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Kuijpers L, Hornung B, van den Hout-van Vroonhoven MCGN, van IJcken WFJ, Grosveld F, Mulugeta E. Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison. BMC Genomics 2024; 25:361. [PMID: 38609853 PMCID: PMC11010347 DOI: 10.1186/s12864-024-10285-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Single-cell sequencing techniques are revolutionizing every field of biology by providing the ability to measure the abundance of biological molecules at a single-cell resolution. Although single-cell sequencing approaches have been developed for several molecular modalities, single-cell transcriptome sequencing is the most prevalent and widely applied technique. SPLiT-seq (split-pool ligation-based transcriptome sequencing) is one of these single-cell transcriptome techniques that applies a unique combinatorial-barcoding approach by splitting and pooling cells into multi-well plates containing barcodes. This unique approach required the development of dedicated computational tools to preprocess the data and extract the count matrices. Here we compare eight bioinformatic pipelines (alevin-fry splitp, LR-splitpipe, SCSit, splitpipe, splitpipeline, SPLiTseq-demultiplex, STARsolo and zUMI) that have been developed to process SPLiT-seq data. We provide an overview of the tools, their computational performance, functionality and impact on downstream processing of the single-cell data, which vary greatly depending on the tool used. RESULTS We show that STARsolo, splitpipe and alevin-fry splitp can all handle large amount of data within reasonable time. In contrast, the other five pipelines are slow when handling large datasets. When using smaller dataset, cell barcode results are similar with the exception of SPLiTseq-demultiplex and splitpipeline. LR-splitpipe that is originally designed for processing long-read sequencing data is the slowest of all pipelines. Alevin-fry produced different down-stream results that are difficult to interpret. STARsolo functions nearly identical to splitpipe and produce results that are highly similar to each other. However, STARsolo lacks the function to collapse random hexamer reads for which some additional coding is required. CONCLUSION Our comprehensive comparative analysis aids users in selecting the most suitable analysis tool for efficient SPLiT-seq data processing, while also detailing the specific prerequisites for each of these pipelines. From the available pipelines, we recommend splitpipe or STARSolo for SPLiT-seq data analysis.
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Affiliation(s)
- Lucas Kuijpers
- Department of Cell Biology, Erasmus University Medical Center Rotterdam (Erasmus MC), Wytemaweg 80, Rotterdam, 3015CN, The Netherlands.
| | - Bastian Hornung
- Center for Biomics, Erasmus University Medical Center Rotterdam (Erasmus MC), Rotterdam, The Netherlands
| | | | - Wilfred F J van IJcken
- Center for Biomics, Erasmus University Medical Center Rotterdam (Erasmus MC), Rotterdam, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus University Medical Center Rotterdam (Erasmus MC), Wytemaweg 80, Rotterdam, 3015CN, The Netherlands
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus University Medical Center Rotterdam (Erasmus MC), Wytemaweg 80, Rotterdam, 3015CN, The Netherlands.
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Mirnezami AH, Drami I, Glyn T, Sutton PA, Tiernan J, Behrenbruch C, Guerra G, Waters PS, Woodward N, Applin S, Charles SJ, Rose SA, Denys A, Pape E, van Ramshorst GH, Baker D, Bignall E, Blair I, Davis P, Edwards T, Jackson K, Leendertse PG, Love-Mott E, MacKenzie L, Martens F, Meredith D, Nettleton SE, Trotman MP, van Hecke JJM, Weemaes AMJ, Abecasis N, Angenete E, Aziz O, Bacalbasa N, Barton D, Baseckas G, Beggs A, Brown K, Buchwald P, Burling D, Burns E, Caycedo-Marulanda A, Chang GJ, Coyne PE, Croner RS, Daniels IR, Denost QD, Drozdov E, Eglinton T, Espín-Basany E, Evans MD, Flatmark K, Folkesson J, Frizelle FA, Gallego MA, Gil-Moreno A, Goffredo P, Griffiths B, Gwenaël F, Harris DA, Iversen LH, Kandaswamy GV, Kazi M, Kelly ME, Kokelaar R, Kusters M, Langheinrich MC, Larach T, Lydrup ML, Lyons A, Mann C, McDermott FD, Monson JRT, Neeff H, Negoi I, Ng JL, Nicolaou M, Palmer G, Parnaby C, Pellino G, Peterson AC, Quyn A, Rogers A, Rothbarth J, Abu Saadeh F, Saklani A, Sammour T, Sayyed R, Smart NJ, Smith T, Sorrentino L, Steele SR, Stitzenberg K, Taylor C, Teras J, Thanapal MR, Thorgersen E, Vasquez-Jimenez W, Waller J, Weber K, Wolthuis A, Winter DC, Brangan G, Vimalachandran D, Aalbers AGJ, Abdul Aziz N, Abraham-Nordling M, Akiyoshi T, Alahmadi R, Alberda W, Albert M, Andric M, Angeles M, Antoniou A, Armitage J, Auer R, Austin KK, Aytac E, Baker RP, Bali M, Baransi S, Bebington B, Bedford M, Bednarski BK, Beets GL, Berg PL, Bergzoll C, Biondo S, Boyle K, Bordeianou L, Brecelj E, Bremers AB, Brunner M, Bui A, Burgess A, Burger JWA, Campain N, Carvalhal S, Castro L, Ceelen W, Chan KKL, Chew MH, Chok AK, Chong P, Christensen HK, Clouston H, Collins D, Colquhoun AJ, Constantinides J, Corr A, Coscia M, Cosimelli M, Cotsoglou C, Damjanovic L, Davies M, Davies RJ, Delaney CP, de Wilt JHW, Deutsch C, Dietz D, Domingo S, Dozois EJ, Duff M, Egger E, Enrique-Navascues JM, Espín-Basany E, Eyjólfsdóttir B, Fahy M, Fearnhead NS, Fichtner-Feigl S, Fleming F, Flor B, Foskett K, Funder J, García-Granero E, García-Sabrido JL, Gargiulo M, Gava VG, Gentilini L, George ML, George V, Georgiou P, Ghosh A, Ghouti L, Giner F, Ginther N, Glover T, Golda T, Gomez CM, Harris C, Hagemans JAW, Hanchanale V, Harji DP, Helbren C, Helewa RM, Hellawell G, Heriot AG, Hochman D, Hohenberger W, Holm T, Holmström A, Hompes R, Hornung B, Hurton S, Hyun E, Ito M, Jenkins JT, Jourand K, Kaffenberger S, Kapur S, Kanemitsu Y, Kaufman M, Kelley SR, Keller DS, Kersting S, Ketelaers SHJ, Khan MS, Khaw J, Kim H, Kim HJ, Kiran R, Koh CE, Kok NFM, Kontovounisios C, Kose F, Koutra M, Kraft M, Kristensen HØ, Kumar S, Lago V, Lakkis Z, Lampe B, Larsen SG, Larson DW, Law WL, Laurberg S, Lee PJ, Limbert M, Loria A, Lynch AC, Mackintosh M, Mantyh C, Mathis KL, Margues CFS, Martinez A, Martling A, Meijerink WJHJ, Merchea A, Merkel S, Mehta AM, McArthur DR, McCormick JJ, McGrath JS, McPhee A, Maciel J, Malde S, Manfredelli S, Mikalauskas S, Modest D, Morton JR, Mullaney TG, Navarro AS, Neto JWM, Nguyen B, Nielsen MB, Nieuwenhuijzen GAP, Nilsson PJ, Nordkamp S, O’Dwyer ST, Paarnio K, Pappou E, Park J, Patsouras D, Peacock O, Pfeffer F, Piqeur F, Pinson J, Poggioli G, Proud D, Quinn M, Oliver A, Radwan RW, Rajendran N, Rao C, Rasheed S, Rasmussen PC, Rausa E, Regenbogen SE, Reims HM, Renehan A, Rintala J, Rocha R, Rochester M, Rohila J, Rottoli M, Roxburgh C, Rutten HJT, Safar B, Sagar PM, Sahai A, Schizas AMP, Schwarzkopf E, Scripcariu D, Scripcariu V, Seifert G, Selvasekar C, Shaban M, Shaikh I, Shida D, Simpson A, Skeie-Jensen T, Smart P, Smith JJ, Solbakken AM, Solomon MJ, Sørensen MM, Spasojevic M, Steffens D, Stocchi L, Stylianides NA, Swartling T, Sumrien H, Swartking T, Takala H, Tan EJ, Taylor D, Tejedor P, Tekin A, Tekkis PP, Thaysen HV, Thurairaja R, Toh EL, Tsarkov P, Tolenaar J, Tsukada Y, Tsukamoto S, Tuech JJ, Turner G, Turner WH, Tuynman JB, Valente M, van Rees J, van Zoggel D, Vásquez-Jiménez W, Verhoef C, Vierimaa M, Vizzielli G, Voogt ELK, Uehara K, Wakeman C, Warrier S, Wasmuth HH, Weiser MR, Westney OL, Wheeler JMD, Wild J, Wilson M, Yano H, Yip B, Yip J, Yoo RN, Zappa MA. The empty pelvis syndrome: a core data set from the PelvEx collaborative. Br J Surg 2024; 111:znae042. [PMID: 38456677 PMCID: PMC10921833 DOI: 10.1093/bjs/znae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/15/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Empty pelvis syndrome (EPS) is a significant source of morbidity following pelvic exenteration (PE), but is undefined. EPS outcome reporting and descriptors of radicality of PE are inconsistent; therefore, the best approaches for prevention are unknown. To facilitate future research into EPS, the aim of this study is to define a measurable core outcome set, core descriptor set and written definition for EPS. Consensus on strategies to mitigate EPS was also explored. METHOD Three-stage consensus methodology was used: longlisting with systematic review, healthcare professional event, patient engagement, and Delphi-piloting; shortlisting with two rounds of modified Delphi; and a confirmatory stage using a modified nominal group technique. This included a selection of measurement instruments, and iterative generation of a written EPS definition. RESULTS One hundred and three and 119 participants took part in the modified Delphi and consensus meetings, respectively. This encompassed international patient and healthcare professional representation with multidisciplinary input. Seventy statements were longlisted, seven core outcomes (bowel obstruction, enteroperineal fistula, chronic perineal sinus, infected pelvic collection, bowel obstruction, morbidity from reconstruction, re-intervention, and quality of life), and four core descriptors (magnitude of surgery, radiotherapy-induced damage, methods of reconstruction, and changes in volume of pelvic dead space) reached consensus-where applicable, measurement of these outcomes and descriptors was defined. A written definition for EPS was agreed. CONCLUSIONS EPS is an area of unmet research and clinical need. This study provides an agreed definition and core data set for EPS to facilitate further research.
