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Weikum J, van Dyck JF, Subramani S, Klebl DP, Storflor M, Muench SP, Abel S, Sobott F, Morth JP. The bacterial magnesium transporter MgtA reveals highly selective interaction with specific cardiolipin species. Biochim Biophys Acta Mol Cell Res 2024; 1871:119614. [PMID: 37879515 DOI: 10.1016/j.bbamcr.2023.119614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/13/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023]
Abstract
The bacterial magnesium transporter A (MgtA) is a specialized P-type ATPase important for Mg2+ import into the cytoplasm; disrupted magnesium homeostasis is linked to intrinsic ribosome instability and antibacterial resistance in Salmonella strains. Here, we show that MgtA has functional specificity for cardiolipin 18:1. Still, it reaches maximum activity only in combination with cardiolipin 16:0, equivalent to the major components of native cardiolipin found in E. coli membranes. Native mass spectrometry indicates the presence of two binding sites for cardiolipin, agreeing with the kinetic studies revealing that a cooperative relationship likely exists between the two cardiolipin variants. This is the first experimental evidence of cooperative effects between lipids of the same class, with only minor variations in their acyl chain composition, acting on a membrane protein. In summary, our results reveal that MgtA exhibits a highly complex interaction with one cardiolipin 18:1 and one cardiolipin 16:0, affecting protein activity and stability, contributing to our understanding of the particular interactions between lipid environment and membrane proteins. Further, a better understanding of Mg2+ homeostasis in bacteria, due to its role as a virulence regulator, will provide further insights into the regulation and mechanism of bacterial infections.
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Affiliation(s)
- Julia Weikum
- Membrane Transport Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, P.O. Box 1137, Blindern, 0318 Oslo, Norway; Enzyme and Protein Chemistry, Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark
| | - Jeroen F van Dyck
- Department of Chemistry, University of Antwerp, Campus Groenenborger, Groenenborgerlaan 171, G.V. 418, 2020 Antwerpen, Belgium
| | - Saranya Subramani
- Membrane Transport Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, P.O. Box 1137, Blindern, 0318 Oslo, Norway
| | - David P Klebl
- School of Biomedical Sciences & The Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Merete Storflor
- Infections Biology Lab, Department of Pharmacy, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Stephen P Muench
- School of Biomedical Sciences & The Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Sören Abel
- Infections Biology Lab, Department of Pharmacy, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Frank Sobott
- Department of Chemistry, University of Antwerp, Campus Groenenborger, Groenenborgerlaan 171, G.V. 418, 2020 Antwerpen, Belgium; School of Molecular and Cellular Biology & The Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom.
| | - J Preben Morth
- Membrane Transport Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, P.O. Box 1137, Blindern, 0318 Oslo, Norway; Enzyme and Protein Chemistry, Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark; Institute for Experimental Medical Research (IEMR), Oslo University Hospital, Ullevål PB 4956 Nydalen, NO-0424 Oslo, Norway.
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Chahine Z, Abel S, Hollin T, Chung JH, Barnes GL, Daub ME, Renard I, Choi JY, Pratap V, Pal A, Alba-Argomaniz M, Banks CAS, Kirkwood J, Saraf A, Camino I, Castaneda P, Cuevas MC, De Mercado-Arnanz J, Fernandez-Alvaro E, Garcia-Perez A, Ibarz N, Viera-Morilla S, Prudhomme J, Joyner CJ, Bei AK, Florens L, Ben Mamoun C, Vanderwal CD, Le Roch KG. A Potent Kalihinol Analogue Disrupts Apicoplast Function and Vesicular Trafficking in P. falciparum Malaria. bioRxiv 2023:2023.11.21.568162. [PMID: 38045341 PMCID: PMC10690269 DOI: 10.1101/2023.11.21.568162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Here we report the discovery of MED6-189, a new analogue of the kalihinol family of isocyanoterpene (ICT) natural products. MED6-189 is effective against drug-sensitive and -resistant P. falciparum strains blocking both intraerythrocytic asexual replication and sexual differentiation. This compound was also effective against P. knowlesi and P. cynomolgi. In vivo efficacy studies using a humanized mouse model of malaria confirms strong efficacy of the compound in animals with no apparent hemolytic activity or apparent toxicity. Complementary chemical biology, molecular biology, genomics and cell biological analyses revealed that MED6-189 primarily targets the parasite apicoplast and acts by inhibiting lipid biogenesis and cellular trafficking. Genetic analyses in P. falciparum revealed that a mutation in PfSec13, which encodes a component of the parasite secretory machinery, reduced susceptibility to the drug. The high potency of MED6-189 in vitro and in vivo, its broad range of efficacy, excellent therapeutic profile, and unique mode of action make it an excellent addition to the antimalarial drug pipeline.
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Affiliation(s)
- Z Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - S Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - T Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - JH Chung
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - GL Barnes
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - ME Daub
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - I Renard
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - JY Choi
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - V Pratap
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - A Pal
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - M Alba-Argomaniz
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - CAS Banks
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - J Kirkwood
- Metabolomics Core Facility, University of California, Riverside, CA 92521, USA
| | - A Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - I Camino
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - P Castaneda
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - MC Cuevas
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | | | | | - A Garcia-Perez
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - N Ibarz
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - S Viera-Morilla
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - J Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - CJ Joyner
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - AK Bei
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - L Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - C Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - CD Vanderwal
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - KG Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
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Shamsesfandabadi P, Ponnapalli S, Spencer K, Patel A, Yin Y, Abel S, Beriwal S, Wegner RE, Patel AK, Horne ZD. CT vs. MRI: Which is More Accurate in Grading Rectal Wall Infiltration after Hydrogel Spacer Placement for Prostate Cancer Patients? Int J Radiat Oncol Biol Phys 2023; 117:e436-e437. [PMID: 37785418 DOI: 10.1016/j.ijrobp.2023.06.1608] [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: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) The purpose of this study was to evaluate the incidence and severity of rectal wall infiltration (RWI) in prostate cancer patients after rectal hydrogel spacer implantation, a commonly used procedure to minimize rectal radiation exposure during prostate radiotherapy. The study aimed to determine correlation of RWI using computed tomography (CT) scans and magnetic resonance imaging (MRI) scans in order to determine the optimal post-placement imaging modality. MATERIALS/METHODS This retrospective study was conducted on 370 patients diagnosed with localized prostate cancer who underwent rectal hydrogel spacer placement from 2020 to 2022. CT scans were performed on all patients, with a smaller subset also undergoing MRI scans. The images were independently evaluated by three radiation oncologists to grade RWI levels using a standardized scoring system based on CT and MRI images after hydrogel placement. The levels were categorized as 0 (no RWI), 1 (focal RWI), 2 (moderate RWI), and 3 (significant RWI). RESULTS Any grade of RWI was identified in 79.8% of men with the majority (41%) being RWI grade 1. The median time for CT scans was 9 days after hydrogel spacer placement and 14.5 days for MRI scans. For the subset of patients with both CT and MRI scans after spacer (mostly SpaceOAR Vue), RWI was detected in 58.33% of patients based on CT and 61.11% of patients based on MRI. Table 1 shows the mean percentage of patients with each score of RWI for each imaging modality. MRI was more likely to lead to a designation of RWI of any grade compared to CT and more often led to detection of RWI grades 2-3. CONCLUSION Our findings demonstrate that the incidence and severity of RWI may be higher than previously reported in clinical trials and that MRI may be a more sensitive imaging modality. Caution is needed in the utilization of rectal spacer gels given the potential for complications with misplacement prior to radiation therapy. Further study is warranted to determine the potential impact of low-grade RWI on the safety of subsequent treatment.
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Affiliation(s)
- P Shamsesfandabadi
- Allegheny Health Network Cancer Institute, Department of Radiation Oncology, Pittsburgh, PA
| | - S Ponnapalli
- Drexel University College of Medicine, Philadelphia, PA
| | - K Spencer
- Drexel University College of Medicine, Philadelphia, PA
| | - A Patel
- Drexel University College of Medicine, Philadelphia, PA
| | - Y Yin
- Allegheny Health Network, Pittsburgh, PA
| | - S Abel
- Allegheny Health Network Cancer Institute, Department of Radiation Oncology, Pittsburgh, PA
| | - S Beriwal
- Allegheny Health Network Cancer Institute, Department of Radiation Oncology, Pittsburgh, PA
| | - R E Wegner
- Allegheny Health Network Cancer Institute, Department of Radiation Oncology, Pittsburgh, PA
| | - A K Patel
- Allegheny Health Network Cancer Institute, Department of Radiation Oncology, Pittsburgh, PA
| | - Z D Horne
- Allegheny Health Network Cancer Institute, Department of Radiation Oncology, Pittsburgh, PA
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Chahine Z, Gupta M, Lenz T, Hollin T, Abel S, Banks CAS, Saraf A, Prudhomme J, Florens L, Le Roch KG. PfMORC protein regulates chromatin accessibility and transcriptional repression in the human malaria parasite, P. falciparum. bioRxiv 2023:2023.09.11.557253. [PMID: 37745554 PMCID: PMC10515874 DOI: 10.1101/2023.09.11.557253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The environmental challenges the human malaria parasite, Plasmodium falciparum, faces during its progression into its various lifecycle stages warrant the use of effective and highly regulated access to chromatin for transcriptional regulation. Microrchidia (MORC) proteins have been implicated in DNA compaction and gene silencing across plant and animal kingdoms. Accumulating evidence has shed light into the role MORC protein plays as a transcriptional switch in apicomplexan parasites. In this study, using CRISPR/Cas9 genome editing tool along with complementary molecular and genomics approaches, we demonstrate that PfMORC not only modulates chromatin structure and heterochromatin formation throughout the parasite erythrocytic cycle, but is also essential to the parasite survival. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) experiments suggest that PfMORC binds to not only sub-telomeric regions and genes involved in antigenic variation but is also most likely a key modulator of stage transition. Protein knockdown experiments followed by chromatin conformation capture (Hi-C) studies indicate that downregulation of PfMORC induces the collapse of the parasite heterochromatin structure leading to its death. All together these findings confirm that PfMORC plays a crucial role in chromatin structure and gene regulation, validating this factor as a strong candidate for novel antimalarial strategies.
