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Deen J, Patel J, Kittleson M, Chang D, Singer-Englar T, Patel N, Nikolova A, Ramzy D, Czer L, Kobashigawa J. Efficacy of Tocilizumab for Refractory Sensitized Patients Awaiting Heart Transplantation. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.1402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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2
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Mésange P, Bonnet M, Deen J. 1144P When AI-based image analysis gets in clinical trials. Ann Oncol 2021. [PMCID: PMC8454335 DOI: 10.1016/j.annonc.2021.08.785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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3
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Vernieuwe L, Van de Putte P, Deen J, Bouchez S. Focus on PoCUS or hocus pocus? Integrating point-of-care ultrasound into residency and clinical practice. Acta Anaest Belg 2020. [DOI: 10.56126/71.2.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Point-of care ultrasound (PoCUS) is a new clinical diagnostic paradigm that plays an instrumental role in the ongoing anesthesiologist’s evolving role towards a perioperative physician. Currently, there are few approved curricula that incorporate a PoCUS program into anesthesia residency. This article examines relevant PoCUS applications for anesthesiologists, presents an overview of existing international guidelines for education and training, and reflects on the need for specialty-wide standards. We present a possible framework, that could offer a first move towards a structured PoCUS pathway for Belgian anesthesia residents and facilitate its incorporation into national anesthesia practice.
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4
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Bouwens A, Deen J, Vitale R, D’Huys L, Goyvaerts V, Descloux A, Borrenberghs D, Grussmayer K, Lukes T, Camacho R, Su J, Ruckebusch C, Lasser T, Van De Ville D, Hofkens J, Radenovic A, Frans Janssen KP. Identifying microbial species by single-molecule DNA optical mapping and resampling statistics. NAR Genom Bioinform 2020; 2:lqz007. [PMID: 33575560 PMCID: PMC7671359 DOI: 10.1093/nargab/lqz007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 08/30/2019] [Accepted: 09/12/2019] [Indexed: 12/13/2022] Open
Abstract
Single-molecule DNA mapping has the potential to serve as a powerful complement to high-throughput sequencing in metagenomic analysis. Offering longer read lengths and forgoing the need for complex library preparation and amplification, mapping stands to provide an unbiased view into the composition of complex viromes and/or microbiomes. To fully enable mapping-based metagenomics, sensitivity and specificity of DNA map analysis and identification need to be improved. Using detailed simulations and experimental data, we first demonstrate how fluorescence imaging of surface stretched, sequence specifically labeled DNA fragments can yield highly sensitive identification of targets. Second, a new analysis technique is introduced to increase specificity of the analysis, allowing even closely related species to be resolved. Third, we show how an increase in resolution improves sensitivity. Finally, we demonstrate that these methods are capable of identifying species with long genomes such as bacteria with high sensitivity.
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Affiliation(s)
- Arno Bouwens
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jochem Deen
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Raffaele Vitale
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- LASIR CNRS, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Laurens D’Huys
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Vince Goyvaerts
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Adrien Descloux
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Kristin Grussmayer
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Tomas Lukes
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Rafael Camacho
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Jia Su
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Cyril Ruckebusch
- LASIR CNRS, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Theo Lasser
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Dimitri Van De Ville
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Center for Neuroprosthetics, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Department of Radiology and Medical Informatics, Université de Genève, 1205 Genève, Switzerland
| | - Johan Hofkens
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Aleksandra Radenovic
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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Deen J, Wang S, Van Snick S, Leen V, Janssen K, Hofkens J, Neely RK. A general strategy for direct, enzyme-catalyzed conjugation of functional compounds to DNA. Nucleic Acids Res 2019; 46:e64. [PMID: 29546351 PMCID: PMC6009647 DOI: 10.1093/nar/gky184] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 12/22/2017] [Accepted: 03/02/2018] [Indexed: 12/13/2022] Open
Abstract
The methyltransferase enzymes can be applied to deliver a range of modifications to pre-determined sites on large DNA molecules with exceptional specificity and efficiency. To date, however, a limited number of modifications have been delivered in this way because of the complex chemical synthesis that is needed to produce a cofactor analogue carrying a specific function, such as a fluorophore. Here, we describe a method for the direct transfer of a series of functional compounds (seven fluorescent dyes, biotin and polyethylene glycol) to the DNA duplex. Our approach uses a functional cofactor analogue, whose final preparative step is performed alongiside the DNA modification reaction in a single pot, with no purification needed. We show that fluorophore conjugation efficiency in these mixtures is significantly improved compared to two-step labeling approaches. Our experiments highlight the remarkable malleability and selectivity of the methyltransferases tested. Additional analysis using high resolution localization of the fluorophore distribution indicates that target sites for the methyltransferase are predominantly labeled on a single strand of their palindromic site and that a small and randomly-distributed probability of off-site labeling exists.
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Affiliation(s)
- Jochem Deen
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Su Wang
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Sven Van Snick
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Volker Leen
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Kris Janssen
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Johan Hofkens
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Robert K Neely
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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Sokolova A, Deen J, Perry-Keene J. A case of nonuraemic calciphylaxis presenting as a chronic ulcer in a diabetic patient. Pathology 2018. [DOI: 10.1016/j.pathol.2017.11.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Abstract
Pigs that grow slower than their contemporaries can cause complications for animal welfare and profitability. This study was conducted to investigate factors that may contribute to slow growth of pigs. Pigs ( = 440) farrowed by 65 sows were monitored from birth to market. Pigs were categorized as slow, average, and fast growers based on market weight adjusted to 170 d of age (slow growers were <105 kg, average growers were between 105 and 125 kg, and fast growers were >125 kg). Blood samples were collected from 48 focal pigs at 9 and 21 wk of age and analyzed for hormone and free AA concentrations. Data were analyzed using the Mixed and Logistic procedures of SAS. Slow-growing pigs accounted for 10% of pigs marketed, average growers accounted for 49% of pigs marketed, and fast growers accounted for 41% of pigs marketed. Compared with fast growers, slow growers were lighter at birth ( < 0.01), at weaning ( < 0.01), and at nursery exit ( < 0.01) and had less backfat ( < 0.01) and smaller loin muscle area ( < 0.01) at marketing at 21 wk of age. Slow growers had lower plasma concentrations of IGF-1 ( = 0.03) and insulin ( < 0.001) during the nursery period and lower concentrations of leptin ( < 0.001) and insulin ( < 0.001) during the finishing period compared with average and fast growers. Serum concentrations of several essential, nonessential, and total free AA were less for slow growers during both the nursery and finishing periods compared with average and fast growers. Gilts were more likely to become slow growers than barrows (odds ratio = 2.17, 95% confidence interval = 1.19 to 3.96, = 0.01). Litter size and parity of the pigs' dam were not associated with slow growth. These results suggest that low concentrations of IGF-1, insulin, leptin, and AA may contribute to or be associated with slow growth in pigs.