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West CT, West MA, Mirnezami AH, Drami I, Denys A, Glyn T, Sutton PA, Tiernan J, Behrenbruch C, Guerra G, Waters PS, Woodward N, Applin S, Charles SJ, Rose SA, Pape E, van Ramshorst GH, Aalbers AGJ, Abdul AN, Abecasis N, Abraham-Nordling M, Akiyoshi T, Alahmadi R, Alberda W, Albert M, Andric M, Angeles M, Angenete E, Antoniou A, Armitage J, Auer R, Austin KK, Aytac E, Aziz O, Bacalbasa N, Baker RP, Bali M, Baransi S, Baseckas G, Bebington B, Bedford M, Bednarski BK, Beets GL, Berg PL, Bergzoll C, Biondo S, Boyle K, Bordeianou L, Brecelj E, Bremers AB, Brown K, Brunner M, Buchwald P, Bui A, Burgess A, Burger JWA, Burling D, Burns E, Campain N, Carvalhal S, Castro L, Caycedo-Marulanda A, Ceelen W, Chan KKL, Chang GJ, Chew MH, Chok AK, Chong P, Christensen HK, Clouston H, Collins D, Colquhoun AJ, Constantinides J, Corr A, Coscia M, Cosimelli M, Cotsoglou C, Coyne PE, Croner RS, Damjanovic L, Daniels IR, Davies M, Davies RJ, Delaney CP, de Wilt JHW, Denost QD, Deutsch C, Dietz D, Domingo S, Dozois EJ, Drozdov E, Duff M, Egger E, Eglinton T, Enrique-Navascues JM, Espín-Basany E, Evans MD, Eyjólfsdóttir B, Fahy M, Fearnhead NS, Fichtner-Feigl S, Flatmark K, Fleming F, Flor B, Folkesson J, Foskett K, Frizelle FA, Funder J, Gallego MA, García-Granero E, García-Sabrido JL, Gargiulo M, Gava VG, Gentilini L, George ML, George V, Georgiou P, Ghosh A, Ghouti L, Gil-Moreno A, Giner F, Ginther N, Glover T, Goffredo P, Golda T, Gomez CM, Griffiths B, Gwenaël F, Harris C, Harris DA, Hagemans JAW, Hanchanale V, Harji DP, Helbren C, Helewa RM, Hellawell G, Heriot AG, Hochman D, Hohenberger W, Holm T, Holmström A, Hompes R, Hornung B, Hurton S, Hyun E, Ito M, Iversen LH, Jenkins JT, Jourand K, Kaffenberger S, Kandaswamy GV, Kapur S, Kanemitsu Y, Kaufman M, Kazi M, Kelley SR, Keller DS, Kelly ME, Kersting S, Ketelaers SHJ, Khan MS, Khaw J, Kim H, Kim HJ, Kiran R, Koh CE, Kok NFM, Kokelaar R, Kontovounisios C, Kose F, Koutra M, Kraft M, Kristensen HØ, Kumar S, Kusters M, Lago V, Lakkis Z, Lampe B, Langheinrich MC, Larach T, Larsen SG, Larson DW, Law WL, Laurberg S, Lee PJ, Limbert M, Loria A, Lydrup ML, Lyons A, Lynch AC, Mackintosh M, Mann C, Mantyh C, Mathis KL, Margues CFS, Martinez A, Martling A, Meijerink WJHJ, Merchea A, Merkel S, Mehta AM, McArthur DR, McCormick JJ, McDermott FD, McGrath JS, McPhee A, Maciel J, Malde S, Manfredelli S, Mikalauskas S, Modest D, Monson JRT, Morton JR, Mullaney TG, Navarro AS, Neeff H, Negoi I, Neto JWM, Nguyen B, Nielsen MB, Nieuwenhuijzen GAP, Nilsson PJ, Nordkamp S, O’Dwyer ST, Paarnio K, Palmer G, Pappou E, Park J, Patsouras D, Peacock A, Pellino G, Peterson AC, Pfeffer F, Piqeur F, Pinson J, Poggioli G, Proud D, Quinn M, Oliver A, Quyn A, Radwan RW, Rajendran N, Rao C, Rasheed S, Rasmussen PC, Rausa E, Regenbogen SE, Reims HM, Renehan A, Rintala J, Rocha R, Rochester M, Rohila J, Rothbarth J, Rottoli M, Roxburgh C, Rutten HJT, Safar B, Sagar PM, Sahai A, Saklani A, Sammour T, Sayyed R, Schizas AMP, Schwarzkopf E, Scripcariu D, Scripcariu V, Seifert G, Selvasekar C, Shaban M, Shaikh I, Shida D, Simpson A, Skeie-Jensen T, Smart NJ, Smart P, Smith JJ, Smith T, Solbakken AM, Solomon MJ, Sørensen MM, Spasojevic M, Steele SR, Steffens D, Stitzenberg K, Stocchi L, Stylianides NA, Swartling T, Sumrien H, Swartking T, Takala H, Tan EJ, Taylor C, Taylor D, Tejedor P, Tekin A, Tekkis PP, Teras J, Thanapal MR, Thaysen HV, Thorgersen E, Thurairaja R, Toh EL, Tsarkov P, Tolenaar J, Tsukada Y, Tsukamoto S, Tuech JJ, Turner G, Turner WH, Tuynman JB, Valente M, van Rees J, van Zoggel D, Vásquez-Jiménez W, Verhoef C, Vierimaa M, Vizzielli G, Voogt ELK, Uehara K, Wakeman C, Warrier S, Wasmuth HH, Weber K, Weiser MR, Westney OL, Wheeler JMD, Wild J, Wilson M, Wolthuis A, Yano H, Yip B, Yip J, Yoo RN, Zappa MA, Winter DC. Empty pelvis syndrome: PelvEx Collaborative guideline proposal. Br J Surg 2023; 110:1730-1731. [PMID: 37757457 PMCID: PMC10805575 DOI: 10.1093/bjs/znad301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
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Arumapperuma T, Li J, Hornung B, Soler NM, Goddard-Borger ED, Terrapon N, Williams SJ. A subfamily classification to choreograph the diverse activities within glycoside hydrolase family 31. J Biol Chem 2023; 299:103038. [PMID: 36806678 PMCID: PMC10074150 DOI: 10.1016/j.jbc.2023.103038] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 12/13/2022] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
The Carbohydrate-Active Enzyme classification groups enzymes that breakdown, assemble, or decorate glycans into protein families based on sequence similarity. The glycoside hydrolases (GH) are arranged into over 170 enzyme families, with some being very large and exhibiting distinct activities/specificities towards diverse substrates. Family GH31 is a large family that contains more than 20,000 sequences with a wide taxonomic diversity. Less than 1% of GH31 members are biochemically characterized and exhibit many different activities that include glycosidases, lyases, and transglycosidases. This diversity of activities limits our ability to predict the activities and roles of GH31 family members in their host organism and our ability to exploit these enzymes for practical purposes. Here, we established a subfamily classification using sequence similarity networks that was further validated by a structural analysis. While sequence similarity networks provide a sequence-based separation, we obtained good segregation between activities among the subfamilies. Our subclassification consists of 20 subfamilies with sixteen subfamilies containing at least one characterized member and eleven subfamilies that are monofunctional based on the available data. We also report the biochemical characterization of a member of the large subfamily 2 (GH31_2) that lacked any characterized members: RaGH31 from Rhodoferax aquaticus is an α-glucosidase with activity on a range of disaccharides including sucrose, trehalose, maltose, and nigerose. Our subclassification provides improved predictive power for the vast majority of uncharacterized proteins in family GH31 and highlights the remaining sequence space that remains to be functionally explored.