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Affiliation(s)
- Z Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - M Gupta
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - T Lenz
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - T Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - S Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - CAS Banks
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - A Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - J Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - L Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - KG Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
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Poghosyan AH, Abel S, Koetz J. Simulation of AOT reverse micelles with polyethylenimine in hexane. Colloid Polym Sci 2023. [DOI: 10.1007/s00396-023-05059-4] [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: 02/05/2023]
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Abel S, Shamsesfandabadi P, Renz P, Monga D, Wegner R. Utilization of Advanced Radiation Techniques in Neuroendocrine Carcinoma of the Pancreas. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.1089] [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]
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Hemez C, Clarelli F, Palmer AC, Bleis C, Abel S, Chindelevitch L, Cohen T, Abel zur Wiesch P. Mechanisms of antibiotic action shape the fitness landscapes of resistance mutations. Comput Struct Biotechnol J 2022; 20:4688-4703. [PMID: 36147681 PMCID: PMC9463365 DOI: 10.1016/j.csbj.2022.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 11/15/2022] Open
Abstract
Antibiotic-resistant pathogens are a major public health threat. A deeper understanding of how an antibiotic's mechanism of action influences the emergence of resistance would aid in the design of new drugs and help to preserve the effectiveness of existing ones. To this end, we developed a model that links bacterial population dynamics with antibiotic-target binding kinetics. Our approach allows us to derive mechanistic insights on drug activity from population-scale experimental data and to quantify the interplay between drug mechanism and resistance selection. We find that both bacteriostatic and bactericidal agents can be equally effective at suppressing the selection of resistant mutants, but that key determinants of resistance selection are the relationships between the number of drug-inactivated targets within a cell and the rates of cellular growth and death. We also show that heterogeneous drug-target binding within a population enables resistant bacteria to evolve fitness-improving secondary mutations even when drug doses remain above the resistant strain's minimum inhibitory concentration. Our work suggests that antibiotic doses beyond this "secondary mutation selection window" could safeguard against the emergence of high-fitness resistant strains during treatment.
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Affiliation(s)
- Colin Hemez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Graduate Program in Biophysics, Harvard University, Boston, MA 02115, USA
- Corresponding authors at: Broad Institute, 75 Ames St, Room 3035, Cambridge, MA 02412, USA (C. Hemez). Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway (P. Abel zur Wiesch).
| | - Fabrizio Clarelli
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Adam C. Palmer
- Department of Pharmacology, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christina Bleis
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sören Abel
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Division of Infection Control, Norwegian Institute of Public Health, Oslo 0318, Norway
| | - Leonid Chindelevitch
- Department of Infectious Disease Epidemiology, Imperial College, London SW7 2AZ, UK
| | - Theodore Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA
| | - Pia Abel zur Wiesch
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Division of Infection Control, Norwegian Institute of Public Health, Oslo 0318, Norway
- Corresponding authors at: Broad Institute, 75 Ames St, Room 3035, Cambridge, MA 02412, USA (C. Hemez). Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway (P. Abel zur Wiesch).
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Johnson P, Chan JK, Vavasour IM, Abel S, Lee LE, Yong H, Laule C, Li DKB, Tam R, Traboulsee A, Carruthers RL, Kolind SH. Quantitative MRI findings indicate diffuse white matter damage in Susac Syndrome. Mult Scler J Exp Transl Clin 2022; 8:20552173221078834. [PMID: 35186315 PMCID: PMC8851927 DOI: 10.1177/20552173221078834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/21/2022] [Indexed: 11/15/2022] Open
Abstract
Background Susac Syndrome (SuS) is an autoimmune endotheliopathy impacting the brain, retina and cochlea that can clinically mimic multiple sclerosis (MS). Objective To evaluate non-lesional white matter demyelination changes in SuS compared to MS and healthy controls (HC) using quantitative MRI. Methods 3T MRI including myelin water imaging and diffusion basis spectrum imaging were acquired for 7 SuS, 10 MS and 10 HC participants. Non-lesional white matter was analyzed in the corpus callosum (CC) and normal appearing white matter (NAWM). Groups were compared using ANCOVA with Tukey correction. Results SuS CC myelin water fraction (mean 0.092) was lower than MS(0.11, p = 0.01) and HC(0.11, p = 0.04). Another myelin marker, radial diffusivity, was increased in SuS CC(0.27μm2/ms) compared to HC(0.21μm2/ms, p = 0.008) and MS(0.23μm2/ms, p = 0.05). Fractional anisotropy was lower in SuS CC(0.82) than HC(0.86, p = 0.04). Fiber fraction (reflecting axons) did not differ from HC or MS. In NAWM, radial diffusivity and apparent diffusion coefficient were significantly increased in SuS compared to HC(p < 0.001 for both measures) and MS(p = 0.003, p < 0.001 respectively). Conclusions Our results provided evidence of myelin damage in SuS, particularly in the CC, and more extensive microstructural injury in NAWM, supporting the hypothesis that there are widespread microstructural changes in SuS syndrome including diffuse demyelination.
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Affiliation(s)
| | - JK Chan
- Department of Medicine (Neurology), University of British Columbia, Canada
| | - IM Vavasour
- Department of Radiology, University of British Columbia, Canada
- International Collaboration on Repair Discoveries (ICORD)
| | | | | | - H Yong
- Department of Medicine (Neurology), University of British Columbia, Canada
| | - C Laule
- Department of Radiology, University of British Columbia, Canada
- International Collaboration on Repair Discoveries (ICORD)
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
- Department of Physics and Astronomy, University of British Columbia, Canada
| | - DKB Li
- Department of Medicine (Neurology), University of British Columbia, Canada
- Department of Radiology, University of British Columbia, Canada
| | - R Tam
- Department of Radiology, University of British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Canada
| | | | - RL Carruthers
- Department of Medicine (Neurology), University of British Columbia, Canada
| | - SH Kolind
- Department of Medicine (Neurology), University of British Columbia, Canada
- Department of Radiology, University of British Columbia, Canada
- International Collaboration on Repair Discoveries (ICORD)
- Department of Physics and Astronomy, University of British Columbia, Canada
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Abel S, Colonias A, Beriwal S, Weksler B, Finley G, Long S, Wegner R. Comparing Clinicopathologic Factors and Survival in Stage III Adenocarcinoma and Squamous Cell Carcinoma of the Lung Following Definitive Chemoradiotherapy. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2021.10.183] [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: 10/19/2022]
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10
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Gillman AN, Helleux A, Abel S. A single step three-strain in vivo Gateway reaction. Plasmid 2021; 118:102608. [PMID: 34801582 DOI: 10.1016/j.plasmid.2021.102608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 10/19/2022]
Abstract
We developed a simplified, highly efficient Gateway reaction that recombines target DNA to expression (destination) plasmids in vivo and subsequently conjugates the final vector into a recipient strain, all in a single step. This recipient strain does not need to contain any selective marker and can be freely chosen as long as it is sensitive to ccdB counterselection and can be targeted by the RP4α conjugation system. Our protocol is simple, robust, and cost effective. It works in 96-well plate format and performs across a range of temperatures. We designed modular, minimal destination vectors containing a modified Gateway insert to ease vector design by providing locations for insertion of tags, promoters, or conjugations. To demonstrate the utility of our system, we created destination vectors with split adenylate cyclase tags for bacterial two-hybrid (B2H) studies and screened a library of diguanylate cyclases for protein-protein interactions in a single step.
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Affiliation(s)
- Aaron Nicholas Gillman
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway; Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Alexandra Helleux
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway
| | - Sören Abel
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway; Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; Centre for Molecular Medicine Norway, Nordic EMBL Partnership, 0318 Oslo, Norway; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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11
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Abel S, Renz P, Colonias A, Raj M, Wegner R. PD-0847 Dose escalation in locally advanced NSCLC: comparing outcomes in adenocarcinoma and squamous cell carcinoma. Radiother Oncol 2021. [DOI: 10.1016/s0167-8140(21)07126-7] [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: 12/01/2022]
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12
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Mahmutovic A, Gillman AN, Lauksund S, Robson Moe NA, Manzi A, Storflor M, Abel Zur Wiesch P, Abel S. RESTAMP - Rate estimates by sequence-tag analysis of microbial populations. Comput Struct Biotechnol J 2021; 19:1035-1051. [PMID: 33613869 PMCID: PMC7878984 DOI: 10.1016/j.csbj.2021.01.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 12/31/2022] Open
Abstract
Microbial division rates determine the speed of mutation accumulation and thus the emergence of antimicrobial resistance. Microbial death rates are affected by antibiotic action and the immune system. Therefore, measuring these rates has advanced our understanding of host-pathogen interactions and antibiotic action. Several methods based on marker-loss or few inheritable neutral markers exist that allow estimating microbial division and death rates, each of which has advantages and limitations. Technical bottlenecks, i.e., experimental sampling events, during the experiment can distort the rate estimates and are typically unaccounted for or require additional calibration experiments. In this work, we introduce RESTAMP (Rate Estimates by Sequence Tag Analysis of Microbial Populations) as a method for determining bacterial division and death rates. This method uses hundreds of fitness neutral sequence barcodes to measure the rates and account for experimental bottlenecks at the same time. We experimentally validate RESTAMP and compare it to established plasmid loss methods. We find that RESTAMP has a number of advantages over plasmid loss or previous marker based techniques. (i) It enables to correct the distortion of rate estimates by technical bottlenecks. (ii) Rate estimates are independent of the sequence tag distribution in the starting culture allowing the use of an arbitrary number of tags. (iii) It introduces a bottleneck sensitivity measure that can be used to maximize the accuracy of the experiment. RESTAMP allows studying microbial population dynamics with great resolution over a wide dynamic range and can thus advance our understanding of host-pathogen interactions or the mechanisms of antibiotic action.