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8
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Deen J, Vranken C, Leen V, Neely RK, Janssen KPF, Hofkens J. Methyltransferase-Directed Labeling of Biomolecules and its Applications. Angew Chem Int Ed Engl 2017; 56:5182-5200. [PMID: 27943567 PMCID: PMC5502580 DOI: 10.1002/anie.201608625] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Indexed: 01/01/2023]
Abstract
Methyltransferases (MTases) form a large family of enzymes that methylate a diverse set of targets, ranging from the three major biopolymers to small molecules. Most of these MTases use the cofactor S-adenosyl-l-Methionine (AdoMet) as a methyl source. In recent years, there have been significant efforts toward the development of AdoMet analogues with the aim of transferring moieties other than simple methyl groups. Two major classes of AdoMet analogues currently exist: doubly-activated molecules and aziridine based molecules, each of which employs a different approach to achieve transalkylation rather than transmethylation. In this review, we discuss the various strategies for labelling and functionalizing biomolecules using AdoMet-dependent MTases and AdoMet analogues. We cover the synthetic routes to AdoMet analogues, their stability in biological environments and their application in transalkylation reactions. Finally, some perspectives are presented for the potential use of AdoMet analogues in biology research, (epi)genetics and nanotechnology.
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Affiliation(s)
- Jochem Deen
- Laboratory of Nanoscale BiologySchool of Engineering, EPFL, STI IBI-STI LBEN BM 5134 (Bâtiment BM)Station 17CH-1015LausanneSwitzerland
| | - Charlotte Vranken
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
| | - Volker Leen
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
| | - Robert K. Neely
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Kris P. F. Janssen
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
| | - Johan Hofkens
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
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9
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Deen J, Vranken C, Leen V, Neely RK, Janssen KPF, Hofkens J. Die Methyltransferase-gesteuerte Markierung von Biomolekülen und ihre Anwendungen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201608625] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Jochem Deen
- Laboratory of Nanoscale Biology; School of Engineering, EPFL, STI IBI-STI LBEN BM 5134 (Bâtiment BM); Station 17 CH-1015 Lausanne Schweiz
| | - Charlotte Vranken
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
| | - Volker Leen
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
| | - Robert K. Neely
- School of Chemistry; University of Birmingham; Edgbaston Birmingham B15 2TT Großbritannien
| | - Kris P. F. Janssen
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
| | - Johan Hofkens
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
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Lauer MH, Vranken C, Deen J, Frederickx W, Vanderlinden W, Wand N, Leen V, Gehlen MH, Hofkens J, Neely RK. Methyltransferase-directed covalent coupling of fluorophores to DNA. Chem Sci 2017; 8:3804-3811. [PMID: 28580113 PMCID: PMC5436541 DOI: 10.1039/c6sc04229e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 09/21/2016] [Accepted: 03/13/2017] [Indexed: 12/25/2022] Open
Abstract
Highly efficient DNA labelling using an enzymatically-directed, strain-promoted azide–alkyne cycloaddition.
We report an assay for determining the number of fluorophores conjugated to single plasmid DNA molecules and apply this to compare the efficiency of fluorophore coupling strategies for covalent DNA labelling. We compare a copper-catalyzed azide–alkyne cycloaddition reaction, amine to N-hydroxysuccinimidyl ester coupling reaction and strain-promoted azide–alkyne cycloaddition reaction for fluorescent DNA labelling. We found increased labelling efficiency going from the amine to N-hydroxysuccinimidyl ester coupling reaction to the copper-catalyzed azide–alkyne cycloaddition and found the highest degree of DNA labelling with the strain-promoted azide–alkyne cycloaddition reaction. We also examined the effect of labelling on the DNA structure using atomic force microscopy. We observe no distortions or damage to the DNA that was labeled using the amine to N-hydroxysuccinimidyl ester and strain-promoted azide–alkyne cycloaddition coupling reactions. This was in contrast to the copper-catalyzed azide–alkyne cycloaddition reaction, which, despite the use of copper-coordinating ligands in the labelling mixture, leads to some structural DNA damage (single-stranded DNA breaks).
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Affiliation(s)
- Milena Helmer Lauer
- Department of Chemistry , KU Leuven , Celestijnenlaan , 3001 Heverlee , Belgium.,Institute of Chemistry of São Carlos , University of São Paulo , Brazil
| | - Charlotte Vranken
- Department of Chemistry , KU Leuven , Celestijnenlaan , 3001 Heverlee , Belgium
| | - Jochem Deen
- Department of Chemistry , KU Leuven , Celestijnenlaan , 3001 Heverlee , Belgium
| | - Wout Frederickx
- Department of Chemistry , KU Leuven , Celestijnenlaan , 3001 Heverlee , Belgium
| | - Willem Vanderlinden
- Department of Chemistry , KU Leuven , Celestijnenlaan , 3001 Heverlee , Belgium
| | - Nathaniel Wand
- School of Chemistry , University of Birmingham , Edgbaston , Birmingham B15 2TT , UK .
| | - Volker Leen
- Department of Chemistry , KU Leuven , Celestijnenlaan , 3001 Heverlee , Belgium
| | - Marcelo H Gehlen
- Institute of Chemistry of São Carlos , University of São Paulo , Brazil
| | - Johan Hofkens
- Department of Chemistry , KU Leuven , Celestijnenlaan , 3001 Heverlee , Belgium
| | - Robert K Neely
- School of Chemistry , University of Birmingham , Edgbaston , Birmingham B15 2TT , UK .