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Affiliation(s)
- Thimali Arumapperuma
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and University of Melbourne, Parkville, Victoria, Australia
| | - Jinling Li
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and University of Melbourne, Parkville, Victoria, Australia
| | - Bastian Hornung
- AFMB, UMR 7257 CNRS Aix-Marseille Univ., USC 1408 INRAE, Marseille, France
| | - Niccolay Madiedo Soler
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Ethan D Goddard-Borger
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Nicolas Terrapon
- AFMB, UMR 7257 CNRS Aix-Marseille Univ., USC 1408 INRAE, Marseille, France
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and University of Melbourne, Parkville, Victoria, Australia.
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Fahy MR, Kelly ME, Aalbers AGJ, Abdul Aziz N, Abecasis N, Abraham-Nordling M, Akiyoshi T, Alberda W, Albert M, Andric M, Angeles MA, Angenete E, Antoniou A, Auer R, Austin KK, Aytac E, Aziz O, Bacalbasa N, Baker RP, Bali M, Baransi S, Baseckas G, Bebington B, Bedford M, Bednarski BK, Beets GL, Berg PL, Bergzoll C, Beynon J, Biondo S, Boyle K, Bordeianou L, Brecelj E, Bremers AB, Brunner M, Buchwald P, Bui A, Burgess A, Burger JWA, Burling D, Burns E, Campain N, Carvalhal S, Castro L, Caycedo-Marulanda A, Ceelan W, Chan KKL, Chang GJ, Chang M, Chew MH, Chok AY, Chong P, Clouston H, Codd M, Collins D, Colquhoun AJ, Constantinides J, Corr A, Coscia M, Cosimelli M, Cotsoglou C, Coyne PE, Croner RS, Damjanovich L, Daniels IR, Davies M, Delaney CP, de Wilt JHW, Denost Q, Deutsch C, Dietz D, Domingo S, Dozois EJ, Drozdov E, Duff M, Eglinton T, Enriquez-Navascues JM, Espín-Basany E, Evans MD, Eyjólfsdóttir B, Fearnhead NS, Ferron G, Flatmark K, Fleming FJ, Flor B, Folkesson J, Frizelle FA, Funder J, Gallego MA, Gargiulo M, García-Granero E, García-Sabrido JL, Gargiulo M, Gava VG, Gentilini L, George ML, George V, Georgiou P, Ghosh A, Ghouti L, Gil-Moreno A, Giner F, Ginther DN, Glyn T, Glynn R, Golda T, Griffiths B, Harris DA, Hagemans JAW, Hanchanale V, Harji DP, Helewa RM, Hellawell G, Heriot AG, Hochman D, Hohenberger W, Holm T, Hompes R, Hornung B, Hurton S, Hyun E, Ito M, Iversen LH, Jenkins JT, Jourand K, Kaffenberger S, Kandaswamy GV, Kapur S, Kanemitsu Y, Kazi M, Kelley SR, Keller DS, Ketelaers SHJ, Khan MS, Kiran RP, Kim H, Kim HJ, Koh CE, Kok NFM, Kokelaar R, Kontovounisios C, Kose F, Koutra M, Kristensen HØ, Kroon HM, Kumar S, Kusters M, Lago V, Lampe B, Lakkis Z, Larach JT, Larkin JO, Larsen SG, Larson DW, Law WL, Lee PJ, Limbert M, Loria A, Lydrup ML, Lyons A, Lynch AC, Maciel J, Manfredelli S, Mann C, Mantyh C, Mathis KL, Marques CFS, Martinez A, Martling A, Mehigan BJ, Meijerink WJHJ, Merchea A, Merkel S, Mehta AM, Mikalauskas S, McArthur DR, McCormick JJ, McCormick P, McDermott FD, McGrath JS, Malde S, Mirnezami A, Monson JRT, Navarro AS, Negoi I, Neto JWM, Ng JL, Nguyen B, Nielsen MB, Nieuwenhuijzen GAP, Nilsson PJ, Nordkamp S, Nugent T, Oliver A, O’Dwyer ST, O’Sullivan NJ, Paarnio K, Palmer G, Pappou E, Park J, Patsouras D, Peacock O, Pellino G, Peterson AC, Pinson J, Poggioli G, Proud D, Quinn M, Quyn A, Rajendran N, Radwan RW, Rajendran N, Rao C, Rasheed S, Rausa E, Regenbogen SE, Reims HM, Renehan A, Rintala J, Rocha R, Rochester M, Rohila J, Rothbarth J, Rottoli M, Roxburgh C, Rutten HJT, Safar B, Sagar PM, Sahai A, Saklani A, Sammour T, Sayyed R, Schizas AMP, Schwarzkopf E, Scripcariu D, Scripcariu V, Selvasekar C, Shaikh I, Simpson A, Skeie-Jensen T, Smart NJ, Smart P, Smith JJ, Solbakken AM, Solomon MJ, Sørensen MM, Sorrentino L, Steele SR, Steffens D, Stitzenberg K, Stocchi L, Stylianides NA, Swartling T, Spasojevic M, Sumrien H, Sutton PA, Swartking T, Takala H, Tan EJ, Taylor C, Tekin A, Tekkis PP, Teras J, Thaysen HV, Thurairaja R, Thorgersen EB, Toh EL, Tsarkov P, Tsukada Y, Tsukamoto S, Tuech JJ, Turner WH, Tuynman JB, Valente M, van Ramshorst GH, van Zoggel D, Vasquez-Jimenez W, Vather R, Verhoef C, Vierimaa M, Vizzielli G, Voogt ELK, Uehara K, Urrejola G, Wakeman C, Warrier SK, Wasmuth HH, Waters PS, Weber K, Weiser MR, Wheeler JMD, Wild J, Williams A, Wilson M, Wolthuis A, Yano H, Yip B, Yip J, Yoo RN, Zappa MA, Winter DC. Minimum standards of pelvic exenterative practice: PelvEx Collaborative guideline. Br J Surg 2022; 109:1251-1263. [PMID: 36170347 DOI: 10.1093/bjs/znac317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/18/2022] [Accepted: 08/18/2022] [Indexed: 12/31/2022]
Abstract
This document outlines the important aspects of caring for patients who have been diagnosed with advanced pelvic cancer. It is primarily aimed at those who are establishing a service that adequately caters to this patient group. The relevant literature has been summarized and an attempt made to simplify the approach to management of these complex cases.
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Sánchez-Andrea I, van der Graaf CM, Hornung B, Bale NJ, Jarzembowska M, Sousa DZ, Rijpstra WIC, Sinninghe Damsté JS, Stams AJM. Acetate Degradation at Low pH by the Moderately Acidophilic Sulfate Reducer Acididesulfobacillus acetoxydans gen. nov. sp. nov. Front Microbiol 2022; 13:816605. [PMID: 35391737 PMCID: PMC8982180 DOI: 10.3389/fmicb.2022.816605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/31/2022] [Indexed: 11/19/2022] Open
Abstract
In acid drainage environments, biosulfidogenesis by sulfate-reducing bacteria (SRB) attenuates the extreme conditions by enabling the precipitation of metals as their sulfides, and the neutralization of acidity through proton consumption. So far, only a handful of moderately acidophilic SRB species have been described, most of which are merely acidotolerant. Here, a novel species within a novel genus of moderately acidophilic SRB is described, Acididesulfobacillus acetoxydans gen. nov. sp. nov. strain INE, able to grow at pH 3.8. Bioreactor studies with strain INE at optimum (5.0) and low (3.9) pH for growth showed that strain INE alkalinized its environment, and that this was more pronounced at lower pH. These studies also showed the capacity of strain INE to completely oxidize organic acids to CO2, which is uncommon among acidophilic SRB. Since organic acids are mainly in their protonated form at low pH, which increases their toxicity, their complete oxidation may be an acid stress resistance mechanism. Comparative proteogenomic and membrane lipid analysis further indicated that the presence of saturated ether-bound lipids in the membrane, and their relative increase at lower pH, was a protection mechanism against acid stress. Interestingly, other canonical acid stress resistance mechanisms, such as a Donnan potential and increased active charge transport, did not appear to be active.