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Affiliation(s)
- Anel Mahmutovic
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway
| | - Aaron Nicholas Gillman
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway.,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, PA 16802, USA
| | - Silje Lauksund
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway
| | - Natasha-Anne Robson Moe
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway
| | - Aime Manzi
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway
| | - Merete Storflor
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway.,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, PA 16802, USA
| | - Pia Abel Zur Wiesch
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway.,Centre for Molecular Medicine Norway, Nordic EMBL Partnership, 0318 Oslo, Norway.,Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sören Abel
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, 9037 Tromsø, Norway.,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, PA 16802, USA.,Centre for Molecular Medicine Norway, Nordic EMBL Partnership, 0318 Oslo, Norway.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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Cotte L, Hocqueloux L, Lefebvre M, Pradat P, Bani-Sadr F, Huleux T, Poizot-Martin I, Pugliese P, Rey D, Cabié A, Chirouze C, Drobacheff-Thiébaut C, Foltzer A, Bouiller K, Hustache-Mathieu L, Lepiller Q, Bozon F, Babre O, Brunel AS, Muret P, Chevalier E, Jacomet C, Laurichesse H, Lesens O, Vidal M, Mrozek N, Aumeran C, Baud O, Corbin V, Goncalvez E, Mirand A, brebion A, Henquell C, Lamaury I, Fabre I, Curlier E, Ouissa R, Herrmann-Storck C, Tressieres B, Receveur MC, Boulard F, Daniel C, Clavel C, Roger PM, Markowicz S, Chellum Rungen N, Merrien D, Perré P, Guimard T, Bollangier O, Leautez S, Morrier M, Laine L, Boucher D, Point P, Cotte L, Ader F, Becker A, Boibieux A, Brochier C, Brunel-Dalmas F, Cannesson O, Chiarello P, Chidiac C, Degroodt S, Ferry T, Godinot M, Livrozet JM, Makhloufi D, Miailhes P, Perpoint T, Perry M, Pouderoux C, Roux S, Triffault-Fillit C, Valour F, Charre C, Icard V, Tardy JC, Trabaud MA, Ravaux I, Ménard A, Belkhir AY, Colson P, Dhiver C, Madrid A, Martin-Degioanni M, Meddeb L, Mokhtari M, Motte A, Raoux A, Toméi C, Tissot-Dupont H, Poizot-Martin I, Brégigeon S, Zaegel-Faucher O, Obry-Roguet V, Laroche H, Orticoni M, Soavi MJ, Ressiot E, Ducassou MJ, Jaquet I, Galie S, Colson H, Ritleng AS, Ivanova A, Debreux C, Lions C, Rojas-Rojas T, Cabié A, Abel S, Bavay J, Bigeard B, Cabras O, Cuzin L, Dupin de Majoubert R, Fagour L, Guitteaud K, Marquise A, Najioullah F, Pierre-François S, Pasquier J, Richard P, Rome K, Turmel JM, Varache C, Atoui N, Bistoquet M, Delaporte E, Le Moing V, Makinson A, Meftah N, Merle de Boever C, Montes B, Montoya Ferrer A, Tuaillon E, Reynes J, Lefèvre B, Jeanmaire E, Hénard S, Frentiu E, Charmillon A, Legoff A, Tissot N, André M, Boyer L, Bouillon MP, Delestan M, Goehringer F, Bevilacqua S, Rabaud C, May T, Raffi F, Allavena C, Aubry O, Billaud E, Biron C, Bonnet B, Bouchez S, Boutoille D, Brunet-Cartier C, Deschanvres C, Gaborit BJ, Grégoire A, Grégoire M, Grossi O, Guéry R, Jovelin T, Lefebvre M, Le Turnier P, Lecomte R, Morineau P, Reliquet V, Sécher S, Cavellec M, Paredes E, Soria A, Ferré V, André-Garnier E, Rodallec A, Pugliese P, Breaud S, Ceppi C, Chirio D, Cua E, Dellamonica P, Demonchy E, De Monte A, Durant J, Etienne C, Ferrando S, Garraffo R, Michelangeli C, Mondain V, Naqvi A, Oran N, Perbost I, Carles M, Klotz C, Maka A, Pradier C, Prouvost-Keller B, Risso K, Rio V, Rosenthal E, Touitou I, Wehrlen-Pugliese S, Zouzou G, Hocqueloux L, Prazuck T, Gubavu C, Sève A, Giaché S, Rzepecki V, Colin M, Boulard C, Thomas G, Cheret A, Goujard C, Quertainmont Y, Teicher E, Lerolle N, Jaureguiberry S, Colarino R, Deradji O, Castro A, Barrail-Tran A, Yazdanpanah Y, Landman R, Joly V, Ghosn J, Rioux C, Lariven S, Gervais A, Lescure FX, Matheron S, Louni F, Julia Z, Le GAC S, Charpentier C, Descamps D, Peytavin G, Duvivier C, Aguilar C, Alby-Laurent F, Amazzough K, Benabdelmoumen G, Bossi P, Cessot G, Charlier C, Consigny PH, Jidar K, Lafont E, Lanternier F, Leporrier J, Lortholary O, Louisin C, Lourenco J, Parize P, Pilmis B, Rouzaud C, Touam F, Valantin MA, Tubiana R, Agher R, Seang S, Schneider L, PaLich R, Blanc C, Katlama C, Bani-Sadr F, Berger JL, N’Guyen Y, Lambert D, Kmiec I, Hentzien M, Brunet A, Romaru J, Marty H, Brodard V, Arvieux C, Tattevin P, Revest M, Souala F, Baldeyrou M, Patrat-Delon S, Chapplain JM, Benezit F, Dupont M, Poinot M, Maillard A, Pronier C, Lemaitre F, Morlat C, Poisson-Vannier M, Jovelin T, Sinteff JP, Gagneux-Brunon A, Botelho-Nevers E, Frésard A, Ronat V, Lucht F, Rey D, Fischer P, Partisani M, Cheneau C, Priester M, Mélounou C, Bernard-Henry C, de Mautort E, Fafi-Kremer S, Delobel P, Alvarez M, Biezunski N, Debard A, Delpierre C, Gaube G, Lansalot P, Lelièvre L, Marcel M, Martin-Blondel G, Piffaut M, Porte L, Saune K, Robineau O, Ajana F, Aïssi E, Alcaraz I, Alidjinou E, Baclet V, Bocket L, Boucher A, Digumber M, Huleux T, Lafon-Desmurs B, Meybeck A, Pradier M, Tetart M, Thill P, Viget N, Valette M. Microelimination or Not? The Changing Epidemiology of Human Immunodeficiency Virus-Hepatitis C Virus Coinfection in France 2012–2018. Clin Infect Dis 2021; 73:e3266-e3274. [DOI: 10.1093/cid/ciaa1940] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/01/2021] [Indexed: 01/15/2023] Open
Abstract
Abstract
Background
The arrival of highly effective, well-tolerated, direct-acting antiviral agents (DAA) led to a dramatic decrease in hepatitis C virus (HCV) prevalence. Human immunodeficiency virus (HIV)-HCV–coinfected patients are deemed a priority population for HCV elimination, while a rise in recently acquired HCV infections in men who have sex with men (MSM) has been described. We describe the variations in HIV-HCV epidemiology in the French Dat’AIDS cohort.
Methods
This was a retrospective analysis of a prospective cohort of persons living with HIV (PLWH) from 2012 to 2018. We determined HCV prevalence, HCV incidence, proportion of viremic patients, treatment uptake, and mortality rate in the full cohort and by HIV risk factors.
Results
From 2012 to 2018, 50 861 PLWH with a known HCV status were followed up. During the period, HCV prevalence decreased from 15.4% to 13.5%. HCV prevalence among new HIV cases increased from 1.9% to 3.5% in MSM but remained stable in other groups. Recently acquired HCV incidence increased from 0.36/100 person-years to 1.25/100 person-years in MSM. The proportion of viremic patients decreased from 67.0% to 8.9%. MSM became the first group of viremic patients in 2018 (37.9%). Recently acquired hepatitis represented 59.2% of viremic MSM in 2018. DAA treatment uptake increased from 11.4% to 61.5%. More treatments were initiated in MSM in 2018 (41.2%) than in intravenous drug users (35.6%). In MSM, treatment at the acute phase represented 30.0% of treatments in 2018.
Conclusions
A major shift in HCV epidemiology was observed in PLWH in France from 2012 to 2018, leading to a unique situation in which the major group of HCV transmission in 2018 was MSM.
Clinical Trials Registration. NCT02898987.
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Affiliation(s)
- Laurent Cotte
- Department of Infectious Diseases, Croix-Rousse Hospital, Hospices Civils de Lyon, Lyon, Institut National de la Santé et de la Recherche Médicale (INSERM) U1052, Lyon, France
| | - Laurent Hocqueloux
- Department of Infectious Diseases, Centre Hospitalier Régional d’Orléans – La Source, Orléans, France
| | - Maeva Lefebvre
- Department of Infectious Diseases, Centre Hospitalier Universitaire Hôtel-Dieu, Nantes; Centre d’Investigation Clinique (CIC) 1413, INSERM, Nantes, France
| | - Pierre Pradat
- Center for Clinical Research, Croix-Rousse Hospital, Hospices Civils de Lyon, Lyon, France
| | - Firouze Bani-Sadr
- Department of Internal Medicine, Clinical Immunology and Infectious Diseases, Robert Debré Hospital, University Hospital, Reims, France
| | - Thomas Huleux
- Department of Infectious Diseases and Travel Diseases, Centre Hospitalier Gustave-Dron, Tourcoing, France
| | - Isabelle Poizot-Martin
- Immuno-Hematology Clinic, Assistance Publique–Hôpitaux de Marseille, Hôpital Sainte-Marguerite, Marseille, Aix-MarseilleUniversity–Inserm–Institut de Recherche pour le Développement (IRD), Sciences Economiques & Sociales de la Santé & Traitement de l’Information Médicale, Marseille, France
| | - Pascal Pugliese
- Department of Infectious Diseases, Centre Hospitalier Universitaire de Nice, Hôpital l’Archet, Nice, France
| | - David Rey
- HIV Infection Care Centre, Hôpitaux Universitaires, Strasbourg
| | - André Cabié
- Department of Infectious Diseases, Centre Hospitalier Universitaire de Martinique, Fort de France, Université des Antilles EA4537, Fort de France, INSERM CIC1424, Fort-de-France, France
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Abel S, Karlovits S, Yu A, Renz P, Xu L, Wegner R. Patterns Of Care In The Non-Operative Management Of Elderly Patients With NSCLC Brain Metastases. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.054] [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: 10/23/2022]
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15
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Bregigeon S, Obry-Roguet V, Delpierre C, Cotte L, Duvivier C, Pugliese P, Abel S, Huleux T, Poizot-Martin I. Impact de la zone géographique de résidence dans la prévalence du surpoids et de l’obésité au sein de la cohorte Dat’AIDS. Med Mal Infect 2020. [DOI: 10.1016/j.medmal.2020.06.024] [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: 10/23/2022]
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Clarelli F, Palmer A, Singh B, Storflor M, Lauksund S, Cohen T, Abel S, Abel zur Wiesch P. Drug-target binding quantitatively predicts optimal antibiotic dose levels in quinolones. PLoS Comput Biol 2020; 16:e1008106. [PMID: 32797079 PMCID: PMC7449454 DOI: 10.1371/journal.pcbi.1008106] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 04/03/2020] [Revised: 08/26/2020] [Accepted: 06/30/2020] [Indexed: 11/19/2022] Open
Abstract
Antibiotic resistance is rising and we urgently need to gain a better quantitative understanding of how antibiotics act, which in turn would also speed up the development of new antibiotics. Here, we describe a computational model (COMBAT-COmputational Model of Bacterial Antibiotic Target-binding) that can quantitatively predict antibiotic dose-response relationships. Our goal is dual: We address a fundamental biological question and investigate how drug-target binding shapes antibiotic action. We also create a tool that can predict antibiotic efficacy a priori. COMBAT requires measurable biochemical parameters of drug-target interaction and can be directly fitted to time-kill curves. As a proof-of-concept, we first investigate the utility of COMBAT with antibiotics belonging to the widely used quinolone class. COMBAT can predict antibiotic efficacy in clinical isolates for quinolones from drug affinity (R2>0.9). To further challenge our approach, we also do the reverse: estimate the magnitude of changes in drug-target binding based on antibiotic dose-response curves. We overexpress target molecules to infer changes in antibiotic-target binding from changes in antimicrobial efficacy of ciprofloxacin with 92-94% accuracy. To test the generality of our approach, we use the beta-lactam ampicillin to predict target molecule occupancy at MIC from antimicrobial action with 90% accuracy. Finally, we apply COMBAT to predict antibiotic concentrations that can select for resistance due to novel resistance mutations. Using ciprofloxacin and ampicillin as well defined test cases, our work demonstrates that drug-target binding is a major predictor of bacterial responses to antibiotics. This is surprising because antibiotic action involves many additional effects downstream of drug-target binding. In addition, COMBAT provides a framework to inform optimal antibiotic dose levels that maximize efficacy and minimize the rise of resistant mutants.
