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Santosuosso E, Leguillette R, Vinardell T, Filho S, Massie S, McCrae P, Johnson S, Rolian C, David F. Kinematic Analysis During Straight Line Free Swimming in Horses: Part 2 - Hindlimbs. Front Vet Sci 2022; 8:761500. [PMID: 35174237 PMCID: PMC8843043 DOI: 10.3389/fvets.2021.761500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/08/2021] [Indexed: 11/24/2022] Open
Abstract
Background Swimming is used for rehabilitation and conditioning purposes in equine sports medicine. We described the swimming kinematics of the equine forelimbs in Part 1. The aim of Part 2 is to assess stifle, tarsus, and hind fetlock joints kinematics in swimming horses. The objectives were 1- to calculate and compare joint angles during swimming against passive mobilizations (PM), 2- to determine joints angular velocities during a swimming stride cycle. Methods Eleven elite endurance horses were used to swim in a 100-meter straight pool. Underwater (swimming) and overground PM videos were recorded from the horses' left side. Joint markers were applied on the lateral hoof wall, lateral metatarsal epicondyle, lateral aspect of the talus, lateral femoral epicondyle, and great trochanter of the femur. As a reference, maximal fetlock, tarsus, and stifle flexion/extension angles were determined during PM overground. Differences between angle extrema, angular velocities, and range of motion (ROM) were statistically compared. Results The tarsus ROM was similar during PM and swimming. The stifle and fetlock ROM were greater during PM, although the stifle flexion was greater during swimming. The stifle and tarsus had the greatest hindlimb angular velocity during the swimming cycle. Greater angular velocities were observed during the retraction phase for all the hindlimb joints. Conclusion A short retraction phase with great angular velocity for the joints of interest characterized the swimming pattern observed. Swimming may be beneficial in horses when an increased ROM of the tarsus and stifle or a reduced fetlock extension is indicated for rehabilitation purposes.
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Affiliation(s)
- Emma Santosuosso
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Renaud Leguillette
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Tatiana Vinardell
- Equine Veterinary Medical Center, Member of Qatar Foundation, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Member of Qatar Foundation, Doha, Qatar
| | - Silvio Filho
- Al Shaqab's Endurance Department, Member of Qatar Foundation, Doha, Qatar
| | - Shannon Massie
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Persephone McCrae
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Sarah Johnson
- Equine Veterinary Medical Center, Member of Qatar Foundation, Doha, Qatar
| | - Campbell Rolian
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Florent David
- Equine Veterinary Medical Center, Member of Qatar Foundation, Doha, Qatar
- *Correspondence: Florent David ;
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Santosuosso E, Leguillette R, Vinardell T, Filho S, Massie S, McCrae P, Johnson S, Rolian C, David F. Kinematic Analysis During Straight Line Free Swimming in Horses: Part 1 - Forelimbs. Front Vet Sci 2021; 8:752375. [PMID: 34722709 PMCID: PMC8553013 DOI: 10.3389/fvets.2021.752375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/17/2021] [Indexed: 11/28/2022] Open
Abstract
Background: Swimming is used for rehabilitation and conditioning purposes in equine sports medicine despite the lack of understanding of equine swimming kinematics. The aim of this study was to assess forelimb joints kinematics (elbow, carpus, and fetlock) in swimming horses. The specific objectives were 1- to calculate and compare joint angles in swimming vs. passive mobilizations (PM), 2- to determine joint angular velocities during a swimming stride cycle. Methods: Eleven elite endurance horses swam in a 100-m straight pool. Underwater (swimming) and overground (PM) videos were recorded from the horses' left side. Joint markers were applied on the lateral hoof wall, lateral metacarpal epicondyle, ulnar carpal bone, lateral humeral epicondyle, and the greater tubercle of humerus, from which elbow, carpus and fetlock angles, and angular velocities were obtained. As a reference, maximal fetlock, carpus, and elbow flexion/extension angles were determined during PM overground. Differences between angle extrema, angular velocities and range of motion (ROM) were compared. Results: Carpus and fetlock ROM were significantly smaller (p < 0.001) during swimming when compared with PM, while there was no difference in elbow ROM between both situations. The carpus had the greatest ROM of all joints during swimming. Absolute angular velocities values of all joints during swimming were greater during retraction than protraction (p < 0.001). When compared to other joints during protraction, the carpus joint reached the highest angular velocity. Conclusion: Swimming, as a rehabilitation exercise, has the potential to benefit horses where great elbow ROM with a moderate carpus and fetlock extension are wanted.