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Zheng X, Cheng Z, Deen J, Peng H, Xing L. SU-C-206-01: Impact of Charge Sharing Effect On Sub-Pitch Resolution for CZT-Based Photon Counting CT Systems. Med Phys 2016. [DOI: 10.1118/1.4955583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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12
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Cheng Z, Zheng X, Deen J, Peng H, Xing L. TH-CD-207B-07: Noise Modeling of Single Photon Avalanche Diode (SPAD) for Photon Counting CT Applications. Med Phys 2016. [DOI: 10.1118/1.4958213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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13
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Deen J. 013 Six questions for veterinarians. J Anim Sci 2016. [DOI: 10.2527/msasas2016-013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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14
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He Y, Cui S, Deen J, Shurson GC, Li Y. 009 Effects of feeder space allowance on behavior of slow-growing pigs during the nursery period. J Anim Sci 2016. [DOI: 10.2527/msasas2016-009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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15
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Deen J, Sempels W, De Dier R, Vermant J, Dedecker P, Hofkens J, Neely RK. Combing of genomic DNA from droplets containing picograms of material. ACS Nano 2015; 9:809-816. [PMID: 25561163 PMCID: PMC4344373 DOI: 10.1021/nn5063497] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 11/06/2014] [Accepted: 01/05/2015] [Indexed: 05/30/2023]
Abstract
Deposition of linear DNA molecules is a critical step in many single-molecule genomic approaches including DNA mapping, fiber-FISH, and several emerging sequencing technologies. In the ideal situation, the DNA that is deposited for these experiments is absolutely linear and uniformly stretched, thereby enabling accurate distance measurements. However, this is rarely the case, and furthermore, current approaches for the capture and linearization of DNA on a surface tend to require complex surface preparation and large amounts of starting material to achieve genomic-scale mapping. This makes them technically demanding and prevents their application in emerging fields of genomics, such as single-cell based analyses. Here we describe a simple and extremely efficient approach to the deposition and linearization of genomic DNA molecules. We employ droplets containing as little as tens of picograms of material and simply drag them, using a pipet tip, over a polymer-coated coverslip. In this report we highlight one particular polymer, Zeonex, which is remarkably efficient at capturing DNA. We characterize the method of DNA capture on the Zeonex surface and find that the use of droplets greatly facilitates the efficient deposition of DNA. This is the result of a circulating flow in the droplet that maintains a high DNA concentration at the interface of the surface/solution. Overall, our approach provides an accessible route to the study of genomic structural variation from samples containing no more than a handful of cells.
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Affiliation(s)
- Jochem Deen
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Wouter Sempels
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Raf De Dier
- Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46, Heverlee 3001, Belgium
| | - Jan Vermant
- Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46, Heverlee 3001, Belgium
- Department of Materials, ETH Zürich, Vladimir Prelog Weg 5, CH 8093 Zürich, Switzerland
| | - Peter Dedecker
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Robert K. Neely
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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16
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Hopper A, Deen J, Smith C, Campillo A, Vilke G, Castillo E, Wilson M. 393 Hypotensive Effects of Oral Second Generation Antipsychotics in the Emergency Department. Ann Emerg Med 2014. [DOI: 10.1016/j.annemergmed.2014.07.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Phillips CE, Farmer C, Anderson JE, Johnston LJ, Shurson GC, Deen J, Keisler DH, Conner AM, Li YZ. Preweaning mortality in group-housed lactating sows: Hormonal differences between high risk and low risk sows. J Anim Sci 2014; 92:2603-11. [DOI: 10.2527/jas.2014-7624] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- C. E. Phillips
- College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, St. Paul 55108
| | - C. Farmer
- Agriculture and Agri-Food Canada, Dairy and Swine R & D Centre, Sherbrooke, QC, Canada J1M 0C8
| | | | - L. J. Johnston
- West Central Research and Outreach Center, University of Minnesota Morris, 56267
| | - G. C. Shurson
- College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, St. Paul 55108
| | - J. Deen
- College of Veterinary Medicine, University of Minnesota, St. Paul 55108
| | - D. H. Keisler
- Division of Animal Science, University of Missouri, Columbia 65211
| | - A. M. Conner
- Division of Animal Science, University of Missouri, Columbia 65211
| | - Y. Z. Li
- West Central Research and Outreach Center, University of Minnesota Morris, 56267
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18
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Vranken C, Deen J, Dirix L, Stakenborg T, Dehaen W, Leen V, Hofkens J, Neely RK. Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry. Nucleic Acids Res 2014; 42:e50. [PMID: 24452797 PMCID: PMC3985630 DOI: 10.1093/nar/gkt1406] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [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] [Indexed: 12/23/2022] Open
Abstract
We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes transalkylate DNA with the cofactor we tested (a readily prepared s-adenosyl-l-methionine analogue).
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Affiliation(s)
- Charlotte Vranken
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium, Life Science Technologies, Imec, Kapeldreef 75, 3001 Heverlee, Belgium and Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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von Seidlein L, Jiddawi M, Grais RF, Luquero F, Lucas M, Deen J. The Value of and Challenges for Cholera Vaccines in Africa. J Infect Dis 2013; 208 Suppl 1:S8-14. [DOI: 10.1093/infdis/jit194] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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21
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Naha A, Chowdhury G, Ghosh-Banerjee J, Senoh M, Takahashi T, Ley B, Thriemer K, Deen J, Seidlein LV, Ali SM, Khatib A, Ramamurthy T, Nandy RK, Nair GB, Takeda Y, Mukhopadhyay AK. Molecular characterization of high-level-cholera-toxin-producing El Tor variant Vibrio cholerae strains in the Zanzibar Archipelago of Tanzania. J Clin Microbiol 2013; 51:1040-5. [PMID: 23325815 PMCID: PMC3592071 DOI: 10.1128/jcm.03162-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 01/08/2013] [Indexed: 01/09/2023] Open
Abstract
Analysis of 1,180 diarrheal stool samples in Zanzibar detected 247 Vibrio cholerae O1, Ogawa strains in 2009. Phenotypic traits and PCR-based detection of rstR, rtxC, and tcpA alleles showed that they belonged to the El Tor biotype. Genetic analysis of ctxB of these strains revealed that they were classical type, and production of classical cholera toxin B (CTB) was confirmed by Western blotting. These strains produced more CT than the prototype El Tor and formed a separate cluster by pulsed-field gel electrophoresis (PFGE) analysis.
