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Kramer S, Karolak NK, Odenwald J, Gabiatti B, Castañeda Londoño P, Zavřelová A, Freire E, Almeida K, Braune S, Moreira C, Eder A, Goos C, Field M, Carrington M, Holetz F, Górna M, Zoltner M. A unique mRNA decapping complex in trypanosomes. Nucleic Acids Res 2023; 51:7520-7540. [PMID: 37309887 PMCID: PMC10415143 DOI: 10.1093/nar/gkad497] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 06/14/2023] Open
Abstract
Removal of the mRNA 5' cap primes transcripts for degradation and is central for regulating gene expression in eukaryotes. The canonical decapping enzyme Dcp2 is stringently controlled by assembly into a dynamic multi-protein complex together with the 5'-3'exoribonuclease Xrn1. Kinetoplastida lack Dcp2 orthologues but instead rely on the ApaH-like phosphatase ALPH1 for decapping. ALPH1 is composed of a catalytic domain flanked by C- and N-terminal extensions. We show that T. brucei ALPH1 is dimeric in vitro and functions within a complex composed of the trypanosome Xrn1 ortholog XRNA and four proteins unique to Kinetoplastida, including two RNA-binding proteins and a CMGC-family protein kinase. All ALPH1-associated proteins share a unique and dynamic localization to a structure at the posterior pole of the cell, anterior to the microtubule plus ends. XRNA affinity capture in T. cruzi recapitulates this interaction network. The ALPH1 N-terminus is not required for viability in culture, but essential for posterior pole localization. The C-terminus, in contrast, is required for localization to all RNA granule types, as well as for dimerization and interactions with XRNA and the CMGC kinase, suggesting possible regulatory mechanisms. Most significantly, the trypanosome decapping complex has a unique composition, differentiating the process from opisthokonts.
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Affiliation(s)
| | - Natalia Katarzyna Karolak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | | | - Bernardo Gabiatti
- Biocenter, University of Würzburg, Würzburg, Germany
- Carlos Chagas Institute (ICC), FIOCRUZ/PR, Curitiba, Brazil
| | | | - Anna Zavřelová
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
| | | | | | - Silke Braune
- Biocenter, University of Würzburg, Würzburg, Germany
| | - Claudia Moreira
- Biocenter, University of Würzburg, Würzburg, Germany
- Carlos Chagas Institute (ICC), FIOCRUZ/PR, Curitiba, Brazil
| | - Amelie Eder
- Biocenter, University of Würzburg, Würzburg, Germany
| | - Carina Goos
- Biocenter, University of Würzburg, Würzburg, Germany
| | - Mark Field
- School of Life Sciences, University of Dundee, Dundee, UK
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Fabiola Holetz
- Carlos Chagas Institute (ICC), FIOCRUZ/PR, Curitiba, Brazil
| | - Maria Wiktoria Górna
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Martin Zoltner
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
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Smitherman EA, Chahine RA, Beukelman T, Lewandowski LB, Rahman AKMF, Wenderfer SE, Curtis JR, Hersh AO, Abulaban K, Adams A, Adams M, Agbayani R, Aiello J, Akoghlanian S, Alejandro C, Allenspach E, Alperin R, Alpizar M, Amarilyo G, Ambler W, Anderson E, Ardoin S, Armendariz S, Baker E, Balboni I, Balevic S, Ballenger L, Ballinger S, Balmuri N, Barbar‐Smiley F, Barillas‐Arias L, Basiaga M, Baszis K, Becker M, Bell‐Brunson H, Beltz E, Benham H, Benseler S, Bernal W, Beukelman T, Bigley T, Binstadt B, Black C, Blakley M, Bohnsack J, Boland J, Boneparth A, Bowman S, Bracaglia C, Brooks E, Brothers M, Brown A, Brunner H, Buckley M, Buckley M, Bukulmez H, Bullock D, Cameron B, Canna S, Cannon L, Carper P, Cartwright V, Cassidy E, Cerracchio L, Chalom E, Chang J, Chang‐Hoftman A, Chauhan V, Chira P, Chinn T, Chundru K, Clairman H, Co D, Confair A, Conlon H, Connor R, Cooper