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Affiliation(s)
- Fabrizio Clarelli
- Department of Pharmacy, Faculty of Health Sciences, UiT—The Arctic University of Norway, Tromsø, Norway
- Department of Biology, Eberly College of Science, The Pennsylvania State University, University Park, PA, United States of America
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States of America
| | - Adam Palmer
- Department of Pharmacology, Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Bhupender Singh
- Department of Pharmacy, Faculty of Health Sciences, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Merete Storflor
- Department of Pharmacy, Faculty of Health Sciences, UiT—The Arctic University of Norway, Tromsø, Norway
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, PA, United States of America
| | - Silje Lauksund
- Department of Pharmacy, Faculty of Health Sciences, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States of America
| | - Sören Abel
- Department of Pharmacy, Faculty of Health Sciences, UiT—The Arctic University of Norway, Tromsø, Norway
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States of America
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, PA, United States of America
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, Oslo, Norway
| | - Pia Abel zur Wiesch
- Department of Pharmacy, Faculty of Health Sciences, UiT—The Arctic University of Norway, Tromsø, Norway
- Department of Biology, Eberly College of Science, The Pennsylvania State University, University Park, PA, United States of America
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States of America
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, Oslo, Norway
- * E-mail:
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Horne Z, Abel S, Wegner R, Colonias A. Patterns of care and outcomes of early-stage sarcomatoid squamous cell carcinomas of the larynx. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2019.11.218] [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: 11/24/2022]
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Wegner R, Verma V, Abel S, Hasan S, Weksler B, Colonias A. P1.12-20 Surgical Resection Versus Stereotactic Body Radiation Therapy for T1-2 N0 Typical Bronchopulmonary Carcinoid Tumors. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.1133] [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: 10/25/2022]
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Abel S, Schiffman S, Monga D, Finley G, Williams H, Thakkar S, Kirichenko A, Wegner R. Neoadjuvant Stereotactic Body Radiotherapy in Addition to Chemotherapy and Its Effect on Outcome in Resected Pancreatic Cancer. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.2000] [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: 11/16/2022]
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Martinecz A, Clarelli F, Abel S, Abel Zur Wiesch P. Reaction Kinetic Models of Antibiotic Heteroresistance. Int J Mol Sci 2019; 20:E3965. [PMID: 31443146 PMCID: PMC6719119 DOI: 10.3390/ijms20163965] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 11/16/2022] Open
Abstract
Bacterial heteroresistance (i.e., the co-existence of several subpopulations with different antibiotic susceptibilities) can delay the clearance of bacteria even with long antibiotic exposure. Some proposed mechanisms have been successfully described with mathematical models of drug-target binding where the mechanism's downstream of drug-target binding are not explicitly modeled and subsumed in an empirical function, connecting target occupancy to antibiotic action. However, with current approaches it is difficult to model mechanisms that involve multi-step reactions that lead to bacterial killing. Here, we have a dual aim: first, to establish pharmacodynamic models that include multi-step reaction pathways, and second, to model heteroresistance and investigate which molecular heterogeneities can lead to delayed bacterial killing. We show that simulations based on Gillespie algorithms, which have been employed to model reaction kinetics for decades, can be useful tools to model antibiotic action via multi-step reactions. We highlight the strengths and weaknesses of current models and Gillespie simulations. Finally, we show that in our models, slight normally distributed variances in the rates of any event leading to bacterial death can (depending on parameter choices) lead to delayed bacterial killing (i.e., heteroresistance). This means that a slowly declining residual bacterial population due to heteroresistance is most likely the default scenario and should be taken into account when planning treatment length.
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Affiliation(s)
- Antal Martinecz
- Department of Pharmacy, Faculty of Health Sciences, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Fabrizio Clarelli
- Department of Pharmacy, Faculty of Health Sciences, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Sören Abel
- Department of Pharmacy, Faculty of Health Sciences, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
- Centre for Molecular Medicine Norway, P.O. Box 1137, Blindern, 0318 Oslo, Norway
| | - Pia Abel Zur Wiesch
- Department of Pharmacy, Faculty of Health Sciences, UiT-The Arctic University of Norway, 9037 Tromsø, Norway.
- Centre for Molecular Medicine Norway, P.O. Box 1137, Blindern, 0318 Oslo, Norway.
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Warr AR, Hubbard TP, Munera D, Blondel CJ, Abel zur Wiesch P, Abel S, Wang X, Davis BM, Waldor MK. Transposon-insertion sequencing screens unveil requirements for EHEC growth and intestinal colonization. PLoS Pathog 2019; 15:e1007652. [PMID: 31404118 PMCID: PMC6705877 DOI: 10.1371/journal.ppat.1007652] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 02/15/2019] [Revised: 08/22/2019] [Accepted: 08/01/2019] [Indexed: 12/28/2022] Open
Abstract
Enterohemorrhagic Escherichia coli O157:H7 (EHEC) is an important food-borne pathogen that colonizes the colon. Transposon-insertion sequencing (TIS) was used to identify genes required for EHEC and E. coli K-12 growth in vitro and for EHEC growth in vivo in the infant rabbit colon. Surprisingly, many conserved loci contribute to EHEC's but not to K-12's growth in vitro. There was a restrictive bottleneck for EHEC colonization of the rabbit colon, which complicated identification of EHEC genes facilitating growth in vivo. Both a refined version of an existing analytic framework as well as PCA-based analysis were used to compensate for the effects of the infection bottleneck. These analyses confirmed that the EHEC LEE-encoded type III secretion apparatus is required for growth in vivo and revealed that only a few effectors are critical for in vivo fitness. Over 200 mutants not previously associated with EHEC survival/growth in vivo also appeared attenuated in vivo, and a subset of these putative in vivo fitness factors were validated. Some were found to contribute to efficient type-three secretion while others, including tatABC, oxyR, envC, acrAB, and cvpA, promote EHEC resistance to host-derived stresses. cvpA is also required for intestinal growth of several other enteric pathogens, and proved to be required for EHEC, Vibrio cholerae and Vibrio parahaemolyticus resistance to the bile salt deoxycholate, highlighting the important role of this previously uncharacterized protein in pathogen survival. Collectively, our findings provide a comprehensive framework for understanding EHEC growth in the intestine.
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Affiliation(s)
- Alyson R. Warr
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Troy P. Hubbard
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Diana Munera
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Carlos J. Blondel
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pia Abel zur Wiesch
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sören Abel
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xiaoxue Wang
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Brigid M. Davis
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Matthew K. Waldor
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- HHMI, Boston, Massachusetts, United States of America
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Abel S, Muller C, Sasanti B. Effect of alternating total mixed ration and pasture feeding on the fatty acid content and health indices of Jersey and Fleckvieh x Jersey milk. S AFR J ANIM SCI 2019. [DOI: 10.4314/sajas.v49i3.4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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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Abel S, Whitehead LC, Coppell KJ. Making dietary changes following a diagnosis of prediabetes: a qualitative exploration of barriers and facilitators. Diabet Med 2018; 35:1693-1699. [PMID: 30092618 DOI: 10.1111/dme.13796] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/06/2018] [Indexed: 11/30/2022]
Abstract
AIM To explore the experiences of people recently diagnosed with prediabetes and overweight or obese in making dietary changes following a six-month primary care nurse-delivered dietary intervention pilot. METHODS Semi-structured interviews were conducted with 20 participants, purposefully selected to ensure a mix of ethnicity, gender and glycaemic outcome. Thematic analysis of interview data was undertaken. RESULTS Participants described feeling shocked when they received the diagnosis of prediabetes. Three core themes, each containing subthemes, emerged: (i) supportive factors - determination not to develop diabetes, clear information and manageable strategies, and supportive relationships; (ii) barriers - lack of family support, financial constraints, social expectations around food, and chronic health issues; and (iii) overcoming challenges - growing and sharing food, using frozen vegetables and planning. Challenges related to cultural expectations around providing and partaking of food were more evident for indigenous Māori participants. CONCLUSIONS A diagnosis of prediabetes provides a window of opportunity for healthcare professionals to work with those diagnosed and their families to make healthful dietary changes. Dietary guidance is likely to be most effective when individuals' life circumstances are taken into account. Clear information and supportive relationships to facilitate lifestyle change are extremely important. (Clinical Trials Registry No; ANZCTR ACTRN1261500080656).
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Affiliation(s)
- S Abel
- Kaupapa Consulting Ltd, Napier, New Zealand
| | - L C Whitehead
- School of Nursing and Midwifery, Edith Cowan University, Joondalup, Australia
| | - K J Coppell
- Department of Medicine, University of Otago, Dunedin, New Zealand
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Burger HM, Abel S, Gelderblom WCA. Modulation of key lipid raft constituents in primary rat hepatocytes by fumonisin B 1 - Implications for cancer promotion in the liver. Food Chem Toxicol 2018; 115:34-41. [PMID: 29510220 DOI: 10.1016/j.fct.2018.03.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 02/07/2018] [Accepted: 03/02/2018] [Indexed: 01/15/2023]
Abstract
Fumonisin B1 (FB1), a group 2B natural occurring carcinogenic mycotoxin, modulated lipid and fatty acid (FA) constituents of lipid rafts isolated from primary hepatocytes following exposure to a cytotoxic concentration of FB1 (250 μM). The major effects observed in rafts, included a significant (p < 0.05) increase in raft cholesterol (CHOL) and glycerophospholipid such as phosphatidylethanolamine (PE), whereas sphingomyelin (SM) decreased (p < 0.05). Changes in lipid constituents resulted in the disruption of important membrane fluidity parameters represented as a decreased (p < 0.05) in the phosphatidylcholine (PC)/PE and PC/(PE+SM) ratios and an increase (p < 0.05) in the CHOL/PL (PL=PC+PE) ratio, suggesting the preservation of lipid raft rigidity and integrity. Observed FA changes in the raft PE fraction included a significant (p < 0.05) increase in C18:2ω-6, C20:3ω-6, C20:4ω-6, C22:4ω-6, C22:5ω-3 and C22:6ω-3, with an increase in total ω-6 and ω-3 polyunsaturated fatty acids (PUFAs). Modulation of the FA content in PE, specifically the C20:4ω-6 PC/PE ratio and PUFA levels, together with changes in CHOL and SM are key determinants regulating the integrity and function of lipid rafts. In primary hepatocytes these changes are associated with the inhibition of cell proliferation and induction of apoptosis. A lipogenic mechanism is proposed whereby FB1 modulates lipid rafts and differentially target cell survival indices of normal and preneoplastic hepatocytes during cancer promotion in the liver.
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Affiliation(s)
- H-M Burger
- Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa.
| | - S Abel
- Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa.
| | - W C A Gelderblom
- Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa; Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa.