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Affiliation(s)
- A. Naha
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - G. Chowdhury
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - M. Senoh
- Collaborative Research Center of Okayama University for Infectious Diseases at NICED, Kolkata, India
| | - T. Takahashi
- Collaborative Research Center of Okayama University for Infectious Diseases at NICED, Kolkata, India
| | - B. Ley
- The International Vaccine Institute, Seoul, Republic of Korea
| | - K. Thriemer
- The International Vaccine Institute, Seoul, Republic of Korea
| | - J. Deen
- The International Vaccine Institute, Seoul, Republic of Korea
| | - L. V. Seidlein
- Menzies School of Health Research, Casuarina, Northern Territory, Australia
| | - S. M. Ali
- Ministry of Health and Social Welfare, Zanzibar, Tanzania
- Public Health Laboratory, Pemba, Zanzibar, Tanzania
| | - A. Khatib
- Ministry of Health and Social Welfare, Zanzibar, Tanzania
| | - T. Ramamurthy
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - R. K. Nandy
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - G. B. Nair
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Y. Takeda
- Collaborative Research Center of Okayama University for Infectious Diseases at NICED, Kolkata, India
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Neely RK, Deen J, Hofkens J. Erratum: “Review: Optical Mapping of DNA: Single-Molecule-Based Methods for Mapping Genomes” Biopolymers 95(5), 298-311, (2011). Biopolymers 2011. [DOI: 10.1002/bip.21682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Neely RK, Deen J, Hofkens J. Optical mapping of DNA: Single-molecule-based methods for mapping genomes. Biopolymers 2011; 95:298-311. [DOI: 10.1002/bip.21579] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 12/15/2010] [Accepted: 12/15/2010] [Indexed: 11/09/2022]
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Dee S, Spronk G, Reicks D, Ruen P, Deen J. Further assessment of air filtration for preventing PRRSV infection in large breeding pig herds. Vet Rec 2010; 167:976-7. [DOI: 10.1136/vr.c6788] [Citation(s) in RCA: 14] [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: 11/04/2022]
Affiliation(s)
- S. Dee
- Swine Disease Eradication Center; College of Veterinary Medicine; University of Minnesota; 1988 Fitch Avenue St Paul MN 55108 USA
| | - G. Spronk
- Pipestone Veterinary Clinic; PO Box 188, 1300 S Highway 75 Pipestone MN 56164 USA
| | - D. Reicks
- Swine Vet Center; 1608 S Minnesota Avenue St Peter MN 56082 USA
| | - P. Ruen
- Fairmont Veterinary Clinic; 1275 Highway 15 South Fairmont MN 56031 USA
| | - J. Deen
- Swine Disease Eradication Center; College of Veterinary Medicine; University of Minnesota; 1988 Fitch Avenue St Paul MN 55108 USA
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Rutten-Ramos S, Deen J. An investigation of the success of production-based sow removal and replacement in the context of herd performance. J Anim Sci 2009; 87:1794-800. [PMID: 19151155 DOI: 10.2527/jas.2008-0986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Production-based removal and replacement has been used as a method to improve sow herd performance. Limited data are available as to the reliability of this approach. The purpose of this investigation was to use a retrospective case-control study to assess the success of replacement events when herd productivity was greater or less than the mean for removal events attributed to problems with fertility, fecundity, or old age. For each of 3 herds, 1,000 consecutive sows removed between parities 1 and 6 for reasons of fertility, fecundity, or old age were matched to sows with similar histories that were retained in the herd (controls) and to gilts that were first bred into the herd around the time of the case removal events. Controls and gilts were followed until their next parity or removal event, and the outcome was measured as a standardized calculation of born alive per mated female per year. Herd performance at the time of the case removal events was categorized according to greater or less than the mean for fertility or fecundity on monthly farrowing rates and average piglets born alive per litter. Success of removal/replacement events were evaluated according to removal reason and contemporary herd performance. A model was developed to estimate production and financial implications of changes to productivity-based culling, using a Monte Carlo simulation with a 1,000-iteration run. Born alive per mated female per year from gilts was greater (P = 0.0001) than from controls in 1 of 3 herds when herd fertility was greater than the mean, 1 of 3 herds when herd fertility was less than the mean (P = 0.0065), 3 of 3 herds when herd fecundity was greater than the mean (P < 0.030), and 2 of 3 herds when herd fecundity was less than the mean (P < 0.020). The financial model sensitivity analysis indicated greater likelihood of economic advantage for a scenario without production-based removals in parities 1 to 6.
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Affiliation(s)
- S Rutten-Ramos
- University of Minnesota, 1988 Fitch Avenue, St. Paul 55108, USA.
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Larriestra AJ, Wattanaphansak S, Neumann EJ, Bradford J, Morrison RB, Deen J. Pig characteristics associated with mortality and light exit weight for the nursery phase. Can Vet J 2006; 47:560-6. [PMID: 16808228 PMCID: PMC1461411] [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: 05/10/2023]
Abstract
One thousand and ten weaned pigs that were reared in 1 nursery in Iowa from weaning (17 +/- 2 days ) until 10 weeks of age were evaluated. A weaning weight threshold of 3.6 kg maximized the sensitivity and specificity to correctly predict the likelihood of dying or being light in weight at exit from the nursery (< or = 14.5 kg). Weaning weight < or = 3.6 kg (OR = 2.92), barrow (OR = 1.75), and sow unit (A versus B, OR = 2.14) were significant predictors of mortality in the nursery. Birth weight < or = 1.0 kg (OR = 2.66), weaning weight < or = 3.6 kg (OR = 8.75), gilt (OR = 1.4), sow unit (OR = 2.38), and gilt as nursing sow at weaning (OR = 1.66) were significant predictors of being lightweight at nursery exit. Eighteen per cent of the nursery deaths and almost half of lightweight nursery pigs could be prevented if there were no lightweight pigs at weaning.
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Affiliation(s)
- A J Larriestra
- College of Veterinary Medicine, Department of Clinical and Population Sciences, University of Minnesota, St. Paul, Minnesota 55108, USA.