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Affiliation(s)
- Emma Santosuosso
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Renaud Leguillette
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Tatiana Vinardell
- Equine Veterinary Medical Center, Member of Qatar Foundation, Doha, Qatar
- College of Health & Life Sciences, Hamad Bin Khalifa University, Member of Qatar Foundation, Doha, Qatar
| | - Silvio Filho
- Al Shaqab - Endurance Department, Member of Qatar Foundation, Doha, Qatar
| | - Shannon Massie
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Persephone McCrae
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Sarah Johnson
- Equine Veterinary Medical Center, Member of Qatar Foundation, Doha, Qatar
| | - Campbell Rolian
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Florent David
- Equine Veterinary Medical Center, Member of Qatar Foundation, Doha, Qatar
- College of Health & Life Sciences, Hamad Bin Khalifa University, Member of Qatar Foundation, Doha, Qatar
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Giannopoulos G, Sullivan MJ, Hartop KR, Rowley G, Gates AJ, Watmough NJ, Richardson DJ. Tuning the modular Paracoccus denitrificans respirome to adapt from aerobic respiration to anaerobic denitrification. Environ Microbiol 2017; 19:4953-4964. [PMID: 29076595 DOI: 10.1111/1462-2920.13974] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 10/10/2017] [Accepted: 10/16/2017] [Indexed: 12/31/2022]
Abstract
Bacterial denitrification is a respiratory process that is a major source and sink of the potent greenhouse gas nitrous oxide. Many denitrifying bacteria can adjust to life in both oxic and anoxic environments through differential expression of their respiromes in response to environmental signals such as oxygen, nitrate and nitric oxide. We used steady-state oxic and anoxic chemostat cultures to demonstrate that the switch from aerobic to anaerobic metabolism is brought about by changes in the levels of expression of relatively few genes, but this is sufficient to adjust the configuration of the respirome to allow the organism to efficiently respire nitrate without the significant release of intermediates, such as nitrous oxide. The regulation of the denitrification respirome in strains deficient in the transcription factors FnrP, Nnr and NarR was explored and revealed that these have both inducer and repressor activities, possibly due to competitive binding at similar DNA binding sites. This may contribute to the fine tuning of expression of the denitrification respirome and so adds to the understanding of the regulation of nitrous oxide emission by denitrifying bacteria in response to different environmental signals.
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Affiliation(s)
- Georgios Giannopoulos
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Matthew J Sullivan
- School of Medical Science, Griffith University, Gold Coast campus, Southport, Australia
| | - Katherine R Hartop
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Gary Rowley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew J Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Nicholas J Watmough
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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von der Haar M, Lindner P, Scheper T, Stahl F. Array Analysis Manager-An automated DNA microarray analysis tool simplifying microarray data filtering, bias recognition, normalization, and expression analysis. Eng Life Sci 2017; 17:841-846. [PMID: 32624831 PMCID: PMC6999572 DOI: 10.1002/elsc.201700046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/18/2017] [Accepted: 05/16/2017] [Indexed: 11/11/2022] Open
Abstract
Desoxyribonucleic acid (DNA) microarray experiments generate big datasets. To successfully harness the potential information within, multiple filtering, normalization, and analysis methods need to be applied. An in-depth knowledge of underlying physical, chemical, and statistical processes is crucial to the success of this analysis. However, due to the interdisciplinarity of DNA microarray applications and experimenter backgrounds, the published analyses differ greatly, for example, in methodology. This severely limits the comprehensibility and comparability among studies and research fields. In this work, we present a novel end-user software, developed to automatically filter, normalize, and analyze two-channel microarray experiment data. It enables the user to analyze single chip, dye-swap, and loop experiments with an extended dynamic intensity range using a multiscan approach. Furthermore, to our knowledge, this is the first analysis software solution, that can account for photobleaching, automatically detected by an artificial neural network. The user gets feedback on the effectiveness of each applied normalization regarding bias minimization. Standardized methods for expression analysis are included as well as the possibility to export the results in the Gene Expression Omnibus (GEO) format. This software was designed to simplify the microarray analysis process and help the experimenter to make educated decisions about the analysis process to contribute to reproducibility and comparability.