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Affiliation(s)
- Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- *Correspondence: Irene Sánchez-Andrea,
| | | | - Bastian Hornung
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Monika Jarzembowska
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Diana Z. Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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7
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Atashgahi S, Oosterkamp MJ, Peng P, Frank J, Kraft B, Hornung B, Schleheck D, Lücker S, Jetten MSM, Stams AJM, Smidt H. Proteogenomic analysis of Georgfuchsia toluolica revealed unexpected concurrent aerobic and anaerobic toluene degradation. Environ Microbiol Rep 2021; 13:841-851. [PMID: 34374217 PMCID: PMC9290046 DOI: 10.1111/1758-2229.12996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Denitrifying Betaproteobacteria play a key role in the anaerobic degradation of monoaromatic hydrocarbons. We performed a multi-omics study to better understand the metabolism of the representative organism Georgfuchsia toluolica strain G5G6 known as a strict anaerobe coupling toluene oxidation with dissimilatory nitrate and Fe(III) reduction. Despite the genomic potential for degradation of different carbon sources, we did not find sugar or organic acid transporters, in line with the inability of strain G5G6 to use these substrates. Using a proteomics analysis, we detected proteins of fumarate-dependent toluene activation, membrane-bound nitrate reductase, and key components of the metal-reducing (Mtr) pathway under both nitrate- and Fe(III)-reducing conditions. High abundance of the multiheme cytochrome MtrC implied that a porin-cytochrome complex was used for respiratory Fe(III) reduction. Remarkably, strain G5G6 contains a full set of genes for aerobic toluene degradation, and we detected enzymes of aerobic toluene degradation under both nitrate- and Fe(III)-reducing conditions. We further detected an ATP-dependent benzoyl-CoA reductase, reactive oxygen species detoxification proteins, and cytochrome c oxidase indicating a facultative anaerobic lifestyle of strain G5G6. Correspondingly, we found diffusion through the septa a substantial source of oxygen in the cultures enabling concurrent aerobic and anaerobic toluene degradation by strain G5G6.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
- Department of Microbiology, IWWRRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Margreet J. Oosterkamp
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
- Sub‐department of Environmental TechnologyWageningen University & Research, Bornse weilanden 9Wageningen6708 DWThe Netherlands
| | - Peng Peng
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
- Department of Civil and Environmental EngineeringUniversity of Michigan, 1351 Beal AvenueAnn ArborMI48109‐2125USA
| | - Jeroen Frank
- Department of Microbiology, IWWRRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Beate Kraft
- Nordic Center for Earth EvolutionUniversity of Southern DenmarkOdenseDK‐5230Denmark
| | - Bastian Hornung
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, 163 avenue de Luminy13288 Aix Marseille UniversitéMarseilleFrance
| | - David Schleheck
- Department of BiologyUniversity of KonstanzKonstanz78457Germany
| | - Sebastian Lücker
- Department of Microbiology, IWWRRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology, IWWRRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Alfons J. M. Stams
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135Nijmegen6525 AJThe Netherlands
- Centre of Biological EngineeringUniversity of Minho, Campus de GualtarBraga4710‐057Portugal
| | - Hauke Smidt
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
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8
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Sánchez-Andrea I, Guedes IA, Hornung B, Boeren S, Lawson CE, Sousa DZ, Bar-Even A, Claassens NJ, Stams AJM. The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans. Nat Commun 2020; 11:5090. [PMID: 33037220 PMCID: PMC7547702 DOI: 10.1038/s41467-020-18906-7] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 09/14/2020] [Indexed: 12/30/2022] Open
Abstract
Six CO2 fixation pathways are known to operate in photoautotrophic and chemoautotrophic microorganisms. Here, we describe chemolithoautotrophic growth of the sulphate-reducing bacterium Desulfovibrio desulfuricans (strain G11) with hydrogen and sulphate as energy substrates. Genomic, transcriptomic, proteomic and metabolomic analyses reveal that D. desulfuricans assimilates CO2 via the reductive glycine pathway, a seventh CO2 fixation pathway. In this pathway, CO2 is first reduced to formate, which is reduced and condensed with a second CO2 to generate glycine. Glycine is further reduced in D. desulfuricans by glycine reductase to acetyl-P, and then to acetyl-CoA, which is condensed with another CO2 to form pyruvate. Ammonia is involved in the operation of the pathway, which is reflected in the dependence of the autotrophic growth rate on the ammonia concentration. Our study demonstrates microbial autotrophic growth fully supported by this highly ATP-efficient CO2 fixation pathway.
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Affiliation(s)
- Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Iame Alves Guedes
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Bastian Hornung
- Leids Universitair Medisch Centrum (LUMC), Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Christopher E Lawson
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
- Center of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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9
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Shannon RJ, Hornung B, Tew DP, Glowacki DR. Anharmonic Molecular Mechanics: Ab Initio Based Morse Parametrizations for the Popular MM3 Force Field. J Phys Chem A 2019; 123:2991-2999. [PMID: 30793911 DOI: 10.1021/acs.jpca.8b12006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methodologies for creating reactive potential energy surfaces from molecular mechanics force-fields are becoming increasingly popular. To date, molecular mechanics force-fields in biochemistry and small molecule organic chemistry tend to use harmonic expressions to treat bonding stretches, which is a poor approximation in reactive and nonequilibirum molecular dynamics simulations since bonds are often displaced significantly from their equilibrium positions. For such applications there is need for a better treatment of anharmonicity. In this contribution, Morse bonding potentials have been extensively parametrized for the atom types in the MM3 force field of Allinger and co-workers using high level CCSD(T)(F12*) energies. To our knowledge this is among the first instances of a comprehensive parametrization of Morse potentials in a popular organic chemistry force field. In the context of molecular dynamics simulations, these data will: (1) facilitate the fitting of reactive potential energy surfaces using empirical valence bond approaches and (2) enable more accurate treatments of energy transfer.
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Affiliation(s)
- R J Shannon
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K.,Department of Mechanical Engineering , Stanford University , 452 Escondido Mall , Stanford , California 94305 , United States
| | - B Hornung
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K
| | - D P Tew
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K
| | - D R Glowacki
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K.,Department of Computer Science , University of Bristol , Bristol BS8 1UB , U.K
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10
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Gerritsen J, Umanets A, Staneva I, Hornung B, Ritari J, Paulin L, Rijkers GT, de Vos WM, Smidt H. Romboutsia hominis sp. nov., the first human gut-derived representative of the genus Romboutsia, isolated from ileostoma effluent. Int J Syst Evol Microbiol 2018; 68:3479-3486. [PMID: 30226461 DOI: 10.1099/ijsem.0.003012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A Gram-stain-positive, motile, rod-shaped, obligately anaerobic bacterium, designated FRIFIT, was isolated from human ileostoma effluent and characterized. On the basis of 16S rRNA gene sequence similarity, strain FRIFIT was most closely related to the species Romboutsia ilealis CRIBT (97.7 %), Romboutsia lituseburensis DSM 797T (97.6 %) and Romboutsia sedimentorum LAM201T (96.6 %). The level of DNA-DNA relatedness between strain FRIFIT and R. ilealis CRIBT was 13.9±3.3 % based on DNA-DNA hybridization. Whole genome sequence-based average nucleotide identity between strain FRIFIT and closely related Romboutsia strains ranged from 78.4-79.1 %. The genomic DNA G+C content of strain FRIFIT was 27.8 mol%. The major cellular fatty acids of strain FRIFIT were saturated and unsaturated straight-chain C12-C19 fatty acids as well as cyclopropane fatty acids, with C16 : 0 being the predominant fatty acid. The polar lipid profile comprised five phospholipids and six glycolipids. These results, together with differences in phenotypic features, support the proposal that strain FRIFIT represents a novel species within the genus Romboutsia, for which the name Romboutsiahominis sp. nov. is proposed. The type strain is FRIFIT (=DSM 28814T=KCTC 15553T).