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Renz P, Hasan S, Abel S, Uemura T, Machado L, Thai N, Kirichenko A. Multimodality Local Therapy Improves Survival Without Hastening Liver Failure in Patients With Locally Advanced Hepatocellular Carcinoma. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.1035] [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: 10/18/2022]
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26
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Hasan S, Abel S, Renz P, Kudithipudi V, Uemura T, Machado L, Thai N, Kirichenko A. The Albumin-Bilirubin Model in Hepatocellular Carcinoma May Better Predict Progression of Cirrhosis in Traditionally Low Risk Patients Following Definitive Stereotactic Body Radiation Therapy. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.964] [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: 10/18/2022]
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Pradat P, Pugliese P, Poizot-Martin I, Valantin MA, Cuzin L, Reynes J, Billaud E, Huleux T, Bani-Sadr F, Rey D, Frésard A, Jacomet C, Duvivier C, Cheret A, Hustache-Mathieu L, Hoen B, Cabié A, Cotte L, Chidiac C, Ferry T, Ader F, Biron F, Boibieux A, Miailhes P, Perpoint T, Schlienger I, Lippmann J, Braun E, Koffi J, Longuet C, Guéripel V, Augustin-Normand C, Brochier C, Degroodt S, Pugliese P, Ceppi C, Cua E, Cottalorda J, Courjon J, Dellamonica P, Demonchy E, De Monte A, Durant J, Etienne C, Ferrando S, Fuzibet J, Garraffo R, Joulie A, Risso K, Mondain V, Naqvi A, Oran N, Perbost I, Pillet S, Prouvost-Keller B, Wehrlen-Pugliese S, Rosenthal E, Sausse S, Rio V, Roger P, Brégigeon S, Faucher O, Obry-Roguet V, Orticoni M, Soavi M, Geneau de Lamarlière P, Laroche H, Ressiot E, Carta M, Ducassou M, Jacquet I, Gallie S, Galinier A, Ritleng A, Ivanova A, Blanco-Betancourt C, Lions C, Debreux C, Obry-Roguet V, Poizot-Martin I, Agher R, Katlama C, Valantin M, Duvivier C, Lortholary O, Lanternier F, Charlier C, Rouzaud C, Aguilar C, Henry B, Lebeaux D, Cessot G, Gergely A, Consigny P, Touam F, Louisin C, Alvarez M, Biezunski N, Cuzin L, Debard A, Delobel P, Delpierre C, Fourcade C, Marchou B, Martin-Blondel G, Porte M, Mularczyk M, Garipuy D, Saune K, Lepain I, Marcel M, Puntis E, Atoui N, Casanova M, Faucherre V, Jacquet J, Le Moing V, Makinson A, Merle De Boever C, Montoya-Ferrer A, Psomas C, Reynes J, Raffi F, Allavena C, Billaud E, Biron C, Bonnet B, Bouchez S, Boutoille D, Brunet C, Jovelin T, Hall N, Bernaud C, Morineau P, Reliquet V, Aubry O, Point P, Besnier M, Larmet L, Hüe H, Pineau S, André-Garnier E, Rodallec A, Choisy P, Vandame S, Huleux T, Ajana F, Alcaraz I, Baclet V, Huleux T, Melliez H, Viget N, Valette M, Aissi E, Allienne C, Meybeck A, Riff B, Bani-Sadr F, Rouger C, Berger J, N'Guyen Y, Lambert D, Kmiec I, Hentzien M, Lebrun D, Migault C, Rey D, Batard M, Bernard-Henry C, Cheneau C, de Mautort E, Fischer P, Partisani M, Priester M, Lucht F, Frésard A, Botelho-Nevers E, Gagneux-Brunon A, Cazorla C, Guglielminotti C, Daoud F, Lutz M, Jacomet C, Laurichesse H, Lesens O, Vidal M, Mrozek N, Corbin V, Aumeran C, Baud O, Casanova S, Coban D, Hustache-Mathieu L, Thiebaut-Drobacheff M, Foltzer A, Gendrin V, Bozon F, Chirouze C, Abel S, Cabié A, Césaire R, Santos GD, Fagour L, Najioullah F, Ouka M, Pierre-François S, Pircher M, Rozé B, Hoen B, Ouissa R, Lamaury I. Direct-acting antiviral treatment against hepatitis C virus infection in HIV-Infected patients - "En route for eradication"? J Infect 2017; 75:234-241. [PMID: 28579302 DOI: 10.1016/j.jinf.2017.05.008] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/17/2017] [Accepted: 05/11/2017] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Direct-Acting Antivirals (DAAs) opened a new era in HCV treatment. We report the impact of HCV treatment in French HIV-HCV coinfected patients. METHODS All HIV-HCV patients from the Dat'AIDS cohort followed between 2012 and 2015 were included. HCV status was defined yearly as naive, spontaneous cure, sustained virological response (SVR12), failure or reinfection. RESULTS Among 32,945 HIV-infected patients, 15.2% were positive for anti-HCV antibodies. From 2012 to 2015, HCV incidence rate increased from 0.35%PY to 0.69%PY in MSM, while median incidence was 0.08%PY in other patients. Median reinfection rate was 2.56%PY in MSM and 0.22%PY in other patients. HCV treatment initiation rate rose from 8.2% in 2012 to 29.6% (48.0% in pre-treated patients vs 22.6% in naïve patients). SVR12 rate increased from 68.7% to 95.2%. By the end of 2015, 62.7% of the patients were cured either spontaneously or following SVR. CONCLUSIONS HCV treatment dramatically increased in HIV-HCV patients in France from 2012 to 2015 resulting in HCV cure in nearly two-thirds of the patients in this cohort. Combined with a declining HCV prevalence, the prevalence of active HCV infection among HIV patients will drastically decrease in the forthcoming years.
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Affiliation(s)
- Pierre Pradat
- Center for Clinical Research, Department of Hepatology, Croix-Rousse Hospital, Hospices Civils de Lyon, Lyon, France.
| | - Pascal Pugliese
- Department of Infectious Diseases, Centre Hospitalier Universitaire de Nice, Hôpital l'Archet, Nice, France
| | - Isabelle Poizot-Martin
- Immuno-hematology Clinic, Assistance Publique - Hôpitaux de Marseille, Hôpital Sainte-Marguerite, Marseille, France; Aix-Marseille University, Inserm U912 (SESSTIM), Marseille, France
| | - Marc-Antoine Valantin
- Department of Infectious Diseases, Assistance Publique - Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, France; Sorbonne Universités, UPMC Université Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
| | - Lise Cuzin
- CHU Toulouse, COREVIH, Toulouse, France; Université de Toulouse III, Toulouse, France; INSERM, UMR, 1027, Toulouse, France
| | - Jacques Reynes
- Department of Infectious Diseases, UMI 233 INSERM U1175, CHU de Montpellier, Montpellier, France
| | - Eric Billaud
- Department of Infectious Diseases, Hotel Dieu Hospital, Nantes, France
| | - Thomas Huleux
- Department of Infectious Diseases and Travel Diseases, Centre Hospitalier Gustave-Dron, Tourcoing, France
| | - Firouze Bani-Sadr
- Department of Internal Medicine, Infectious Diseases and Clinical Immunology, Hôpital Robert Debré, CHU, Reims, France; Université de Reims Champagne-Ardenne, Faculté de médecine, EA-4684/SFR CAP-SANTE, Reims, France
| | - David Rey
- HIV Infection Care Centre, Hôpitaux Universitaires, Strasbourg, France
| | - Anne Frésard
- Department of Infectious Diseases, CHU, Saint-Etienne, France
| | - Christine Jacomet
- Department of Infectious Diseases, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Claudine Duvivier
- Department of Infectious Diseases, Centre d'Infectiologie Necker-Pasteur, IHU Imagine, Assistance Publique - Hôpitaux de Paris, Hôpital Necker-Enfants Malades, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, EA7327, Paris, France
| | - Antoine Cheret
- Department of Internal Medicine, CHU, Bicètre, France; Université Paris Descartes, Sorbonne Paris Cité, EA7327, Paris, France
| | | | - Bruno Hoen
- Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles, and Service de Maladies Infectieuses et Tropicales, Dermatologie et Médecine Interne, and Inserm CIC 1424, Centre Hospitalier Universitaire de Pointe-à-Pitre, Pointe-à-Pitre, France
| | - André Cabié
- Department of Infectious Diseases, CHU de Martinique, Fort-de-France, France; Université des Antilles EA4537 and INSERM CIC1424, Fort-de-France, France
| | - Laurent Cotte
- Department of Infectious Diseases, Croix-Rousse Hospital, Hospices Civils de Lyon, Lyon, France; INSERM U1052, Lyon, France.
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Waring JF, Davis JW, Dumas E, Cohen D, Idler K, Abel S, Georgantas R, Podsadecki T, Dutta S. Epigenetic analysis of the IFNλ3 gene identifies a novel marker for response to therapy in HCV-infected subjects. J Viral Hepat 2017; 24:397-403. [PMID: 27925355 DOI: 10.1111/jvh.12661] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/22/2016] [Indexed: 12/31/2022]
Abstract
Chronic hepatitis C virus (HCV) infection is characterized by high interindividual variability in response to pegylated interferon and ribavirin. A genetic polymorphism on chromosome 19 (rs12979860) upstream of interferon-λ3 (IFNλ3) is associated with a twofold change in sustained virologic response rate after 48 weeks of treatment with pegylated interferon/ribavirin in HCV genotype 1 (GT1) treatment-naïve patients. We conducted epigenetic analysis on the IFNλ3 promoter to investigate whether DNA methylation is associated with response to HCV therapy. DNA samples from HCV GT1-infected subjects receiving an interferon-free paritaprevir-containing combination regimen (N=540) and from HCV-uninfected, healthy controls (N=124) were analysed for IFNλ3 methylation levels. Methylation was strongly associated with rs12979860 allele status whether adjusting for HCV status (r=65.0%, 95% CI: [60.2%, 69.5%]), or not (r=64.4%), both with P<2.2×10-16 . In HCV GT1-infected subjects, C/C genotypes had significantly lower methylation levels relative to C/T or T/T genotypes (P<1×10-14 ), with each T allele resulting in a nine-unit increase in mean methylation level. Methylation levels did not correlate with response in subjects treated for 12 or 24 weeks. However, non-C/C subjects with higher methylation levels were more likely to relapse when treatment duration was 8 weeks. This analysis suggests that methylation status of the IFNλ3 promoter region may be a useful parameter that identifies patients more likely to relapse following HCV therapy; however, continuing therapy for a sufficient duration can overcome this difference. These findings may provide mechanistic insight into the role of IFNλ3 genetic variants in HCV treatment response.
