.07.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Accepted: 07/29/2005] [Indexed: 11/18/2022]
Abstract
A biosensor is a sensor that uses biological selectivity to limit its perception to particular key molecules and can be defined as an analytical device possessing a biological or biologically derived sensing element integrated with or associated closely with a physicochemical transducer. In the future it is likely that a number of key developments in therapeutic monitoring and intelligent drug delivery will rely on real-time feedback information in order to deliver an appropriate response. However due to issues of integration and the fragility and unreliability of the bio-molecule, biosensors are currently unable to fulfil this role. Molecular imprinted polymers are viable alternatives to both antibodies and enzymes and this review considers the current position of molecular imprinted polymer sensing.
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Affiliation(s)
- A L Hillberg
- Welsh School of Pharmacy, Cardiff University, Cardiff, UK
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31
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Easterday WR, Van Ert MN, Simonson TS, Wagner DM, Kenefic LJ, Allender CJ, Keim P. Use of single nucleotide polymorphisms in the plcR gene for specific identification of Bacillus anthracis. J Clin Microbiol 2005; 43:1995-7. [PMID: 15815042 PMCID: PMC1081367 DOI: 10.1128/jcm.43.4.1995-1997.2005] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A TaqMan-minor groove binding assay designed around a nonsense mutation in the plcR gene was used to genotype Bacillus anthracis, B. cereus, and B. thuringiensis isolates. The assay differentiated B. anthracis from these genetic near-neighbors and determined that the nonsense mutation is ubiquitous across 89 globally and genetically diverse B. anthracis strains.
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Affiliation(s)
- W Ryan Easterday
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011-5640, USA
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32
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Allender CJ, Easterday WR, Van Ert MN, Wagner DM, Keim P. High-throughput extraction of arthropod vector and pathogen DNA using bead milling. Biotechniques 2005; 37:730, 732, 734. [PMID: 15560126 DOI: 10.2144/04375bm03] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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33
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Achtman M, Morelli G, Zhu P, Wirth T, Diehl I, Kusecek B, Vogler AJ, Wagner DM, Allender CJ, Easterday WR, Chenal-Francisque V, Worsham P, Thomson NR, Parkhill J, Lindler LE, Carniel E, Keim P. Microevolution and history of the plague bacillus, Yersinia pestis. Proc Natl Acad Sci U S A 2004; 101:17837-42. [PMID: 15598742 PMCID: PMC535704 DOI: 10.1073/pnas.0408026101] [Citation(s) in RCA: 327] [Impact Index Per Article: 16.4] [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: 05/07/2004] [Indexed: 11/18/2022] Open
Abstract
The association of historical plague pandemics with Yersinia pestis remains controversial, partly because the evolutionary history of this largely monomorphic bacterium was unknown. The microevolution of Y. pestis was therefore investigated by three different multilocus molecular methods, targeting genomewide synonymous SNPs, variation in number of tandem repeats, and insertion of IS100 insertion elements. Eight populations were recognized by the three methods, and we propose an evolutionary tree for these populations, rooted on Yersinia pseudotuberculosis. The tree invokes microevolution over millennia, during which enzootic pestoides isolates evolved. This initial phase was followed by a binary split 6,500 years ago, which led to populations that are more frequently associated with human disease. These populations do not correspond directly to classical biovars that are based on phenotypic properties. Thus, we recommend that henceforth groupings should be based on molecular signatures. The age of Y. pestis inferred here is compatible with the dates of historical pandemic plague. However, it is premature to infer an association between any modern molecular grouping and a particular pandemic wave that occurred before the 20th century.
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Affiliation(s)
- Mark Achtman
- Department of Molecular Biology, Max-Planck Institut für Infektionsbiologie, D-10117 Berlin, Germany.