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Affiliation(s)
- Jacoline Gerritsen
- 1Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,2Winclove Probiotics, Hulstweg 11, 1032 LB Amsterdam, The Netherlands
| | - Alexander Umanets
- 1Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ivelina Staneva
- 1Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Bastian Hornung
- 1Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,3Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jarmo Ritari
- 4Department of Veterinary Biosciences, FI-00014 University of Helsinki, Finland
| | - Lars Paulin
- 5Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Ger T Rijkers
- 6Laboratory for Medical Microbiology and Immunology, St. Antonius Hospital, 3430 EM Nieuwegein, The Netherlands.,7Department of Science, University College Roosevelt, 4330 AB Middelburg, The Netherlands
| | - Willem M de Vos
- 1Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,4Department of Veterinary Biosciences, FI-00014 University of Helsinki, Finland.,8Immunobiology Research Program, Department of Bacteriology and Immunology, FI-00014, University of Helsinki, Helsinki, Finland
| | - Hauke Smidt
- 1Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Hornung B, Martins Dos Santos VAP, Smidt H, Schaap PJ. Studying microbial functionality within the gut ecosystem by systems biology. Genes Nutr 2018; 13:5. [PMID: 29556373 PMCID: PMC5840735 DOI: 10.1186/s12263-018-0594-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 02/13/2018] [Indexed: 12/13/2022]
Abstract
Humans are not autonomous entities. We are all living in a complex environment, interacting not only with our peers, but as true holobionts; we are also very much in interaction with our coexisting microbial ecosystems living on and especially within us, in the intestine. Intestinal microorganisms, often collectively referred to as intestinal microbiota, contribute significantly to our daily energy uptake by breaking down complex carbohydrates into simple sugars, which are fermented to short-chain fatty acids and subsequently absorbed by human cells. They also have an impact on our immune system, by suppressing or enhancing the growth of malevolent and beneficial microbes. Our lifestyle can have a large influence on this ecosystem. What and how much we consume can tip the ecological balance in the intestine. A "western diet" containing mainly processed food will have a different effect on our health than a balanced diet fortified with pre- and probiotics. In recent years, new technologies have emerged, which made a more detailed understanding of microbial communities and ecosystems feasible. This includes progress in the sequencing of PCR-amplified phylogenetic marker genes as well as the collective microbial metagenome and metatranscriptome, allowing us to determine with an increasing level of detail, which microbial species are in the microbiota, understand what these microorganisms do and how they respond to changes in lifestyle and diet. These new technologies also include the use of synthetic and in vitro systems, which allow us to study the impact of substrates and addition of specific microbes to microbial communities at a high level of detail, and enable us to gather quantitative data for modelling purposes. Here, we will review the current state of microbiome research, summarizing the computational methodologies in this area and highlighting possible outcomes for personalized nutrition and medicine.
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Affiliation(s)
- Bastian Hornung
- 1Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Vitor A P Martins Dos Santos
- 1Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Hauke Smidt
- 2Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Peter J Schaap
- 1Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
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12
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Smits WK, Weese JS, Roberts AP, Harmanus C, Hornung B. A helicase-containing module defines a family of pCD630-like plasmids in Clostridium difficile. Anaerobe 2018; 49:78-84. [DOI: 10.1016/j.anaerobe.2017.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/07/2017] [Accepted: 12/11/2017] [Indexed: 12/18/2022]
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13
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Gerritsen J, Hornung B, Renckens B, van Hijum SA, Martins dos Santos VA, Rijkers GT, Schaap PJ, de Vos WM, Smidt H. Genomic and functional analysis of Romboutsia ilealis CRIB T reveals adaptation to the small intestine. PeerJ 2017; 5:e3698. [PMID: 28924494 PMCID: PMC5598433 DOI: 10.7717/peerj.3698] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/26/2017] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host. METHODS The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired-end, mate-pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) after growth on three different carbohydrate sources, and short chain fatty acids were measured via HPLC. RESULTS We present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed identification of the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides. DISCUSSION This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available.
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Affiliation(s)
- Jacoline Gerritsen
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Winclove Probiotics, Amsterdam, The Netherlands
| | - Bastian Hornung
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Bernadette Renckens
- Nijmegen Centre for Molecular Life Sciences, CMBI, Radboud UMC, Nijmegen, The Netherlands
| | - Sacha A.F.T. van Hijum
- Nijmegen Centre for Molecular Life Sciences, CMBI, Radboud UMC, Nijmegen, The Netherlands
- NIZO, Ede, The Netherlands
| | - Vitor A.P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
- LifeGlimmer GmbH, Berlin, Germany
| | - Ger T. Rijkers
- Laboratory for Medical Microbiology and Immunology, St. Antonius Hospital, Nieuwegein, The Netherlands
- Department of Science, University College Roosevelt, Middelburg, The Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Departments of Microbiology and Immunology and Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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14
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Brouard M, Chadwick H, Gordon SDS, Hornung B, Nichols B, Aoiz FJ, Stolte S. Stereodynamics in NO(X) + Ar inelastic collisions. J Chem Phys 2017; 144:224301. [PMID: 27306001 DOI: 10.1063/1.4952649] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The effect of orientation of the NO(X) bond axis prior to rotationally inelastic collisions with Ar has been investigated experimentally and theoretically. A modification to conventional velocity-map imaging ion optics is described, which allows the orientation of hexapole state-selected NO(X) using a static electric field, followed by velocity map imaging of the resonantly ionized scattered products. Bond orientation resolved differential cross sections are measured experimentally for a series of spin-orbit conserving transitions and compared with quantum mechanical calculations. The agreement between experimental results and those from quantum mechanical calculations is generally good. Parity pairs, which have previously been observed in collisions of unpolarized NO with various rare gases, are not observed due to the coherent superposition of the two j = 1/2, Ω = 1/2 Λ-doublet levels in the orienting field. The normalized difference differential cross sections are found to depend predominantly on the final rotational state, and are not very sensitive to the final Λ-doublet level. The differential steric effect has also been investigated theoretically, by means of quantum mechanical and classical calculations. Classically, the differential steric effect can be understood by considering the steric requirement for different types of trajectories that contribute to different regions of the differential cross section. However, classical effects cannot account quantitatively for the differential steric asymmetry observed in NO(X) + Ar collisions, which reflects quantum interference from scattering at either end of the molecule. This quantum interference effect is dominated by the repulsive region of the potential.
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Affiliation(s)
- M Brouard
- The Department of Chemistry, University of Oxford, The Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - H Chadwick
- The Department of Chemistry, University of Oxford, The Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - S D S Gordon
- The Department of Chemistry, University of Oxford, The Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - B Hornung
- The Department of Chemistry, University of Oxford, The Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - B Nichols
- The Department of Chemistry, University of Oxford, The Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - F J Aoiz
- Departamento de Química Física, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain
| | - S Stolte
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
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15
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Brouard M, Chadwick H, Gordon SDS, Hornung B, Nichols B, Aoiz FJ, Stolte S. Rotational Orientation Effects in NO(X) + Ar Inelastic Collisions. J Phys Chem A 2015; 119:12404-16. [PMID: 26413997 DOI: 10.1021/acs.jpca.5b07846] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rotational angular momentum orientation effects in the rotationally inelastic collisions of NO(X) with Ar have been investigated both experimentally and theoretically at a collision energy of 530 cm(-1). The collision-induced orientation has been determined experimentally using a hexapole electric field to select the ϵ = -1 Λ-doublet level of the NO(X) j = 1/2 initial state. Fully quantum state resolved polarization-dependent differential cross sections were recorded experimentally using a crossed molecular beam apparatus coupled with a (1 + 1') resonance-enhanced multiphoton ionization detection scheme and subsequent velocity-map imaging. To determine the NO sense of rotation, the probe radiation was circularly polarized. Experimental orientation polarization-dependent differential cross sections are compared with those obtained from quantum mechanical scattering calculations and are found to be in good agreement. The origin of the collision-induced orientation has been investigated by means of close-coupled quantum mechanical, quantum mechanical hard shell, quasi-classical trajectory (QCT), and classical hard shell calculations at the same collision energy. Although there is evidence for the operation of limiting classical mechanisms, the rotational orientation cannot be accounted for by QCT calculations and is found to be strongly influenced by quantum mechanical effects.