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Affiliation(s)
| | | | - E Dumas
- AbbVie Inc., North Chicago, IL, USA
| | - D Cohen
- AbbVie Inc., North Chicago, IL, USA
| | - K Idler
- AbbVie Inc., North Chicago, IL, USA
| | - S Abel
- AbbVie Inc., North Chicago, IL, USA
| | | | | | - S Dutta
- AbbVie Inc., North Chicago, IL, USA
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Putot A, Rozé B, Pierre-François S, Pircher M, Vilain R, Miossec C, Desbois N, Hochedez P, Abel S, Cabié A. IST-06 - Réémergence de la syphilis chez les personnes infectées par le VIH en Martinique en 2015. Med Mal Infect 2016. [DOI: 10.1016/s0399-077x(16)30437-1] [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: 10/21/2022]
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Hatzios SK, Abel S, Martell J, Hubbard T, Sasabe J, Munera D, Clark L, Bachovchin DA, Qadri F, Ryan ET, Davis BM, Weerapana E, Waldor MK. Erratum: Chemoproteomic profiling of host and pathogen enzymes active in cholera. Nat Chem Biol 2016; 12:466. [DOI: 10.1038/nchembio0616-466] [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: 11/09/2022]
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Thioune M, Bertolotti A, Césaire R, Carme B, Nacher M, Calmont I, Jean-Marie J, Abel S, Cabié A. COL 7-01 - Prévalence et facteurs de risques associés de la forme chronique du Chikungunya ; une étude de cohorte. Med Mal Infect 2016. [DOI: 10.1016/s0399-077x(16)30286-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Riedel S, Abel S, Burger HM, van der Westhuizen L, Swanevelder S, Gelderblom WCA. Differential modulation of the lipid metabolism as a model for cellular resistance to fumonisin B1-induced cytotoxic effects in vitro. Prostaglandins Leukot Essent Fatty Acids 2016; 109:39-51. [PMID: 27269712 DOI: 10.1016/j.plefa.2016.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/21/2016] [Accepted: 04/21/2016] [Indexed: 12/30/2022]
Abstract
Differential sensitivity of primary hepatocytes and Chang cells to the cancer promoter fumonisin B1 (FB1)-induced cytotoxic effects were investigated in relation to changes in membrane lipid distribution. In contrast to primary hepatocytes, Chang cells were resistant to FB1-induced cytotoxic effects. This was associated with a high cholesterol (Chol) and sphingomyelin (SM) and low phosphatidylcholine (PC) content, resulting in a significant (P<0.05) decrease in phosphatidylethanolamine (PE)/PC ratio, increased Chol/total phosphoglyceride (TPG) ratios and low total polyunsaturated fatty acids (PUFA) content in PC and PE, suggesting a more rigid membrane structure. High levels of C18:1 and reduced polyunsaturated fatty acid (PUFA) levels are likely to provide selective resistance to FB1-induced oxidative stress. FB1-associated lipid changes included decreases in SM and Chol, increases in sphinganine (Sa) and PE with the increases in key saturated, monounsaturated, and PUFAs in PE as key role players in the differential responses to FB1-induced cell growth responses in cells.
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Affiliation(s)
- S Riedel
- Biomedical Research and Innovation Platform, South African Medical Research Council, PO Box 19070, Tygerberg 7505, South Africa.
| | - S Abel
- Mycotoxicology and Chemoprevention Research Group, Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa.
| | - H-M Burger
- Mycotoxicology and Chemoprevention Research Group, Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa.
| | - L van der Westhuizen
- Oxidative Stress Research Centre, Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa.
| | - S Swanevelder
- Biostatistics Unit, South African Medical Research Council, PO Box 19070, Tygerberg, South Africa.
| | - W C A Gelderblom
- Mycotoxicology and Chemoprevention Research Group, Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa; Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa.
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Abstract
Transposon insertion sequencing (TIS) is a powerful approach that can be extensively applied to the genome-wide definition of loci that are required for bacterial growth under diverse conditions. However, experimental design choices and stochastic biological processes can heavily influence the results of TIS experiments and affect downstream statistical analysis. In this Opinion article, we discuss TIS experimental parameters and how these factors relate to the benefits and limitations of the various statistical frameworks that can be applied to the computational analysis of TIS data.
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Affiliation(s)
- Michael C Chao
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA; the Division of Infectious Disease, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; and the Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Sören Abel
- Department of Pharmacy, University of Tromsø, The Arctic University of Norway, 9019 Tromsø, Norway
| | - Brigid M Davis
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA; the Division of Infectious Disease, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; and the Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Matthew K Waldor
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA; the Division of Infectious Disease, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; and the Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
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Abel Zur Wiesch P, Abel S, Gkotzis S, Ocampo P, Engelstädter J, Hinkley T, Magnus C, Waldor MK, Udekwu K, Cohen T. Classic reaction kinetics can explain complex patterns of antibiotic action. Sci Transl Med 2016; 7:287ra73. [PMID: 25972005 DOI: 10.1126/scitranslmed.aaa8760] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Finding optimal dosing strategies for treating bacterial infections is extremely difficult, and improving therapy requires costly and time-intensive experiments. To date, an incomplete mechanistic understanding of drug effects has limited our ability to make accurate quantitative predictions of drug-mediated bacterial killing and impeded the rational design of antibiotic treatment strategies. Three poorly understood phenomena complicate predictions of antibiotic activity: post-antibiotic growth suppression, density-dependent antibiotic effects, and persister cell formation. We show that chemical binding kinetics alone are sufficient to explain these three phenomena, using single-cell data and time-kill curves of Escherichia coli and Vibrio cholerae exposed to a variety of antibiotics in combination with a theoretical model that links chemical reaction kinetics to bacterial population biology. Our model reproduces existing observations, has a high predictive power across different experimental setups (R(2) = 0.86), and makes several testable predictions, which we verified in new experiments and by analyzing published data from a clinical trial on tuberculosis therapy. Although a variety of biological mechanisms have previously been invoked to explain post-antibiotic growth suppression, density-dependent antibiotic effects, and especially persister cell formation, our findings reveal that a simple model that considers only binding kinetics provides a parsimonious and unifying explanation for these three complex, phenotypically distinct behaviours. Current antibiotic and other chemotherapeutic regimens are often based on trial and error or expert opinion. Our "chemical reaction kinetics"-based approach may inform new strategies, which are based on rational design.
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Affiliation(s)
- Pia Abel Zur Wiesch
- Division of Global Health Equity, Brigham and Women's Hospital and Harvard Medical School, 641 Huntington Avenue, Boston, MA 02115, USA. Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, New Haven, CT 06510, USA.
| | - Sören Abel
- Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA. Department of Pharmacy, UiT, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Spyridon Gkotzis
- Department of Neuroscience, Karolinska Institutet, Retzius väg 8, 17177 Stockholm, Sweden
| | - Paolo Ocampo
- Institute of Integrative Biology, ETH Zürich, Universitätsstrasse 16, 8092 Zürich, Switzerland. Department of Environmental Microbiology, EAWAG, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Jan Engelstädter
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Trevor Hinkley
- School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, UK
| | - Carsten Magnus
- Institute of Medical Virology, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA. Howard Hughes Medical Institute, 181 Longwood Avenue, Boston, MA 02115, USA
| | - Klas Udekwu
- Department of Neuroscience, Karolinska Institutet, Retzius väg 8, 17177 Stockholm, Sweden
| | - Ted Cohen
- Division of Global Health Equity, Brigham and Women's Hospital and Harvard Medical School, 641 Huntington Avenue, Boston, MA 02115, USA. Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, New Haven, CT 06510, USA. Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
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Affiliation(s)
- J. Dittmann
- Albert-Ludwigs-Universität, Germanistische Linguistik, Freiburg i. Br
| | - S. Abel
- University of Manchester, School of Psychological Sciences, Manchester, United Kingdom of Great Britain and Northern Ireland
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Waring JF, Dumas EO, Abel S, Coakley E, Cohen DE, Davis JW, Podsadecki T, Dutta S. Serum miR-122 may serve as a biomarker for response to direct acting antivirals: effect of paritaprevir/R with dasabuvir or ombitasvir on miR-122 in HCV-infected subjects. J Viral Hepat 2016; 23:96-104. [PMID: 26436610 DOI: 10.1111/jvh.12470] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/27/2015] [Indexed: 12/14/2022]
Abstract
Circulating microRNAs (miRNA) have been intensely investigated as biomarkers in disease and therapy. Several studies have identified miR-122 as an important regulator of HCV replication. The effect of new therapies that directly target the HCV replication life cycle on circulating microRNA levels has not been elucidated. We performed expression profiling of circulating miRNA in serum in subjects treated with HCV direct-acting antiviral agents (DAAs). Serum miRNA levels were evaluated from two studies in HCV GT1-infected treatment-naïve subjects and prior nonresponders to pegylated interferon (pegIFN) and ribavirin (RBV) who received paritaprevir/ritonavir + dasabuvir + RBV for 12 weeks, and in treatment-naïve genotype (GT)1-3-infected subjects who received paritaprevir/ritonavir + ombitasvir ± RBV for 12 weeks. Over 100 different miRNA species were detected in serum. Of these, levels of miR-122 showed the most consistent change in response to treatment across all HCV genotypes. In all subjects, miR-122 showed an average four-fold reduction between baseline and week 2, and remained below baseline through post-treatment week 12 in subjects who achieved sustained virological response. In contrast, in subjects who did not achieve SVR, miR-122 levels began to return to baseline levels after the second week of treatment. The change in miR-122 levels was similar across genotypes, and was comparable with or without RBV. This is the first report comparing expression levels of circulating miRNA in HCV GT1-3 subjects treated with IFN-free combinations of DAAs. The results suggest that serum levels of miR-122 are reduced following treatment in subjects who achieve SVR, and correlate with HCV RNA levels across genotypes.
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Affiliation(s)
- J F Waring
- Department of Pharmacogenetics and Pharmacogenomics, Clinical Pharmacology, AbbVie, North Chicago, IL, USA
| | - E O Dumas
- Department of Clinical Virology, AbbVie, North Chicago, IL, USA
| | - S Abel
- Department of Pharmacogenetics and Pharmacogenomics, Clinical Pharmacology, AbbVie, North Chicago, IL, USA
| | - E Coakley
- Department of Clinical Virology, AbbVie, North Chicago, IL, USA
| | - D E Cohen
- Department of Clinical Virology, AbbVie, North Chicago, IL, USA
| | - J Wade Davis
- Department of Pharmacogenetics and Pharmacogenomics, Clinical Pharmacology, AbbVie, North Chicago, IL, USA
| | - T Podsadecki
- Department of Clinical Virology, AbbVie, North Chicago, IL, USA
| | - S Dutta
- Department of Pharmacogenetics and Pharmacogenomics, Clinical Pharmacology, AbbVie, North Chicago, IL, USA
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Sasanti B, Abel S, Muller C, Gelderblom W, Schmulian A. Milk fatty acid composition and conjugated linoleic acid content of Jersey and Fleckvieh x Jersey cows in a pasture-based feeding system. S AFR J ANIM SCI 2015. [DOI: 10.4314/sajas.v45i4.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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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Affiliation(s)
- L. Plum
- Medizinische Fakultät, Lehr- und Forschungsgebiet Neuropsychologie, Klinik für Neurologie, RWTH Aachen University
| | - R. Nobis-Bosch
- Referat Fort- und Weiterbildung, Deutscher Bundesverband für Logopädie (dbl) e.V
| | - F. Krzok
- Medizinische Fakultät, Lehr- und Forschungsgebiet Neuropsychologie, Klinik für Neurologie, RWTH Aachen University
| | | | - K. Willmes
- Medizinische Fakultät, Lehr- und Forschungsgebiet Neuropsychologie, Klinik für Neurologie, RWTH Aachen University
| | - S. Abel
- Medizinische Fakultät, Lehr- und Forschungsgebiet Neuropsychologie, Klinik für Neurologie, RWTH Aachen University
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Abstract
Vibrio cholerae is the agent of cholera, a potentially lethal diarrheal disease that remains a significant threat to populations in developing nations. The infant rabbit model of cholera is the only non-surgical small animal model system that closely mimics human cholera. Following orogastric inoculation, V. cholerae colonizes the intestines of infant rabbits, and the animals develop severe cholera-like diarrhea. In this unit, we provide a detailed description of the preparation of the V. cholerae inoculum, the inoculation process and the collection and processing of tissue samples. This infection model is useful for studies of V. cholerae factors and mechanisms that promote its intestinal colonization and enterotoxicity, as well as the host response to infection. The infant rabbit model of cholera enables investigations that will further our understanding of the pathophysiology of cholera and provides a platform for testing new therapeutics.