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Girard JM, Wagner DM, Vogler AJ, Keys C, Allender CJ, Drickamer LC, Keim P. Differential plague-transmission dynamics determine Yersinia pestis population genetic structure on local, regional, and global scales. Proc Natl Acad Sci U S A 2004; 101:8408-13. [PMID: 15173603 PMCID: PMC420407 DOI: 10.1073/pnas.0401561101] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2004] [Accepted: 04/12/2004] [Indexed: 11/18/2022] Open
Abstract
Plague, the disease caused by the bacterium Yersinia pestis, has greatly impacted human civilization. Y. pestis is a successful global pathogen, with active foci on all continents except Australia and Antarctica. Because the Y. pestis genome is highly monomorphic, previous attempts to characterize the population genetic structure within a single focus have been largely unsuccessful. Here we report that highly mutable marker loci allow determination of Y. pestis population genetic structure and tracking of transmission patterns at two spatial scales within a single focus. In addition, we found that in vitro mutation rates for these loci are similar to those observed in vivo, which allowed us to develop a mutation-rate-based model to examine transmission mechanisms. Our model suggests there are two primary components of plague ecology: a rapid expansion phase for population growth and dispersal followed by a slower persistence phase. This pattern seems consistent across local, regional, and even global scales.
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Affiliation(s)
- Jessica M Girard
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011-5640, USA
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35
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Lavignac N, Allender CJ, Brain KR. Current status of molecularly imprinted polymers as alternatives to antibodies in sorbent assays. Anal Chim Acta 2004. [DOI: 10.1016/j.aca.2003.12.066] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Abstract
The endemic cichlid fishes of Lakes Malawi, Tanganyika and Victoria are textbook examples of explosive speciation and adaptive radiation, and their study promises to yield important insights into these processes. Accurate estimates of species richness of lineages in these lakes, and elsewhere, will be a necessary prerequisite for a thorough comparative analysis of the intrinsic and extrinsic factors influencing rates of diversification. This review presents recent findings on the discoveries of new species and species flocks and critically appraises the relevant evidence on species richness from recent studies of polymorphism and assortative mating, generally using behavioural and molecular methods. Within the haplochromines, the most species-rich lineage, there are few reported cases of postzygotic isolation, and these are generally among allopatric taxa that are likely to have diverged a relatively long time in the past. However, many taxa, including many which occur sympatrically and do not interbreed in nature, produce viable, fertile hybrids. Prezygotic barriers are more important, and persist in laboratory conditions in which environmental factors have been controlled, indicating the primary importance of direct mate preferences. Studies to date indicate that estimates of alpha (within-site) diversity appear to be robust. Although within-species colour polymorphisms are common, these have been taken into account in previous estimates of species richness. However, overall estimates of species richness in Lakes Malawi and Victoria are heavily dependent on the assignation of species status to allopatric populations differing in male colour. Appropriate methods for testing the specific status of allopatric cichlid taxa are reviewed and preliminary results presented.
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Affiliation(s)
- G F Turner
- Division of Biodiversity & Ecology, School of Biological Sciences, University of Southampton, SO16 7PX, UK.
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37
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Allender CJ, Brain KR, Heard CM. Molecularly imprinted polymers--preparation, biomedical applications and technical challenges. Prog Med Chem 2000; 36:235-91. [PMID: 10818675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- C J Allender
- Regio & Enantio Selective Interactions Science & Technology Group, Welsh School of Pharmacy, Cardiff University, U.K
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Abstract
Molecular imprinting is a means of introducing sites of specific molecular arrangement into an otherwise uniform polymeric matrix. This is achieved by formation of a pre-polymerisation complex between complementary monomers and the template molecule. Subsequent polymerisation in the presence of a crosslinker, in a porogenic environment, results in the production of a macroporous polymer capable of specific molecular recognition. This paper considers potential roles for molecularly imprinted polymers within a pharmaceutical remit. Applications including controlled release, drug monitoring devices and biological receptor mimetics are discussed. Histamine and ephedrine molecularly imprinted polymers (MIPs) were studied as potential biological receptor mimics whilst a propranolol MIP was investigated for its use as a rate attenuating selective excipient in a transdermal controlled release device. Preliminary studies concerning the preparation of a theophylline selective transcutaneous monitoring device, using a theophylline MIP, are also described.
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Affiliation(s)
- C J Allender
- The RESIST Group, Welsh School of Pharmacy, Cardiff University, Cardiff, UK
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Allender CJ, Brain KR, Heard CM. 6 Molecularly Imprinted Polymers—Preparation, Biomedical Applications and Technical Challenges. Progress in Medicinal Chemistry 1999. [DOI: 10.1016/s0079-6468(08)70049-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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