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Affiliation(s)
- M Brouard
- The Physical and Theoretical Chemistry Laboratory, The Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - H Chadwick
- The Physical and Theoretical Chemistry Laboratory, The Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - S D S Gordon
- The Physical and Theoretical Chemistry Laboratory, The Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - B Hornung
- The Physical and Theoretical Chemistry Laboratory, The Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - B Nichols
- The Physical and Theoretical Chemistry Laboratory, The Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - F J Aoiz
- Departamento de Química Física, Facultad de Química, Universidad Complutense , 28040 Madrid, Spain
| | - S Stolte
- Institute of Atomic and Molecular Physics, Jilin University , Changchun 130012, China.,Department of Physics and Astronomy, LaserLaB, Vrije Universiteit, Amsterdam , De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.,Laboratoire Francis Perrin, Bâtiment 522, DRECEM/SPAM/CEA Saclay, 91191 Gif sur Yvette, France
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16
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Pham M, Kollmer J, Oikonomou D, Bäumer P, Hornung B, Weiler M, Nawroth PP, Bendszus M, Heiland S. Protonendichte: Ein neuer Biomarker in der MR-Neurografie zur Diagnose und Charakterisierung der diabetischen Polyneuropathie. DIABETOL STOFFWECHS 2015. [DOI: 10.1055/s-0035-1549573] [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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17
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Goris T, Hornung B, Kruse T, Reinhold A, Westermann M, Schaap PJ, Smidt H, Diekert G. Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S. Stand Genomic Sci 2015. [PMID: 26203328 PMCID: PMC4511579 DOI: 10.1186/1944-3277-10-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
This genome report describes the draft genome and the physiological characteristics of Desulfitobacterium hafniense PCE-S, a Gram-positive bacterium known to dechlorinate tetrachloroethene (PCE) to dichloroethene by a PCE reductive dehalogenase. The draft genome has a size of 5,666,696 bp with a G + C content of 47.3%. The genome is very similar to the already sequenced Desulfitobacterium hafniense Y51 and the type strain DCB-2. We identified two complete reductive dehalogenase (rdh) genes in the genome of D. hafniense PCE-S, one of which encodes PceA, the PCE reductive dehalogenase, and is located on a transposon. Interestingly, this transposon structure differs from the PceA-containing transposon of D. hafniense Y51. The second rdh encodes an unknown reductive dehalogenase, highly similar to rdhA 7 found in D. hafniense DCB-2, in which the corresponding gene is disrupted. This reductive dehalogenase might be responsible for the reductive dechlorination of 2,4,5-trichlorophenol and pentachlorophenol, which is mediated by D. hafniense PCE-S in addition to the reductive dechlorination of PCE.
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Affiliation(s)
- Tobias Goris
- Institut für Mikrobiologie, Lehrstuhl für Angewandte und Ökologische Mikrobiologie, University of Jena, Philosophenweg 12, Jena D-07743, Germany
| | - Bastian Hornung
- Laboratory of Microbiology, Wageningen University, Wageningen 6703 HB, The Netherlands ; Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen 6703 HB, The Netherlands
| | - Thomas Kruse
- Laboratory of Microbiology, Wageningen University, Wageningen 6703 HB, The Netherlands
| | - Anika Reinhold
- Institut für Mikrobiologie, Lehrstuhl für Angewandte und Ökologische Mikrobiologie, University of Jena, Philosophenweg 12, Jena D-07743, Germany
| | - Martin Westermann
- Electron Microscopy Center of the University Hospital Jena, Friedrich Schiller University, Jena, Germany
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen 6703 HB, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen 6703 HB, The Netherlands
| | - Gabriele Diekert
- Institut für Mikrobiologie, Lehrstuhl für Angewandte und Ökologische Mikrobiologie, University of Jena, Philosophenweg 12, Jena D-07743, Germany
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Nichols B, Chadwick H, Gordon SDS, Eyles CJ, Hornung B, Brouard M, Alexander MH, Aoiz FJ, Gijsbertsen A, Stolte S. Steric effects and quantum interference in the inelastic scattering of NO(X) + Ar. Chem Sci 2015; 6:2202-2210. [PMID: 28694950 PMCID: PMC5485563 DOI: 10.1039/c4sc03842h] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/03/2015] [Indexed: 11/21/2022] Open
Abstract
New measurements of the differential steric effect for NO + Ar inelastic scattering highlight the importance of quantum interference.
Rotationally inelastic collisions of NO(X) with Ar are investigated in unprecedented detail using state-to-state, crossed molecular beam experiments. The NO(X) molecules are selected in the Ω = 0.5, j = 0.5, f state and then oriented such that either the ‘N’ or ‘O’ end of the molecule is directed towards the incoming Ar atom. Velocity map ion imaging is then used to probe the scattered NO molecules in well-defined quantum states. We show that the fully quantum state-resolved differential steric asymmetry, which quantifies how the relative efficiency for scattering off the ‘O’ and the ‘N’ ends of the molecule varies with scattering angle, is strongly affected by quantum interference. Significant changes in both integral and differential cross sections are found depending on whether collisions occur with the N or O ends of the molecule. The results are well accounted for by rigorous quantum mechanical calculations, in contrast to both classical trajectory calculations and more simplistic models that provide, at best, an incomplete picture of the dynamics.
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Affiliation(s)
- B Nichols
- The Department of Chemistry , University of Oxford , The Physical and Theoretical Chemistry Laboratory , South Parks Road , Oxford , OX1 3QZ , United Kingdom .
| | - H Chadwick
- The Department of Chemistry , University of Oxford , The Physical and Theoretical Chemistry Laboratory , South Parks Road , Oxford , OX1 3QZ , United Kingdom .
| | - S D S Gordon
- The Department of Chemistry , University of Oxford , The Physical and Theoretical Chemistry Laboratory , South Parks Road , Oxford , OX1 3QZ , United Kingdom .
| | - C J Eyles
- The Department of Chemistry , University of Oxford , The Physical and Theoretical Chemistry Laboratory , South Parks Road , Oxford , OX1 3QZ , United Kingdom .
| | - B Hornung
- The Department of Chemistry , University of Oxford , The Physical and Theoretical Chemistry Laboratory , South Parks Road , Oxford , OX1 3QZ , United Kingdom .
| | - M Brouard
- The Department of Chemistry , University of Oxford , The Physical and Theoretical Chemistry Laboratory , South Parks Road , Oxford , OX1 3QZ , United Kingdom .
| | - M H Alexander
- Department of Chemistry and Biochemistry and Institute of Physical Science and Technology , University of Maryland , College Park , MD 20742 , USA .
| | - F J Aoiz
- Departamento de Química Física , Facultad de Química , Universidad Complutense , 28040 Madrid , Spain .
| | - A Gijsbertsen
- Institute for Lasers, Life and Biophotonics , Vrije Universiteit , de Boelelaan 1083 , Amsterdam 1081 HV , The Netherlands
| | - S Stolte
- Institute of Atomic and Molecular Physics , Jilin University , Changchun 130012 , China . .,Department of Physics and Astronomy , LaserLaB , Vrije Universiteit , de Boelelaan 1083 , Amsterdam 1081 HV , The Netherlands.,Laboratoire Francis Perrin , Bâtiment 522, DRECEM/SPAM/CEA Saclay , 91191 Gif sur Yvette , France
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Brouard M, Chadwick H, Gordon SDS, Hornung B, Nichols B, Kłos J, Aoiz FJ, Stolte S. Fully quantum state-resolved inelastic scattering of NO(X) + Kr: Differential cross sections and product rotational alignment. J Chem Phys 2014; 141:164306. [DOI: 10.1063/1.4897558] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. Brouard
- The Department of Chemistry, University of Oxford, The Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - H. Chadwick
- The Department of Chemistry, University of Oxford, The Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - S. D. S. Gordon
- The Department of Chemistry, University of Oxford, The Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - B. Hornung
- The Department of Chemistry, University of Oxford, The Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - B. Nichols
- The Department of Chemistry, University of Oxford, The Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - J. Kłos
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - F. J. Aoiz
- Departamento de Química Física, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain
| | - S. Stolte
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
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Abstract
Collision-induced rotational angular momentum orientation is a fundamental property of molecular scattering, which is sensitive to the balance between attractive and repulsive forces at play during collision. Here, we quantify a new mechanism leading to orientation, which is purely quantum mechanical in origin. Although the new mechanism is quite general, and will operate more widely in atomic and molecular scattering, it is observed here for impulsive hard shell collisions, for which the orientation vanishes classically. The quantum mechanism can thus be studied in isolation from other processes. The orientation is proposed to originate from the nonlocal nature of the quantum mechanical collision encounter.