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Affiliation(s)
- Sören Abel
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Pharmacy, Faculty of Health Sciences, UiT, The Arctic University of Norway, Tromsø, Norway
| | - Matthew K Waldor
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts.,Howard Hughes Medical Institute, Boston, Massachusetts
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Affiliation(s)
- Sören Abel
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Pharmacy, University of Tromsø (UiT), The Arctic University of Norway, Tromsø, Norway
- * E-mail: (SA); (MKW)
| | - Pia Abel zur Wiesch
- Department of Pharmacy, University of Tromsø (UiT), The Arctic University of Norway, Tromsø, Norway
- Division of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Brigid M. Davis
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, United States of America
| | - Matthew K. Waldor
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
- * E-mail: (SA); (MKW)
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Riedel S, Abel S, Swanevelder S, Gelderblom WCA. Induction of an altered lipid phenotype by two cancer promoting treatments in rat liver. Food Chem Toxicol 2015; 78:96-104. [PMID: 25656646 DOI: 10.1016/j.fct.2015.01.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 01/06/2015] [Accepted: 01/26/2015] [Indexed: 02/02/2023]
Abstract
Changes in lipid metabolism have been associated with tumor promotion in rat liver. Similarities and differences of lipid parameters were investigated using the mycotoxin fumonisin B1 (FB1) and the 2-acetylaminofluorene/partial hepatectomy (AAF/PH) treatments as cancer promoters in rat liver. A typical lipid phenotype was observed, including increased membranal phosphatidylethanolamine (PE) and cholesterol content, increased levels of C16:0 and monounsaturated fatty acids in PE and phosphatidylcholine (PC), as well as a decrease in C18:0 and long-chained polyunsaturated fatty acids in the PC fraction. The observed lipid changes, which likely resulted in changes in membrane structure and fluidity, may represent a growth stimulus exerted by the cancer promoters that could provide initiated cells with a selective growth advantage. This study provided insight into complex lipid profiles induced by two different cancer promoting treatments and their potential role in the development of hepatocyte nodules, which can be used to identify targets for the development of chemopreventive strategies against cancer promotion in the liver.
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Affiliation(s)
- S Riedel
- Diabetes Discovery Platform, South African Medical Research Council, PO Box 19070, Tygerberg, South Africa.
| | - S Abel
- Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa
| | - S Swanevelder
- Biostatistics Unit, South African Medical Research Council, PO Box 19070, Tygerberg, South Africa
| | - W C A Gelderblom
- Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa; Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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Abel zur Wiesch P, Kouyos R, Abel S, Viechtbauer W, Bonhoeffer S. Cycling empirical antibiotic therapy in hospitals: meta-analysis and models. PLoS Pathog 2014; 10:e1004225. [PMID: 24968123 PMCID: PMC4072793 DOI: 10.1371/journal.ppat.1004225] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [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: 12/06/2013] [Accepted: 05/13/2014] [Indexed: 01/12/2023] Open
Abstract
The rise of resistance together with the shortage of new broad-spectrum antibiotics underlines the urgency of optimizing the use of available drugs to minimize disease burden. Theoretical studies suggest that coordinating empirical usage of antibiotics in a hospital ward can contain the spread of resistance. However, theoretical and clinical studies came to different conclusions regarding the usefulness of rotating first-line therapy (cycling). Here, we performed a quantitative pathogen-specific meta-analysis of clinical studies comparing cycling to standard practice. We searched PubMed and Google Scholar and identified 46 clinical studies addressing the effect of cycling on nosocomial infections, of which 11 met our selection criteria. We employed a method for multivariate meta-analysis using incidence rates as endpoints and find that cycling reduced the incidence rate/1000 patient days of both total infections by 4.95 [9.43–0.48] and resistant infections by 7.2 [14.00–0.44]. This positive effect was observed in most pathogens despite a large variance between individual species. Our findings remain robust in uni- and multivariate metaregressions. We used theoretical models that reflect various infections and hospital settings to compare cycling to random assignment to different drugs (mixing). We make the realistic assumption that therapy is changed when first line treatment is ineffective, which we call “adjustable cycling/mixing”. In concordance with earlier theoretical studies, we find that in strict regimens, cycling is detrimental. However, in adjustable regimens single resistance is suppressed and cycling is successful in most settings. Both a meta-regression and our theoretical model indicate that “adjustable cycling” is especially useful to suppress emergence of multiple resistance. While our model predicts that cycling periods of one month perform well, we expect that too long cycling periods are detrimental. Our results suggest that “adjustable cycling” suppresses multiple resistance and warrants further investigations that allow comparing various diseases and hospital settings. The rise of antibiotic resistance is a major concern for public health. In hospitals, frequent usage of antibiotics leads to high resistance levels; at the same time the patients are especially vulnerable. We therefore urgently need treatment strategies that limit resistance without compromising patient care. Here, we investigate two strategies that coordinate the usage of different antibiotics in a hospital ward: “cycling”, i.e. scheduled changes in antibiotic treatment for all patients, and “mixing”, i.e. random assignment of patients to antibiotics. Previously, theoretical and clinical studies came to different conclusions regarding the usefulness of these strategies. We combine meta-analyses of clinical studies and epidemiological modeling to address this question. Our meta-analyses suggest that cycling is beneficial in reducing the total incidence rate of hospital-acquired infections as well as the incidence rate of resistant infections, and that this is most pronounced at low baseline levels of resistance. We corroborate our findings with theoretical epidemiological models. When incorporating treatment adjustment upon deterioration of a patient's condition (“adjustable cycling”), we find that our theoretical model is in excellent accordance with the clinical data. With this combined approach we present substantial evidence that adjustable cycling can be beneficial for suppressing the emergence of multiple resistance.
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Affiliation(s)
- Pia Abel zur Wiesch
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Division of Global Health Equity, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
| | - Roger Kouyos
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Sören Abel
- Division of Infectious Diseases, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Wolfgang Viechtbauer
- Department of Psychiatry and Psychology, School for Mental Health and Neuroscience, Faculty of Health, Medicine, and Life Sciences, Maastricht University, Maastricht, The Netherlands
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Fumeaux C, Radhakrishnan SK, Ardissone S, Théraulaz L, Frandi A, Martins D, Nesper J, Abel S, Jenal U, Viollier PH. Cell cycle transition from S-phase to G1 in Caulobacter is mediated by ancestral virulence regulators. Nat Commun 2014; 5:4081. [PMID: 24939058 PMCID: PMC4083442 DOI: 10.1038/ncomms5081] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [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: 11/24/2013] [Accepted: 05/09/2014] [Indexed: 11/10/2022] Open
Abstract
Zinc-finger domain transcriptional regulators regulate a myriad of functions in eukaryotes. Interestingly, ancestral versions (MucR) from Alpha-proteobacteria control bacterial virulence/symbiosis. Whether virulence regulators can also control cell cycle transcription is unknown. Here we report that MucR proteins implement a hitherto elusive primordial S→G1 transcriptional switch. After charting G1-specific promoters in the cell cycle model Caulobacter crescentus by comparative ChIP-seq, we use one such promoter as genetic proxy to unearth two MucR paralogs, MucR1/2, as constituents of a quadripartite and homeostatic regulatory module directing the S→G1 transcriptional switch. Surprisingly, MucR orthologues that regulate virulence and symbiosis gene transcription in Brucella, Agrobacterium or Sinorhizobium support this S→G1 switch in Caulobacter. Pan-genomic ChIP-seq analyses in Sinorhizobium and Caulobacter show that this module indeed targets orthologous genes. We propose that MucR proteins and possibly other virulence regulators primarily control bacterial cell cycle (G1-phase) transcription, rendering expression of target (virulence) genes periodic and in tune with the cell cycle. The bacterium Caulobacter crescentus divides asymmetrically to generate a replicative stalk cell and a quiescent swarmer cell. Fumeaux et al. show that MucR zinc-finger transcription factors, which regulate virulence in other species, also control re-entry into quiescence in Caulobacter.
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Affiliation(s)
- Coralie Fumeaux
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Sunish Kumar Radhakrishnan
- 1] Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland [2]
| | - Silvia Ardissone
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Laurence Théraulaz
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Antonio Frandi
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Daniel Martins
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Jutta Nesper
- Biozentrum of the University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Sören Abel
- 1] Biozentrum of the University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland [2]
| | - Urs Jenal
- Biozentrum of the University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Patrick H Viollier
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
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Cabié A, Dorléans F, Courcier D, Najioullah F, Rosine J, Abel S. COL05-05 : Premiers cas autochtones de chikungunya aux Antilles : caractéristiques cliniques des personnes hospitalisées. Med Mal Infect 2014. [DOI: 10.1016/s0399-077x(14)70063-0] [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: 10/25/2022]
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Ronin V, Pierre-François S, Abel S, Césaire R, Cabié A. A-32: Analyse rétrospective des caractéristiques associées aux co-infections HTLV1/VIH. Med Mal Infect 2014. [DOI: 10.1016/s0399-077x(14)70115-5] [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: 10/25/2022]
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Abel S, Bucher T, Nicollier M, Hug I, Kaever V, Abel zur Wiesch P, Jenal U. Bi-modal distribution of the second messenger c-di-GMP controls cell fate and asymmetry during the caulobacter cell cycle. PLoS Genet 2013; 9:e1003744. [PMID: 24039597 PMCID: PMC3764195 DOI: 10.1371/journal.pgen.1003744] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 07/10/2013] [Indexed: 11/23/2022] Open
Abstract
Many bacteria mediate important life-style decisions by varying levels of the second messenger c-di-GMP. Behavioral transitions result from the coordination of complex cellular processes such as motility, surface adherence or the production of virulence factors and toxins. While the regulatory mechanisms responsible for these processes have been elucidated in some cases, the global pleiotropic effects of c-di-GMP are poorly understood, primarily because c-di-GMP networks are inherently complex in most bacteria. Moreover, the quantitative relationships between cellular c-di-GMP levels and c-di-GMP dependent phenotypes are largely unknown. Here, we dissect the c-di-GMP network of Caulobacter crescentus to establish a global and quantitative view of c-di-GMP dependent processes in this organism. A genetic approach that gradually reduced the number of diguanylate cyclases identified novel c-di-GMP dependent cellular processes and unraveled c-di-GMP as an essential component of C. crescentus cell polarity and its bimodal life cycle. By varying cellular c-di-GMP concentrations, we determined dose response curves for individual c-di-GMP-dependent processes. Relating these values to c-di-GMP levels modeled for single cells progressing through the cell cycle sets a quantitative frame for the successive activation of c-di-GMP dependent processes during the C. crescentus life cycle. By reconstructing a simplified c-di-GMP network in a strain devoid of c-di-GMP we defined the minimal requirements for the oscillation of c-di-GMP levels during the C. crescentus cell cycle. Finally, we show that although all c-di-GMP dependent cellular processes were qualitatively restored by artificially adjusting c-di-GMP levels with a heterologous diguanylate cyclase, much higher levels of the second messenger are required under these conditions as compared to the contribution of homologous c-di-GMP metabolizing enzymes. These experiments suggest that a common c-di-GMP pool cannot fully explain spatiotemporal regulation by c-di-GMP in C. crescentus and that individual enzymes preferentially regulate specific phenotypes during the cell cycle. Bacterial processes like virulence, motility or biofilm formation are governed by the second messenger c-di-GMP. In most bacteria, c-di-GMP is produced and degraded by a complex network comprising dozens of enzymes. This has hindered a comprehensive analysis of the cellular role of c-di-GMP. Here we mutate the entire c-di-GMP network in Caulobacter crescentus, a model organism with inherent cell polarity and bimodal life-cycle. We find that a c-di-GMP free strain (cdG0) shows severe developmental defects, a loss of cell polarity and defective cell division. By determining c-di-GMP dose-response curves for individual processes and relating these to c-di-GMP levels, which were modeled for single cells progressing through the cell cycle, we define a quantitative frame for the c-di-GMP dependent program during the C. crescentus life cycle. We then show that the defects of cdG0 can be largely rescued by restoring c-di-GMP levels with a single heterologous enzyme producing c-di-GMP. However, much higher levels of the second messenger are required under these conditions as compared to the contribution of homologous enzymes. Our data argue for specific regulatory fine-tuning of the enzymes mediating c-di-GMP oscillation during the cell cycle and provide evidence for both global as well as insulated c-di-GMP pools.