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Affiliation(s)
| | - Patrick Lindner
- Institut für Technische ChemieLeibniz Universität HannoverHannoverGermany
| | - Thomas Scheper
- Institut für Technische ChemieLeibniz Universität HannoverHannoverGermany
| | - Frank Stahl
- Institut für Technische ChemieLeibniz Universität HannoverHannoverGermany
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Transcriptional and translational adaptation to aerobic nitrate anabolism in the denitrifier Paracoccus denitrificans. Biochem J 2017; 474:1769-1787. [PMID: 28385879 PMCID: PMC5424462 DOI: 10.1042/bcj20170115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/04/2017] [Accepted: 04/06/2017] [Indexed: 01/05/2023]
Abstract
Transcriptional adaptation to nitrate-dependent anabolism by Paracoccus denitrificans PD1222 was studied. A total of 74 genes were induced in cells grown with nitrate as N-source compared with ammonium, including nasTSABGHC and ntrBC genes. The nasT and nasS genes were cotranscribed, although nasT was more strongly induced by nitrate than nasS. The nasABGHC genes constituted a transcriptional unit, which is preceded by a non-coding region containing hairpin structures involved in transcription termination. The nasTS and nasABGHC transcripts were detected at similar levels with nitrate or glutamate as N-source, but nasABGHC transcript was undetectable in ammonium-grown cells. The nitrite reductase NasG subunit was detected by two-dimensional polyacrylamide gel electrophoresis in cytoplasmic fractions from nitrate-grown cells, but it was not observed when either ammonium or glutamate was used as the N-source. The nasT mutant lacked both nasABGHC transcript and nicotinamide adenine dinucleotide (NADH)-dependent nitrate reductase activity. On the contrary, the nasS mutant showed similar levels of the nasABGHC transcript to the wild-type strain and displayed NasG protein and NADH–nitrate reductase activity with all N-sources tested, except with ammonium. Ammonium repression of nasABGHC was dependent on the Ntr system. The ntrBC and ntrYX genes were expressed at low levels regardless of the nitrogen source supporting growth. Mutational analysis of the ntrBCYX genes indicated that while ntrBC genes are required for nitrate assimilation, ntrYX genes can only partially restore growth on nitrate in the absence of ntrBC genes. The existence of a regulation mechanism for nitrate assimilation in P. denitrificans, by which nitrate induction operates at both transcriptional and translational levels, is proposed.
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Cañas RA, Canales J, Muñoz-Hernández C, Granados JM, Ávila C, García-Martín ML, Cánovas FM. Understanding developmental and adaptive cues in pine through metabolite profiling and co-expression network analysis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3113-27. [PMID: 25873654 PMCID: PMC4449534 DOI: 10.1093/jxb/erv118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Conifers include long-lived evergreen trees of great economic and ecological importance, including pines and spruces. During their long lives conifers must respond to seasonal environmental changes, adapt to unpredictable environmental stresses, and co-ordinate their adaptive adjustments with internal developmental programmes. To gain insights into these responses, we examined metabolite and transcriptomic profiles of needles from naturally growing 25-year-old maritime pine (Pinus pinaster L. Aiton) trees over a year. The effect of environmental parameters such as temperature and rain on needle development were studied. Our results show that seasonal changes in the metabolite profiles were mainly affected by the needles' age and acclimation for winter, but changes in transcript profiles were mainly dependent on climatic factors. The relative abundance of most transcripts correlated well with temperature, particularly for genes involved in photosynthesis or winter acclimation. Gene network analysis revealed relationships between 14 co-expressed gene modules and development and adaptation to environmental stimuli. Novel Myb transcription factors were identified as candidate regulators during needle development. Our systems-based analysis provides integrated data of the seasonal regulation of maritime pine growth, opening new perspectives for understanding the complex regulatory mechanisms underlying conifers' adaptive responses. Taken together, our results suggest that the environment regulates the transcriptome for fine tuning of the metabolome during development.