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Affiliation(s)
- M Brouard
- The Department of Chemistry, The Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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21
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Brouard M, Chadwick H, Eyles CJ, Hornung B, Nichols B, Scott JM, Aoiz FJ, Kłos J, Stolte S, Zhang X. The fully quantum state-resolved inelastic scattering of NO(X) + Ne: experiment and theory. Mol Phys 2013. [DOI: 10.1080/00268976.2013.783940] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- M. Brouard
- a Department of Chemistry, The Physical and Theoretical Chemistry Laboratory , University of Oxford , Oxford , United Kingdom
| | - H. Chadwick
- a Department of Chemistry, The Physical and Theoretical Chemistry Laboratory , University of Oxford , Oxford , United Kingdom
| | - C. J. Eyles
- a Department of Chemistry, The Physical and Theoretical Chemistry Laboratory , University of Oxford , Oxford , United Kingdom
| | - B. Hornung
- a Department of Chemistry, The Physical and Theoretical Chemistry Laboratory , University of Oxford , Oxford , United Kingdom
| | - B. Nichols
- a Department of Chemistry, The Physical and Theoretical Chemistry Laboratory , University of Oxford , Oxford , United Kingdom
| | - J. M. Scott
- a Department of Chemistry, The Physical and Theoretical Chemistry Laboratory , University of Oxford , Oxford , United Kingdom
| | - F. J. Aoiz
- b Departamento de Química Física, Facultad de Química , Universidad Complutense , Madrid , Spain
| | - J. Kłos
- c Department of Chemistry and Biochemistry , University of Maryland , College Park , MD , USA
| | - S. Stolte
- d Atomic and Molecular Physics Institute , Jilin University , Changchun , China
- e Laser Center , Vrije Universiteit , Amsterdam , The Netherlands
- f Laboratoire Francis Perrin , Bâtiment 522, DRECEM/SPAM/CEA Saclay, Gif sur Yvette , France
| | - X. Zhang
- d Atomic and Molecular Physics Institute , Jilin University , Changchun , China
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Brouard M, Chadwick H, Eyles CJ, Hornung B, Nichols B, Aoiz FJ, Jambrina PG, Stolte S. Rotational alignment effects in NO(X) + Ar inelastic collisions: an experimental study. J Chem Phys 2013; 138:104310. [PMID: 23514492 DOI: 10.1063/1.4792159] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Rotational angular momentum alignment effects in the rotationally inelastic collisions of NO(X) with Ar have been investigated at a collision energy of 66 meV by means of hexapole electric field initial state selection coupled with velocity-map ion imaging final state detection. The fully quantum state resolved second rank renormalized polarization dependent differential cross sections determined experimentally are reported for a selection of spin-orbit conserving and changing transitions for the first time. The results are compared with the findings of previous theoretical investigations, and in particular with the results of exact quantum mechanical scattering calculations. The agreement between experiment and theory is generally found to be good throughout the entire scattering angle range. The results reveal that the hard shell nature of the interaction potential is predominantly responsible for the rotational alignment of the NO(X) upon collision with Ar.
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Affiliation(s)
- M Brouard
- The Department of Chemistry, University of Oxford, The Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom.
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Brouard M, Chadwick H, Eyles CJ, Hornung B, Nichols B, Aoiz FJ, Jambrina PG, Stolte S, de Miranda MP. Rotational alignment effects in NO(X) + Ar inelastic collisions: A theoretical study. J Chem Phys 2013; 138:104309. [DOI: 10.1063/1.4792158] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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24
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Eyles CJ, Brouard M, Chadwick H, Hornung B, Nichols B, Yang CH, Kłos J, Aoiz FJ, Gijsbertsen A, Wiskerke AE, Stolte S. Fully Λ-doublet resolved state-to-state differential cross-sections for the inelastic scattering of NO(X) with Ar. Phys Chem Chem Phys 2012; 14:5403-19. [PMID: 22434386 DOI: 10.1039/c2cp23258h] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fully Λ-doublet resolved state-to-state differential cross-sections (DCSs) for the collisions of the open-shell NO(X, (2)Π(1/2), ν = 0, j = 0.5) molecule with Ar at a collision energy of 530 cm(-1) are presented. Initial state selection of NO(X, (2)Π(1/2), j = 0.5, f) was performed using a hexapole so that the (low field seeking) parity of ε = -1, corresponding to the f component of the Λ-doublet, could be selected uniquely. Although the Λ-doublet levels lie very close in energy to one another and differ only in their relative parities, they exhibit strikingly different DCSs. Both spin-orbit conserving and spin-orbit changing collisions have been studied, and the previously unobserved structures in the fully quantum state-to-state resolved DCSs are shown to depend sensitively on the change in parity of the wavefunction of the NO molecule on collision. In all cases, the experimental data are shown to be in excellent agreement with rigorous quantum mechanical scattering calculations.
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Affiliation(s)
- C J Eyles
- The Department of Chemistry, University of Oxford, The Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, UK
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McMurray D, Hornung B, Venkateswaran B, Ali Z. Walking on a tightrope: Our experience in the treatment of traumatic ankle syndesmosis rupture. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.injury.2007.11.354] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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26
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Pring C, Hornung B, Burke D, Sagar P. Letter 1: randomized clinical trial of bowel preparation with a single phosphate enema or polyethylene glycol before elective colorectal surgery (Br J Surg 2006; 93: 427-433). Br J Surg 2006; 93:1147; author reply 1147-8. [PMID: 16915583 DOI: 10.1002/bjs.5588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Abstract
The Editors welcome topical correspondence from readers relating to articles published in the Journal. Responses should be sent electronically via the BJS website (www.bjs.co.uk). All letters will be reviewed and, if approved, appear on the website. A selection of these will be edited and published in the Journal. Letters must be no more than 250 words in length.
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Malling HJ, Gayraud J, Papageorgiu-Saxoni P, Hornung B, Rosado-Pinto J, Del Giacco SG. Objectives of training and specialty training core curriculum in allergology and clinical immunology. Allergy 2004; 59:579-88. [PMID: 15147442 DOI: 10.1111/j.1398-9995.2004.00467.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- H-J Malling
- Section/Board of Allergology and Clinical Immunology, European Union of Medical Specialists, Allergy Clinic 4222, National University Hospital, Blegdamsvej 9m DK-2100 Copenhagen, Denmark
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28
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Rebien W, Hornung B. CEFCAP-Workshop „Allergieprävention“. Allergo J 2002. [DOI: 10.1007/bf03360972] [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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Armstrong JS, Steinauer KK, Hornung B, Irish JM, Lecane P, Birrell GW, Peehl DM, Knox SJ. Role of glutathione depletion and reactive oxygen species generation in apoptotic signaling in a human B lymphoma cell line. Cell Death Differ 2002; 9:252-63. [PMID: 11859408 DOI: 10.1038/sj.cdd.4400959] [Citation(s) in RCA: 340] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2001] [Revised: 08/24/2001] [Accepted: 09/09/2001] [Indexed: 12/13/2022] Open
Abstract
The primary objective of this study was to determine the sequence of biochemical signaling events that occur after modulation of the cellular redox state in the B cell lymphoma line, PW, with emphasis on the role of mitochondrial signaling. L-Buthionine sulphoximine (BSO), which inhibits gamma glutamyl cysteine synthetase (gammaGCS), was used to modulate the cellular redox status. The sequence and role of mitochondrial events and downstream apoptotic signals and mediators was studied. After BSO treatment, there was an early decline in cellular glutathione (GSH), followed by an increase in reactive oxygen species (ROS) production, which induced a variety of apoptotic signals (detectable at different time points) in the absence of any external apoptotic stimuli. The sequence of biochemical events accompanying apoptosis included a 95% decrease in total GSH and a partial (25%) preservation of mitochondrial GSH, without a significant increase in ROS production at 24h. Early activation and nuclear translocation of the nuclear factor kappa B subunit Rel A was observed at approximately 3h after BSO treatment. Cytochrome c release into the cytosol was also seen after 24h of BSO treatment. p53 protein expression was unchanged after redox modulation for up to 72 h, and p21waf1 independent loss of cellular proliferation was observed. Surprisingly, a truncated form of p53 was expressed in a time-dependent manner, beginning at 24h after BSO incubation. Irreversible commitment to apoptosis occurred between 48 and 72 h after BSO treatment when mitochondrial GSH was depleted, and there was an increase in ROS production. Procaspase 3 protein levels showed a time-dependent reduction following incubation with BSO, notably after 48 h, that corresponded with increasing ROS levels. At 96 h, caspase 3 cleavage products were detectable. The pan-caspase inhibitor zVADfmk, partially blocked the induction of apoptosis at 48 h, and was ineffective after 72 h. PW cells could be rescued from apoptosis by removing them from BSO after up to 48, but not 72 h incubation with BSO. Mitochondrial transmembrane potential (DeltaPsi(m)) remained intact in most of the cells during the 72 h observation period, indicating that DeltaPsi(m) dissipation is not an early signal for the induction of redox dependent apoptosis in PW cells. These data suggest that a decrease in GSH alone can act as a potent early activator of apoptotic signaling. Increased ROS production following mitochondrial GSH depletion, represents a crucial event, which irreversibly commits PW cells to apoptosis.