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Affiliation(s)
- Sören Abel
- University of Basel, Biozentrum, Basel, Switzerland
- * E-mail: (SA); (UJ)
| | | | | | - Isabelle Hug
- University of Basel, Biozentrum, Basel, Switzerland
| | - Volkhard Kaever
- Hannover Medical School, Institute of Pharmacology, Hannover, Germany
| | - Pia Abel zur Wiesch
- Brigham and Women's Hospital/Harvard Medical School, Global Health Equity, Boston, Massachusetts, United States of America
| | - Urs Jenal
- University of Basel, Biozentrum, Basel, Switzerland
- * E-mail: (SA); (UJ)
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Abel S, Sousa M, Rossel C, Caimi D, Rossell MD, Erni R, Fompeyrine J, Marchiori C. Controlling tetragonality and crystalline orientation in BaTiO₃ nano-layers grown on Si. Nanotechnology 2013; 24:285701. [PMID: 23787908 DOI: 10.1088/0957-4484/24/28/285701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A hybrid growth process was developed in order to epitaxially integrate nano-layers of the multi-functional perovskite BaTiO₃ onto Si(001) substrates. In particular, we combined molecular beam epitaxy (MBE) with radio-frequency sputtering. Due to its strong influence on the functional properties, the crystalline structure of the layers was thoroughly investigated throughout our study. MBE-grown seed layers are tetragonal and c-axis oriented up to a thickness of 20 nm. A transition into a-axis films is visible for thicker layers. When the seed layer thickness exceeds 6 nm, subsequently sputtered BaTiO₃ films are epitaxial. However, their crystalline structure, their orientation with respect to the substrate, and their morphology are strongly dependent on the deposition and post-deposition thermal budget. Consistently with their crystalline symmetry, thin MBE BaTiO₃ films are piezo- and ferroelectric with a spontaneous polarization perpendicular to the surface. Also for thick films, the functional response, as determined via piezo-force microscopy, is in good agreement with the structural properties.
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Affiliation(s)
- S Abel
- IBM Research-Zurich, Säumerstrasse 4, 8803 Rüschlikon, Switzerland.
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Charpentier C, Joly V, Larrouy L, Fagard C, Visseaux B, de Verdiere NC, Raffi F, Yeni P, Descamps D, Aumaitre H, Medus M, Neuville S, Saada M, Abgrall S, Bentata M, Bouchaud O, Cailhol J, Cordel H, Dhote R, Gros H, Honore-Berlureau P, Huynh T, Krivitzky A, Mansouri R, Poupard M, Prendki V, Radia D, Rouges F, Touam F, Warde B, de Castro N, Colin de Verdiere N, Delgado J, Ferret S, Gallien S, Kandel T, Lafaurie M, Lagrange M, Lascoux-Combe C, Le D, Molina JM, Pavie J, Pintado C, Ponscarme D, Rachline A, Rozenbaum W, Sereni D, Taulera O, Estavoyer JM, Faucher JF, Foltzer A, Hoen B, Hustache-Mathieu L, Dupon M, Dutronc H, Neau D, Ragnaud JM, Raymond I, Boucly S, Lortholary O, Viard JP, Bechara C, Delfraissy JF, Ghosn J, Goujard C, Kamouh W, Mole M, Quertainmont Y, Bergmann JF, Boulanger E, Castillo H, Parrinello M, Rami A, Sellier P, Lepeu G, Pichancourt G, Bernard L, Berthe H, Clarissou J, Gory M, Melchior JC, Perronne C, Stegman S, de Truchis P, Derradji O, Malet M, Teicher E, Vittecoq D, Chakvetadze C, Fontaine C, Lukiana T, Pialloux G, Slama L, Bonnet D, Boucherit S, El Alami Talbi N, Fournier I, Gervais A, Joly V, Iordache L, Laurichesse JJ, Leport C, Pahlavan G, Phung BC, Yeni P, Bennamar N, Brunet A, Guillevin L, Salmon-Ceron D, Tahi T, Chesnel C, Dominguez S, Jouve P, Lelievre JD, Levy Y, Melica G, Sobel A, Ben Abdallah S, Bonmarchand M, Bricaire F, Herson S, Iguertsira M, Katlama C, Kouadio H, Schneider L, Simon A, Valantin MA, Abel S, Beaujolais V, Cabie A, Liauthaud B, Pierre Francois S, Abgueguen P, Chennebault JM, Loison J, Pichard E, Rabier V, Delaune J, Louis I, Morlat P, Pertusa MC, Brunel-Delmas F, Chiarello P, Jeanblanc F, Jourdain JJ, Livrozet JM, Makhloufi D, Touraine JL, Augustin-Normand C, Bailly F, Benmakhlouf N, Brochier C, Cotte L, Gueripel V, Koffi K, Lack P, Lebouche B, Maynard M, Miailhes P, Radenne S, Schlienger I, Thoirain V, Trepo C, Drogoul MP, Fabre G, Faucher O, Frixon-Marin V, Gastaut JA, Peyrouse E, Poizot-Martin I, Jacquet JM, Le Facher G, Merle de Boever C, Reynes J, Tramoni C, Allavena C, Billaud E, Biron C, Bonnet B, Bouchez S, Boutoille D, Brunet-Francois C, Hue H, Mounoury O, Raffi F, Reliquet V, Aubry O, Esnault JL, Leautez-Nainville S, Perre P, Suaud I, Breaud S, Ceppi C, Dellamonica P, De Salvador F, Durant J, Ferrando S, Fuzibet JG, Leplatois A, Mondain V, Perbost I, Pugliese P, Rahelinirina V, Rosenthal E, Sanderson F, Vassalo M, Arvieux C, Chapplain JM, Michelet C, Ratajczak M, Revest M, Souala F, Tattevin P, Cheneau C, Fischer P, Lang JM, Partisani M, Rey D, Bastides F, Besnier JM, Le Bret P, Choutet P, Dailloux JF, Guadagnin P, Nau P, Rivalain J, Soufflet A, Aissi E, Melliez H, Pavel S, Mouton Y, Yazdanpanah Y, Boyer L, Burty C, Letranchant L, May T, Wassoumbou S, Blum L, Danne O, Arthus MA, Dion P, Certain A, Tabuteau S, Beuscart A, Agher N, Frosch A, Couffin-Cadiergues S, Diallo A. Role and evolution of viral tropism in patients with advanced HIV disease receiving intensified initial regimen in the ANRS 130 APOLLO trial. J Antimicrob Chemother 2012; 68:690-6. [DOI: 10.1093/jac/dks455] [Citation(s) in RCA: 13] [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: 11/14/2022] Open
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Cabié A, Bissuel F, Huc P, Paturel L, Abel S. Impact of rapid HIV testing on the return rate for routine test results in sexually transmitted infection testing centres. Int J STD AIDS 2012; 22:757-8. [PMID: 22174063 DOI: 10.1258/ijsa.2009.009267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To strengthen HIV screening in the French West Indies (FWI), we evaluated the feasibility of rapid tests in sexually transmitted infection (STI) testing centres. Rapid testing was offered to each user ahead of the standard screening tests. Between October 2007 and December 2008, 847 users had HIV rapid testing, and 1724 users did not have rapid testing. The results of rapid testing were returned to 99.1% of testers. However, clients who underwent rapid testing were significantly more likely than others to have not returned to get the results of their standard screening tests (for HIV and other STIs): 27.4% versus 14.0% with a relative risk of 1.96 (95% confidence interval [CI] 1.67-2.30, P < 0.0001). Rapid HIV testing has the capacity to reduce the return rates for confirmatory results of HIV testing and other STIs.
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Affiliation(s)
- A Cabié
- Infectious and Tropical Diseases Department, CHU de Fort-de-France, Martinique, France.
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Robinson CA, Bottorff JL, Lilly MB, Reid C, Abel S, Lo M, Cummings GG. Stakeholder perspectives on transitions of nursing home residents to hospital emergency departments and back in two Canadian provinces. J Aging Stud 2012; 26:419-27. [PMID: 22939538 DOI: 10.1016/j.jaging.2012.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 05/15/2012] [Accepted: 06/04/2012] [Indexed: 11/25/2022]
Abstract
Major gaps exist in our understanding of transitions in care for older persons living in nursing homes. The purpose of the study was to identify key elements, from multiple stakeholder perspectives, that influence the success of transitions experienced by nursing home residents when they required transfer to a hospital emergency department. This interpretive descriptive study was conducted in two cities in the Canadian provinces of British Columbia and Alberta. Data were collected from 71 participants via focus groups and individual interviews with nursing home residents, family members, and professional healthcare providers working in nursing homes, emergency departments, and emergency medical services. Transcripts were analyzed using constant comparison. The elements contributing to the success of transitions reflected a patient- and family-centered approach to care. Transitions were influenced by the complex interplay of multiple elements that included: knowing the resident; critical geriatric knowledge and skilled assessment; positive relationships; effective communication; and timeliness. When one or more of the elements was absent or compromised, the success of the transition was also compromised. There was consistency about the importance of all the identified elements across all stakeholder groups whether they are residents, family members, or health professionals in nursing homes, emergency departments or emergency medical services. Aspects of many of these elements are modifiable and suggest viable targets for interventions aimed at improving the success of transitions for this vulnerable population.
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Affiliation(s)
- C A Robinson
- School of Nursing, Faculty of Health and Social Development, University of British Columbia, 3333 University Way, Kelowna, BC, Canada.
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