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Sur D, Sarkar BL, Manna B, Deen J, Datta S, Niyogi SK, Ghosh AN, Deb A, Kanungo S, Palit A, Bhattacharya SK. Epidemiological, microbiological & electron microscopic study of a cholera outbreak in a Kolkata slum community. Indian J Med Res 2006; 123:31-6. [PMID: 16567865] [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: 05/08/2023] Open
Abstract
BACKGROUND & OBJECTIVE Epidemics of cholera caused by Vibrio cholerae O1 or O139 have been reported from different parts of India. Factors such as unsafe water supply, poor environmental sanitation, indiscriminate defaecation and lack of personal hygiene are mainly responsible for continued transmission of this disease. We report here epidemiological and microbiological findings of a localized outbreak of cholera, which occurred during March and April 2004 in the eastern part of Kolkata city. METHODS The affected slum area has a population of 4409, predominantly muslims. Patients suffering from acute watery diarrhoea attended the health outposts organized by National Institute of Cholera and Enteric Diseases, Kolkata and International Vaccine Institute, South Korea as part of a routine surveillance programme at the locality as well as the emergency medical camp organized by the Kolkata Municipal Corporation. Stool and water samples were collected and tested for diarrhoeagenic pathogens in the laboratory. Bacteriophages specific for V. cholerae were isolates and studied electron microscopically for morphology. RESULTS A total of 89 diarrhoea cases were reported giving an attack rate of 2 per cent. V. cholerae O1 biotype ElTor, serotype Ogawa was isolated as a sole pathogen from 15 (15.8%) of 89 stool samples screened. Water samples (2 from tube wells, 3 from municipal taps and 1 from well) showed presence of coliform bacilli with high MPN (Most Probable Number) count. Bacteriophages specific to V. cholerae were isolated from 2 of 6 water samples examined. A leakage was detected in the main pipeline supplying drinking water to that area. INTERPRETATION & CONCLUSION The outbreak was caused by V. cholerae O1 (Ogawa) biotype ElTor. The presence of phages in the water samples was an additional indicator for V. cholerae contamination in this community. Occurrences of such outbreaks support vaccination against cholera as an alternative strategy.
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Affiliation(s)
- Dipika Sur
- National Institute of Cholera & Enteric Diseases (ICMR), Kolkata, India
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Gonyou HW, Brumm MC, Bush E, Deen J, Edwards SA, Fangman T, McGlone JJ, Meunier-Salaun M, Morrison RB, Spoolder H, Sundberg PL, Johnson AK. Application of broken-line analysis to assess floor space requirements of nursery and grower-finisher pigs expressed on an allometric basis1. J Anim Sci 2006; 84:229-35. [PMID: 16361511 DOI: 10.2527/2006.841229x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Few issues in swine production are as complex as floor space allowances. One method for pork producers to calculate floor space allowance (A) is to convert BW into a 2-dimensional concept yielding an expression of A = k * BW(0.667). Data on ADG, ADFI, and G:F were obtained from published peer-reviewed studies. Five data sets were created: A = grower-finisher pigs, fully slatted floors, and consistent group size; B = grower-finisher pigs and fully slatted floors (group size did not need to be consistent); C = grower-finisher pigs, partially slatted floors, and consistent group size; D = grower-finisher pigs, partially slatted floors (group size did not need to be consistent); and E = nursery pigs, fully slatted or woven wire floors (group size did not need to be consistent). Each data set was analyzed using a broken-line analysis and a linear regression. For the broken-line analyses, the critical k value, below which a decrease in ADG occurred, varied from 0.0317 to 0.0348. In all cases the effect of space allowance on ADG was significant (P < 0.05). Using the linear analyses based on data with k values of < 0.030, the critical k values for the 4 grower-finisher data sets did not differ from those obtained using the broken-line analysis (0.0358 vs. 0.0336, respectively; P > 0.10); however, none of the linear regressions explained a significant proportion of the variation in ADG. The slopes for the nonplateau portion of the broken-line analyses based on percent values varied among data sets. For every 0.001 decrease in k (approximately 3% of the critical k value), ADG decreased by 0.56 to 1.41%, with an average value of 0.98% for the 5%-based analyses. The use of an allometric approach to express space allowance and broken-line analysis to establish space requirements seem to be useful tools for pig production. The critical k value at which crowding becomes detrimental to the growth of the pig is similar in full- and partial-slat systems and in nursery and grower-finisher stages. The critical point for crowding determined in these analyses approximated current recommendations to ensure the welfare of pigs.
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Affiliation(s)
- H W Gonyou
- Prairie Swine Centre, Inc., Saskatoon, Saskatchewan, S7H 5NP, Canada.
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Dee SA, Deen J, Jacobson L, Rossow KD, Mahlum C, Pijoan C. Laboratory model to evaluate the role of aerosols in the transport of porcine reproductive and respiratory syndrome virus. Vet Rec 2005; 156:501-4. [PMID: 15833966 DOI: 10.1136/vr.156.16.501] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [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: 11/03/2022]
Abstract
The aim of this study was to develop a model to evaluate the aerosol transmission of porcine reproductive and respiratory disease virus (PRRSV). PRRSV (MN 30-100 strain, total dose 3 x 10(6) virus particles) was aerosolised and transported up to 150 m and a portable air sampler was used to collect air samples at 1, 30, 60, 90, 120 and 150 m (five replicates at each distance) and the air samples were tested by TaqMan PCR and virus isolation. The infectivity of the aerosolised PRRSV was tested by exposing six PRRSV-naive pigs for three hours to aerosolised virus that had been transported 150 m. PRRSV RNA was detected in all five replicate air samples collected at 1, 30, 60 and 90 m, in four of the five collected at 120 m, and in three of the five collected at 150 m. Infectious PRRSV was detected by virus isolation at 1 and 30 m (all five replicates), 60, 90 and 120 m (three of the five) and 150 m (two of the five). There was a 50 per cent reduction in the log concentration of PRRSV RNA every 33 m. Three of the six pigs exposed to PRRSV-positive aerosols became infected, and PRRSV RNA was detected in air samples and on swab samples collected from the interior of the chambers that housed the infected pigs while they were being exposed.