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Affiliation(s)
- Rafael A Cañas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071 Málaga, Spain
| | - Javier Canales
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071 Málaga, Spain
| | - Carmen Muñoz-Hernández
- Unidad de Nanoimagen, Centro Andaluz de Nanomedicina y Biotecnología (BIONAND), Parque Tecnológico de Andalucía, C/ Severo Ochoa 35, 29590 Campanillas (Málaga), Spain
| | - Jose M Granados
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071 Málaga, Spain
| | - Concepción Ávila
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071 Málaga, Spain
| | - María L García-Martín
- Unidad de Nanoimagen, Centro Andaluz de Nanomedicina y Biotecnología (BIONAND), Parque Tecnológico de Andalucía, C/ Severo Ochoa 35, 29590 Campanillas (Málaga), Spain
| | - Francisco M Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071 Málaga, Spain
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Mycko MP, Brosnan CF, Raine CS, Fendler W, Selmaj KW. Transcriptional profiling of microdissected areas of active multiple sclerosis lesions reveals activation of heat shock protein genes. J Neurosci Res 2012; 90:1941-8. [DOI: 10.1002/jnr.23079] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 04/06/2012] [Accepted: 04/13/2012] [Indexed: 11/11/2022]
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Knudsen GM, Nielsen MB, Grassby T, Danino-Appleton V, Thomsen LE, Colquhoun IJ, Brocklehurst TF, Olsen JE, Hinton JCD. A third mode of surface-associated growth: immobilization of Salmonella enterica serovar Typhimurium modulates the RpoS-directed transcriptional programme. Environ Microbiol 2012; 14:1855-75. [PMID: 22356617 DOI: 10.1111/j.1462-2920.2012.02703.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Although the growth of bacteria has been studied for more than a century, it is only in recent decades that surface-associated growth has received attention. In addition to the well-characterized biofilm and swarming lifestyles, bacteria can also develop as micro-colonies supported by structured environments in both food products and the GI tract. This immobilized mode of growth has not been widely studied. To develop our understanding of the effects of immobilization upon a food-borne bacterial pathogen, we used the IFR Gel Cassette model. The transcriptional programme and metabolomic profile of Salmonella enterica serovar Typhimurium ST4/74 were compared during planktonic and immobilized growth, and a number of immobilization-specific characteristics were identified. Immobilized S.Typhimurium did not express motility and chemotaxis genes, and electron microscopy revealed the absence of flagella. The expression of RpoS-dependent genes and the level of RpoS protein were increased in immobilized bacteria, compared with planktonic growth. Immobilized growth prevented the induction of SPI1, SPI4 and SPI5 gene expression, likely mediated by the FliZ transcriptional regulator. Using an epithelial cell-based assay, we showed that immobilized S.Typhimurium was significantly less invasive than planktonic bacteria, and we suggest that S.Typhimurium grown in immobilized environments are less virulent than planktonic bacteria. Our findings identify immobilization as a third type of surface-associated growth that is distinct from the biofilm and swarming lifestyles of Salmonella.
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Affiliation(s)
- Gitte M Knudsen
- Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK
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Novel inducers of the envelope stress response BaeSR in Salmonella Typhimurium: BaeR is critically required for tungstate waste disposal. PLoS One 2011; 6:e23713. [PMID: 21886814 PMCID: PMC3160322 DOI: 10.1371/journal.pone.0023713] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 07/22/2011] [Indexed: 11/21/2022] Open
Abstract
The RpoE and CpxR regulated envelope stress responses are extremely important for SalmonellaTyphimurium to cause infection in a range of hosts. Until now the role for BaeSR in both the Salmonella Typhimurium response to stress and its contribution to infection have not been fully elucidated. Here we demonstrate stationary phase growth, iron and sodium tungstate as novel inducers of the BaeRregulon, with BaeR critically required for Salmonella resistance to sodium tungstate. We show that functional overlap between the resistance nodulation-cell division (RND) multidrug transporters, MdtA, AcrD and AcrB exists for the waste disposal of tungstate from the cell. We also point to a role for enterobactinsiderophores in the protection of enteric organisms from tungstate, akin to the scenario in nitrogen fixing bacteria. Surprisingly, BaeR is the first envelope stress response pathway investigated in S. Typhimurium that is not required for murine typhoid in either ityS or ityR mouse backgrounds. BaeR is therefore either required for survival in larger mammals such as pigs or calves, an avian host such as chickens, or survival out with the host altogether where Salmonella and related enterics must survive in soil and water.
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Hébrard M, Kröger C, Sivasankaran SK, Händler K, Hinton JCD. The challenge of relating gene expression to the virulence of Salmonella enterica serovar Typhimurium. Curr Opin Biotechnol 2011; 22:200-10. [PMID: 21388802 DOI: 10.1016/j.copbio.2011.02.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 02/04/2011] [Accepted: 02/10/2011] [Indexed: 12/15/2022]
Abstract
The first decade of transcriptomic studies of Salmonella enterica serovar Typhimurium focused upon gene expression in vitro, and during the infection of mammalian cells. The published regulons and stimulons show that the three Type Three Secretion Systems of S. Typhimurium respond to a diverse range of environmental conditions, and are controlled by a hierarchy of regulatory proteins. The integration of in vitro generated transcriptomic data with global gene expression of S. Typhimurium during infection is beginning to yield valuable information. The coordinated regulation of Salmonella gene expression is a key process for survival, adaptation and virulence capacities of the pathogen.
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Affiliation(s)
- Magali Hébrard
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics & Microbiology, Trinity College, Dublin 2, Ireland
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