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Affiliation(s)
- J S Armstrong
- Department of Radiation Oncology, Stanford University, Stanford, California, CA 94305-5105, USA
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30
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Armstrong JS, Hornung B, Lecane P, Jones DP, Knox SJ. Rotenone-induced G2/M cell cycle arrest and apoptosis in a human B lymphoma cell line PW. Biochem Biophys Res Commun 2001; 289:973-8. [PMID: 11741286 DOI: 10.1006/bbrc.2001.6054] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Concentrations of rotenone (ROT) that block electron flow through mitochondrial complex I (100 nM) did not significantly alter either cell viability or the growth of PW cells. However, 10- to 50-fold higher concentrations (1-5 microM) were found to induce a dose-dependent cell cycle arrest predominantly at the G2/M stage of the cycle and apoptosis. Apoptosis was dependent on the cell cycle arrest, since apoptosis but not the G2/M arrest was prevented with the broad spectrum caspase inhibitor zVADfmk. Biochemical features of apoptosis included mitochondrial cytochrome c release, reactive oxygen species generation, and the activation of procaspase 3. Thus, ROT inhibition of mitochondrial electron transport may be insufficient to induce apoptosis in PW cells. Instead, apoptosis in these cells occurs as a consequence of disruption of the cell cycle and is only indirectly dependent upon mitochondrial electron transport.
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Affiliation(s)
- J S Armstrong
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, California 94305-5105, USA.
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31
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Kösters J, Hornung B, Korbel R. [Ostrich farming from the perspective of veterinarians]. Dtsch Tierarztl Wochenschr 1996; 103:100-4. [PMID: 8721329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The present paper is an attempt to relate the etiology of 54 cases with diseased/deceased ostriches to criterions of keeping, feeding, climate and infectious diseases. Despite the fact that some of the damages diagnosed seem to be avoidable the criterions of the law for the prevention of cruelty to animals are not to be fulfilled since the adverse climatic circumstances in Germany.
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Affiliation(s)
- J Kösters
- Aus dem Institut für Geflügelkrankheiten der Ludwig-Maximilians-Universität München
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32
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Sader R, Zeilhofer HF, Deppe H, Horch HH, Nuber B, Hornung B. [Equipment and transducer-independent 3D ultrasound in the maxillofacial area]. Ultraschall Med 1995; 16:269-274. [PMID: 8584907 DOI: 10.1055/s-2007-1003217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
AIM The use of a new 3D ultrasound system should reduce the drawbacks of former 3D workstations (long image generation time, limited use due to the need for special 3D transducers), so that it is now applicable in daily clinical routine. METHOD An ultrasound 3D workstation was used based on a pentium PC platform, employing a magnetoelectronic position detection system for spatial reconstruction of conventional 2D B-scan image sequences. RESULTS Better assessment of topographico-anatomical spatial relationships was achieved when presenting pathological findings, especially in assessing lymph nodes and salivary stones. Pathological processes in the maxillofacial area occurring during a period of five months were visualised. CONCLUSION The method of 3D reconstruction of standard two-dimensional electronic scans, as presented here, is the first method of its kind enabling applicability in daily clinical routine thanks to rapid imaging. The images can be produced with any ultrasound unit or transducer. First clinical results in maxillofacial surgery clearly show improved diagnostic possibilities although there still room for an improvement of the image quality. The possibility of semi-automatic exact volumetry appears meaningful especially in the investigation of lymph nodes. Integration of colour duplex sonography will further enhance the diagnostic value of this method.
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Affiliation(s)
- R Sader
- Klinik und Poliklinik für Mund-Kiefer-Gesichtschirurgie, Technischen Universität München, Klinikum rechts der Isar
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Sader R, Zeilhofer HF, Deppe H, Horch HH, Nuber B, Hornung B. [New possibilities in computer-assisted image processing for ultrasound diagnosis in mouth-jaw-facial surgery]. Bildgebung 1995; 62:38-43. [PMID: 7756822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The use of a digital image processing system in ultrasound diagnostics offers not only the advantage of a space-saving archiving without loss of quality, but also a clearly higher efficacy of the examination is achieved. An interactive of system findings leads to a more complete examination and evaluation, thus increasing the reliability and the objectivity of the examination. The standardized findings by use of text components mean at the same time a clear saving of time. Moreover, this system is very comfortable not only for the comparison of different images, but also for the scientific evaluation and processing of the image data. By digitalizing the sonographic images the visual data can be processed in a personal computer. Thereby, for maxillofacial surgery a simple and fast dynamic-functional evaluation of the temporomandibular joint was made possible. By archiving without loss of quality and by higher reliability, objectivity and efficacy of the sonographic examination important preconditions for quality care in ultrasound diagnostics have been achieved.
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Affiliation(s)
- R Sader
- Klinik und Poliklinik für Mund-Kiefer-Gesichtschirurgie der Technischen Universität München
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34
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Hesse A, Nuber B, Hornung B. [3-D ultrasound--data acquisition and representation]. Bildgebung 1994; 61:83-86. [PMID: 7919880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A three-dimensional (3D) workstation for data acquisition, processing, registration and presentation of 3D ultrasound information is described. The ultrasound images needed for further processing are generated by a standard diagnostic ultrasound system. The 3D transducers used here include frequencies of 3.5, 5 and 7.5 MHz. The presentation of reconstructed 3D data is performed by computer-assisted projection of volumetric data or by the presentation of user-selectable slices from the 3D object. Besides improved diagnosis of 3D structures, the system enables precise volume measurements.
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Affiliation(s)
- A Hesse
- ViewPoint Bildverarbeitung GmbH, Gilching
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35
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Abstract
In the presence of lauric acid (C12), the production of infectious vesicular stomatitis virus (VSV) was inhibited in a dose-dependent manner. The inhibitory effect was reversible; after removal of C12 the antiviral effect disappeared. In addition, the chain length of the monocarboxylic acids proved to be crucial, as those with shorter or longer chains were less effective or had no antiviral activity. Concomitant with the C12-induced inhibition was the stimulation of triacylglycerol synthesis, increasing the amount up to ninefold. Analysis of the antiviral mechanism of C12 revealed that the correct assembly of the viral components was disturbed, but viral RNA and protein synthesis remained unimpaired. By cell fractionation and Western blot analysis the amount of viral M protein located in the plasma membrane was found to be markedly reduced after treatment with C12, whereas in the cytoplasm the quantity of M protein was similar to that in untreated cells. C12 did not influence M protein synthesis, but prevented the binding of M protein to the host cell membrane, where the protein plays an essential role in virus assembly. Thus, treatment of VSV-infected cells with C12 resulted in inhibition of virus release. It is suggested that the newly synthesized triacylglycerols might interact with the host cell plasma membrane and interfere with virus maturation.
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Affiliation(s)
- B Hornung
- German Cancer Research Centre, Department of Molecular Biology of DNA Tumour Viruses, Heidelberg
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36
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Abstract
In the presence of undecanoic acid (C11) or lauric acid (C12) the synthesis of triacylglycerols was stimulated up to 10-fold both in tumor cell lines and in normal cell lines. Monocarboxylic acids of shorter or longer chain length either had no effect at all or were less effective. The increased triacylglycerol production was demonstrated, on the one hand, by the incorporation of radiolabeled glycerol into triacylglycerols and, on the other, by the incorporation of radiolabeled monocarboxylic acids, the incorporation of all (1-14C)-labeled monocarboxylic acids (C6, C12, C16, C18) regardless of their chain length, being preferentially enhanced by C11 and C12. C12 stimulated the de novo synthesis of triacylglycerols to such a degree that a 7-fold increase in the total amount of triacylglycerols per cell was observed during the first 10 hr of incubation. After removal of C12 from the tissue culture medium levels of triacylglycerols reach initial values again within 6 hr, indicating that the stimulatory effect of C12 is dependent on its continued presence. This led to the speculation that medium chain length monocarboxylic acids might be involved in the control of triacylglycerol synthesis.
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Affiliation(s)
- B Hornung
- German Cancer Research Center, Institute for Virus Research, Heidelberg, Federal Republic of Germany
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37
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Abstract
Three-dimensional reconstruction of an organ requires a coordinated sequence of cross-sectional scans. In ultrasound this can be solved by rotating the scan plane horizontally or vertically. Two scan heads have been built, one to rotate the plane around a horizontal, the second around a vertical axis. There are two ways to reconstruct the scans taken by ultrasound into a three-dimensional image: --to contour the surface of the organ in each scan and to reconstruct these contours to a ring-shaped structure. This procedure needs a lot of time; moreover, contouring must be performed via cursor on the screen. --calculate a transparent image of the organ. To obtain the best spatial image by the "transparent method", the image must be moved on the screen. Both methods of reconstruction are shown and compared in this paper. First experiences show that they can be applied in tumour diagnostic and in the diagnosis of malformations in early pregnancy. Further clinical studies will have to prove this.
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Affiliation(s)
- C Sohn
- Universitätsfrauenklinik Heidelberg
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