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Affiliation(s)
- S A Dee
- Swine Disease Eradication Centre, University of Minnesota College of Veterinary Medicine, Room 385c, 1988 Fitch Avenue, St Paul, MN 55108, USA
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Abstract
The present study investigated risk factors for mortality in grow-finishing pigs of 137 pig herds belonging to one integration company during a period of 2.5 years. Mortality data, expressed as the number of dead pigs divided by the number of pigs placed in the fattening unit were investigated retrospectively. The following potential risk factors were evaluated: type of pig herd, season and year of placement in the fattening unit, pig density in the municipality, management practices (density of the pigs in the barn, origin of the pigs), housing conditions and feeding practices. The overall average mortality percentage was 4.70%. Three variables in a multivariable regression model were significantly associated with mortality: season of placement in the fattening unit, origin of the piglets and duration of the fattening period. Pigs placed in October, November and December, were at higher risk than pigs placed in other months. Herds that purchased pigs from a merchant, used pigs from other herds with an excess of piglets for filling their fattening units or herds that purchased pigs from more than five origin herds also suffered higher mortality. The mortality also increased in case of longer duration of the fattening period. This study documented for the first time that in addition to seasonal effects and a longer duration of the fattening period, purchasing feeder pigs from one or a limited number of herds is of crucial importance to achieve low mortality in the grow-finishing pigs.
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Affiliation(s)
- D G D Maes
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Salisburylaan 133, B-9820 Merelbeke, Ghent University, Ghent, Belgium.
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Larriestra AJ, Maes DG, Deen J, Morrison RB. Mixed models applied to the study of variation of grower-finisher mortality and culling rates of a large swine production system. Can J Vet Res 2005; 69:26-31. [PMID: 15745219 PMCID: PMC1142166] [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: 05/02/2023]
Abstract
Large scale production systems for swine are frequently organized in a hierarchical structure. Consequently, important production parameters, such as mortality and culling, can be analyzed at different levels. The major aims of this study were to assess variance components (VC) of mortality and culling rates attributed to sites and to barns within a site, and subsequently to investigate the impact of average entry weight, days on feed (length of the production turn), and season on the magnitude of the VC. Then, data from a large farm with 3 sites were collected during 5 y. In total, 1720040 pigs distributed in 1502 all-in/all-out grower-finisher groups were included. Linear mixed models were fitted for mortality and culling rates. The barn was modeled as the residual component (barn-to-barn variations) with production turn and site nested within production turn as random intercept variance components. Barn-to-barn pig group variation was the largest VC for mortality (63.08%), when no predictors were included in the models. Predictors, such as pigs placed on quarters 2 and 3, low average entry weight, and shorter production turn length, were associated together with higher mortality. The explained proportion of variance due to these predictors was about 12.05% and the VC for barn, site, and production turn were 67.6%, 17.6%, and 14.8%, respectively. Barn-to-barn variation was also the largest VC for culling rate (46.2%), but the same predictor mentioned above explained only about 1.4% of the variation. The VC for barn, site, and production turn were 46.8%, 21.3%, and 31.8%, respectively. Since the variability among barns far exceeded the variability among sites, the barn should be used as experimental unit in studies with grower-finisher mortality, culling rate, or both, as outcome variables.
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Affiliation(s)
- A J Larriestra
- College of Veterinary Medicine, Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota 55108, USA.
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Otake S, Dee SA, Rossow KD, Joo HS, Deen J, Molitor TW, Pijoan C. Transmission of porcine reproductive and respiratory syndrome virus by needles. Vet Rec 2002; 150:114-5. [PMID: 11838995] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- S Otake
- Center for Swine Disease Eradication, Department of Clinical and Population Sciences, University of Minnesota, College of Veterinary Medicine, St Paul 55108, USA
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Affiliation(s)
- S. Otake
- Center for Swine Disease Eradication, Department of Clinical and Population Sciences; University of Minnesota, College of Veterinary Medicine; 385c Animal Science/Veterinary Medicine Building, 1988 fitch Avenue St Paul MN 55108 USA
| | - S. A. Dee
- Center for Swine Disease Eradication, Department of Clinical and Population Sciences; University of Minnesota, College of Veterinary Medicine; 385c Animal Science/Veterinary Medicine Building, 1988 fitch Avenue St Paul MN 55108 USA
| | - K. D. Rossow
- Veterinary Diagnostic Laboratory; University of Minnesota, College of Veterinary Medicine; 133 Gartner Avenue St Paul MN 55108 USA
| | - H. S. Joo
- Center for Swine Disease Eradication, Department of Clinical and Population Sciences; University of Minnesota, College of Veterinary Medicine; 385c Animal Science/Veterinary Medicine Building, 1988 fitch Avenue St Paul MN 55108 USA
| | - J. Deen
- Center for Swine Disease Eradication, Department of Clinical and Population Sciences; University of Minnesota, College of Veterinary Medicine; 385c Animal Science/Veterinary Medicine Building, 1988 fitch Avenue St Paul MN 55108 USA
| | - T. W. Molitor
- Center for Swine Disease Eradication, Department of Clinical and Population Sciences; University of Minnesota, College of Veterinary Medicine; 385c Animal Science/Veterinary Medicine Building, 1988 fitch Avenue St Paul MN 55108 USA
| | - C. Pijoan
- Center for Swine Disease Eradication, Department of Clinical and Population Sciences; University of Minnesota, College of Veterinary Medicine; 385c Animal Science/Veterinary Medicine Building, 1988 fitch Avenue St Paul MN 55108 USA
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Targett G, Drakeley C, Jawara M, von Seidlein L, Coleman R, Deen J, Pinder M, Doherty T, Sutherland C, Walraven G, Milligan P. Artesunate reduces but does not prevent posttreatment transmission of Plasmodium falciparum to Anopheles gambiae. J Infect Dis 2001; 183:1254-9. [PMID: 11262208 DOI: 10.1086/319689] [Citation(s) in RCA: 186] [Impact Index Per Article: 8.1] [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: 11/06/2000] [Revised: 01/08/2001] [Indexed: 11/03/2022] Open
Abstract
Combination therapy that includes artemisinin derivatives cures most falciparum malaria infections. Lowering transmission by reducing gametocyte infectivity would be an additional benefit. To examine the effect of such therapy on transmission, Gambian children with Plasmodium falciparum malaria were treated with standard regimens of chloroquine or pyrimethamine-sulfadoxine alone or in combination with 1 or 3 doses of artesunate. The infectivity to mosquitoes of gametocytes in peripheral blood was determined 4 or 7 days after treatment. Infection of mosquitoes was observed in all treatment groups and was positively associated with gametocyte density. The probability of transmission was lowest in those who received pyrimethamine-sulfadoxine and 3 doses of artesunate, and it was 8-fold higher in the group that received pyrimethamine-sulfadoxine alone. Artesunate reduced posttreatment infectivity dramatically but did not abolish it completely. The study raises questions about any policy to use pyrimethamine-sulfadoxine alone as the first-line treatment for malaria.
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Affiliation(s)
- G Targett
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom.
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Dee SA, Bierk MD, Deen J, Molitor TW. An evaluation of test and removal for the elimination of porcine reproductive and respiratory syndrome virus from 5 swine farms. Can J Vet Res 2001; 65:22-7. [PMID: 11227190 PMCID: PMC1189637] [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: 02/19/2023]
Abstract
The objective of this field study was to evaluate the protocol of test and removal (T&R) for the elimination of porcine reproductive and respiratory syndrome virus (PRRSV) from 5 chronically infected breeding herds. The T&R protocol involved sampling the entire breeding herd in one day, testing sera by polymerase chain reaction and ELISA to detect previously exposed and/or infected animals, and subsequently removing them from the herd. Following completion of T&R, breeding herds were monitored for 12 consecutive months, using ELISA, for the presence of antibodies to PRRSV. In order to be classified as a PRRSV-negative herd, all samples collected over the 12-month monitoring period were required to be negative by ELISA (s/p ratio < 0.4). At the conclusion of the monitoring period, all 5 farms were PRRSV-negative, according to the defined testing criteria. Approximately 2.2% (74/3408) ELISA false positive samples were detected across all 5 farms during the monitoring period. The diagnostic cost required during the T&R protocol was approximately US $10.66 per animal tested. Limitations of the study were a lack of herds with large (> 2000 sows) breeding herd inventories, and herds with a history of PRRSV vaccination.
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Affiliation(s)
- S A Dee
- Department of Clinical and Population Sciences, University of Minnesota College of Veterinary Medicine, St. Paul 55108, USA.
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Davies PR, Morrow WE, Deen J, Gamble HR, Patton S. Seroprevalence of Toxoplasma gondii and Trichinella spiralis in finishing swine raised in different production systems in North Carolina, USA. Prev Vet Med 1998; 36:67-76. [PMID: 9677628 DOI: 10.1016/s0167-5877(98)00072-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We compared the seroprevalence of both Toxoplasma gondii and Trichinella spiralis in finishing pigs raised in different production systems in North Carolina, USA. Farms were either finishing sites using all-in/all-out management of buildings in multiple-site systems (14 farms) or farrow-to-finish systems using continuous-flow management of finishing barns or outdoor accommodation 14 farms). The two groups of herds differed with respect to several management variables. A total of 13 of 2238 samples (0.58%) were positive for antibodies to Toxoplasma gondii using the modified agglutination test. Of these, 12 were from 63 pigs sampled on a farm where finishing pigs were kept on pasture. Only one of 1752 (0.057%) samples from pigs kept in total confinement systems was seropositive. Only one pig of 2183 (0.046%) tested positive by ELISA for antibodies against T. spiralis. In this region, management practices in modern production systems appear to be adequate to virtually eliminate the risk of infection of finishing pigs with both T. gondii and T. spiralis.
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Affiliation(s)
- P R Davies
- Department of Food Animal and Equine Medicine, College of Veterinary Medicine, North Carolina State University, Raleigh 27606, USA. peter_davies@nc-
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Davies PR, Bovee FG, Funk JA, Morrow WE, Jones FT, Deen J. Isolation of Salmonella serotypes from feces of pigs raised in a multiple-site production system. J Am Vet Med Assoc 1998; 212:1925-9. [PMID: 9638195] [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: 02/07/2023]
Abstract
OBJECTIVE To determine the prevalence and serotypes of Salmonella organisms in feces of pigs raised in a modern, multiple-site production system. DESIGN Cross-sectional study of prevalence. SAMPLE POPULATION Swine housed on 7 farms (1 gilt development farm, 2 breeding farms, 1 nursery farm, and 3 finishing farms) that formed a multiplesite production system. PROCEDURE Fecal samples were obtained from 792 pigs (96 to 202/farm) and submitted for bacteriolgic culture of Salmonella organisms. RESULTS Salmonellae were isolated from pigs on all 7 farms and from 95 of 792 (12%) fecal samples. Prevalence ranged from 3.4% at the gilt development farm to 18 and 22% at the breeding farms. Serotypes identified were Salmonella derby, S typhimurium var. copenhagen, S heidelberg, S typhimurium, S mbandaka, S worthington, and S tennessee. No single serotype was not isolated from all the farms of the production system and the most prevalent serotypes at the 3 finishing farms (S typhimurium or S typhimurium var. copenhagen) were not isolated from the breeding or nursery farms. CLINICAL IMPLICATIONS Upstream infection (pigs infected before arriving at finishing farms) appears to be an unimportant source of Salmonella infection of finished hogs in multiple-site systems. High prevalence of Salmonella shedding in breeding animals suggests that food products derived from culled breeding livestock may be an important source of foodborne disease.
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Affiliation(s)
- P R Davies
- Department of Food Animal and Equine Medicine, College of Veterinary Medicine, North Carolina State University, Raleigh 27606, USA
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Davies PR, Morrow WE, Jones FT, Deen J, Fedorka-Cray PJ, Harris IT. Prevalence of Salmonella in finishing swine raised in different production systems in North Carolina, USA. Epidemiol Infect 1997; 119:237-44. [PMID: 9363023 PMCID: PMC2808846 DOI: 10.1017/s095026889700784x] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.7] [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
We compared the prevalence of salmonella in faecal samples from finishing pigs and in feed samples from swine herds in North Carolina, USA. Farms were either finishing sites using all-in/all-out management of buildings in multiple-site systems (14 farms) or farrow-to-finish systems using continuous flow management of finishing barns (15 farms). The two groups of herds differed with respect to several management variables. Salmonella were isolated from 565 of 2288 (24.6%) faecal samples and from at least 1 faecal sample on 24 of 29 (83%) farms. Predominant serotypes were S. derby, S. typhimurium (including copenhagen), S. heidelberg, S. worthington and S. mbandaka. Fewer farrow-to-finish farms were detected as positive compared with all-in/all-out farms. Prevalence was lower for pigs raised on slotted floors compared with all other floor types, and was highest for pigs raised on dirt lots. Modern methods of raising pigs in multiple-site production systems, using all-in/all-out management of finishing pigs, appear to have no benefit in reducing the prevalence of salmonella compared with conventional farrow-to-finish systems.
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Affiliation(s)
- P R Davies
- Department of Food Animal and Equine Medicine, College of Veterinary Medicine, North Carolina State University, Raleigh 27606, USA
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Lewbart G, Vaden S, Deen J, Manaugh C, Whitt D, Doi A, Smith T, Flammer K. Pharmacokinetics of enrofloxacin in the red pacu (Colossoma brachypomum) after intramuscular, oral and bath administration. J Vet Pharmacol Ther 1997; 20:124-8. [PMID: 9131538 DOI: 10.1046/j.1365-2885.1997.00814.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The intramuscular (i.m.), oral (p.o.), and bath immersion disposition of enrofloxacin were evaluated following administration to a cultured population of red pacu. The half-life for enrofloxacin following i.m. administration was 28.9 h, considerably longer than values calculated for other animals such as dogs, birds, rabbits, and tortoises. The 4 h maximum concentration (Cmax) of 1.64 micrograms/ml, following a single 5.0 mg/kg dosing easily exceeds the in vitro minimum inhibitory concentration (MIC) for 20 bacterial organisms known to infect fish. At 48 h post i.m. administration, the mean plasma enrofloxacin concentration was well above the MIC for most gram-negative fish pathogens. The gavage method of oral enrofloxacin administration produced a Cmax of 0.94 microgram/mL at 6-8 h. This Cmax was well above the reported in vitro MIC. A bath immersion concentration of 2.5 mg/L for 5 h was used in this study. The Cmax of 0.17 microgram/mL was noted on the 2 hour post-treatment plasma sample. Plasma concentrations of enrofloxacin exceeded published in vitro MIC's for most fish bacterial pathogens 72 h after treatment was concluded. Ciprofloxacin, an active metabolite of enrofloxacin, was detected and measured after all methods of drug administration. It is possible and practical to obtain therapeutic blood concentrations of enrofloxacin in the red pacu using p.o., i.m., and bath immersion administration. The i.m. route is the most predictable and results in the highest plasma concentrations of the drug.
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Affiliation(s)
- G Lewbart
- Department of Companion Animal and Special Species Medicine, College of Veterinary Medicine, North Carolina State University, Raleigh 27606, USA
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Davies PR, Morrow WE, Jones FT, Deen J, Fedorka-Cray PJ, Gray JT. Risk of shedding Salmonella organisms by market-age hogs in a barn with open-flush gutters. J Am Vet Med Assoc 1997; 210:386-9. [PMID: 9057924] [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: 02/03/2023]
Abstract
OBJECTIVE To compare prevalence of fecal shedding of Salmonella organisms and serum antibodies to Salmonella sp in market-age pigs housed in barns with partially slotted floors or solid floors with open-flush gutters. DESIGN Cross-sectional study of prevalence. SAMPLE POPULATION Finishing-age pigs deemed by the producer to be within 1 month of slaughter. PROCEDURE Fecal and serum samples were obtained from a group of 121 pigs housed in a barn with solid floors (31 fecal samples, 30 serum samples) and from a group of about 400 pigs housed on partially slotted floors (57 fecal samples, 64 serum samples). Fecal samples were submitted for bacteriologic culture to detect Salmonella organisms, and serum samples were tested for antibodies by use of ELISA. RESULTS Salmonella agona was isolated from 26 of 31 (84%) fecal samples obtained from pigs housed in the open-flush gutter barn, compared with 5 of 57 (9%) fecal samples from pigs in the barn with slotted floors. Median value for optical density was higher for serum samples from pigs housed in the open-flush gutter barn. CLINICAL IMPLICATIONS Housing of finishing-age swine in barns with open-flush gutters may contribute to increased shedding of Salmonella sp. Analysis of our observations indicated that repeated exposure to infected feces is important in prolonging fecal shedding by swine.
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Affiliation(s)
- P R Davies
- Department of Food Animal and Equine Medicine, College of Veterinary Medicine, North Carolina State University, Raleigh 27606, USA
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Davies P, Morrow M, Funk J, Deen J. Erythromycin resistance of Campylobacter isolates from pigs. Vet Rec 1996; 139:244. [PMID: 8883355] [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: 02/02/2023]
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Davies PR, Morrow WE, Miller DC, Deen J. Epidemiologic study of decubital ulcers in sows. J Am Vet Med Assoc 1996; 208:1058-62. [PMID: 8621319] [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: 01/31/2023]
Abstract
OBJECTIVE To determine prevalence and risk factors for decubital ulcers of the shoulder in sows. DESIGN Descriptive cross-sectional study. SAMPLE POPULATION All females of breeding age in a large confinement swine facility. PROCEDURE 1,916 females were examined for lesions of the skin over the tuber of the spine of the scapula and for body condition scoring. Observational data were combined with sow data (parity, date of farrowing, litter size) contained in computerized records. RESULTS Decubital ulcers were observed in 8.3% of females, predominantly lactating sows. Ulcer prevalence was strongly associated with time after farrowing. Lesions apparently healed rapidly after weaning. Ulcer prevalence was associated with low body condition scores, but was not associated with parity. IMPLICATIONS Decubital ulcers are a multifactorial condition. Housing on concrete floors per se did not result in ulcers. Prolonged recumbency during parturition, reduced activity in early lactation, periparturient illness, thin body condition, moist skin, and floor type are potential risk factors.
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Affiliation(s)
- P R Davies
- Department of Food Animal and Equine Medicine, College of Veterinary Medicine, North Carolina State University, Raleigh 27606, USA
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