A, Cooper J, Cooper S, Correll C, Corvalan R, Costanzo D, Cron R, Curiel‐Duran L, Curington T, Curry M, Dalrymple A, Davis A, Davis C, Davis C, Davis T, De Benedetti F, De Ranieri D, Dean J, Dedeoglu F, DeGuzman M, Delnay N, Dempsey V, DeSantis E, Dickson T, Dingle J, Donaldson B, Dorsey E, Dover S, Dowling J, Drew J, Driest K, Du Q, Duarte K, Durkee D, Duverger E, Dvergsten J, Eberhard A, Eckert M, Ede K, Edelheit B, Edens C, Edens C, Edgerly Y, Elder M, Ervin B, Fadrhonc S, Failing C, Fair D, Falcon M, Favier L, Federici S, Feldman B, Fennell J, Ferguson I, Ferguson P, Ferreira B, Ferrucho R, Fields K, Finkel T, Fitzgerald M, Fleming C, Flynn O, Fogel L, Fox E, Fox M, Franco L, Freeman M, Fritz K, Froese S, Fuhlbrigge R, Fuller J, George N, Gerhold K, Gerstbacher D, Gilbert M, Gillispie‐Taylor M, Giverc E, Godiwala C, Goh I, Goheer H, Goldsmith D, Gotschlich E, Gotte A, Gottlieb B, Gracia C, Graham T, Grevich S, Griffin T, Griswold J, Grom A, Guevara M, Guittar P, Guzman M, Hager M, Hahn T, Halyabar O, Hammelev E, Hance M, Hanson A, Harel L, Haro S, Harris J, Harry O, Hartigan E, Hausmann J, Hay A, Hayward K, Heiart J, Hekl K, Henderson L, Henrickson M, Hersh A, Hickey K, Hill P, Hillyer S, Hiraki L, Hiskey M, Hobday P, Hoffart C, Holland M, Hollander M, Hong S, Horwitz M, Hsu J, Huber A, Huggins J, Hui‐Yuen J, Hung C, Huntington J, Huttenlocher A, Ibarra M, Imundo L, Inman C, Insalaco A, Jackson A, Jackson S, James K, Janow G, Jaquith J, Jared S, Johnson N, Jones J, Jones J, Jones J, Jones K, Jones S, Joshi S, Jung L, Justice C, Justiniano A, Karan N, Kaufman K, Kemp A, Kessler E, Khalsa U, Kienzle B, Kim S, Kimura Y, Kingsbury D, Kitcharoensakkul M, Klausmeier T, Klein K, Klein‐Gitelman M, Kompelien B, Kosikowski A, Kovalick L, Kracker J, Kramer S, Kremer C, Lai J, Lam J, Lang B, Lapidus S, Lapin B, Lasky A, Latham D, Lawson E, Laxer R, Lee P, Lee P, Lee T, Lentini L, Lerman M, Levy D, Li S, Lieberman S, Lim L, Lin C, Ling N, Lingis M, Lo M, Lovell D, Lowman D, Luca N, Lvovich S, Madison C, Madison J, Manzoni SM, Malla B, Maller J, Malloy M, Mannion M, Manos C, Marques L, Martyniuk A, Mason T, Mathus S, McAllister L, McCarthy K, McConnell K, McCormick E, McCurdy D, Stokes PM, McGuire S, McHale I, McMonagle A, McMullen‐Jackson C, Meidan E, Mellins E, Mendoza E, Mercado R, Merritt A, Michalowski L, Miettunen P, Miller M, Milojevic D, Mirizio E, Misajon E, Mitchell M, Modica R, Mohan S, Moore K, Moorthy L, Morgan S, Dewitt EM, Moss C, Moussa T, Mruk V, Murphy A, Muscal E, Nadler R, Nahal B, Nanda K, Nasah N, Nassi L, Nativ S, Natter M, Neely J, Nelson B, Newhall L, Ng L, Nicholas J, Nicolai R, Nigrovic P, Nocton J, Nolan B, Oberle E, Obispo B, O'Brien B, O'Brien T, Okeke O, Oliver M, Olson J, O'Neil K, Onel K, Orandi A, Orlando M, Osei‐Onomah S, Oz R, Pagano E, Paller A, Pan N, Panupattanapong S, Pardeo M, Paredes J, Parsons A, Patel J, Pentakota K, Pepmueller P, Pfeiffer T, Phillippi K, Marafon DP, Phillippi K, Ponder L, Pooni R, Prahalad S, Pratt S, Protopapas S, Puplava B, Quach J, Quinlan‐Waters M, Rabinovich C, Radhakrishna S, Rafko J, Raisian J, Rakestraw A, Ramirez C, Ramsay E, Ramsey S, Randell R, Reed A, Reed A, Reed A, Reid H, Remmel K, Repp A, Reyes A, Richmond A, Riebschleger M, Ringold S, Riordan M, Riskalla M, Ritter M, Rivas‐Chacon R, Robinson A, Rodela E, Rodriquez M, Rojas K, Ronis T, Rosenkranz M, Rosolowski B, Rothermel H, Rothman D, Roth‐Wojcicki E, Rouster – Stevens K, Rubinstein T, Ruth N, Saad N, Sabbagh S, Sacco E, Sadun R, Sandborg C, Sanni A, Santiago L, Sarkissian A, Savani S, Scalzi L, Schanberg L, Scharnhorst S, Schikler K, Schlefman A, Schmeling H, Schmidt K, Schmitt E, Schneider R, Schollaert‐Fitch K, Schulert G, Seay T, Seper C, Shalen J, Sheets R, Shelly A, Shenoi S, Shergill K, Shirley J, Shishov M, Shivers C, Silverman E, Singer N, Sivaraman V, Sletten J, Smith A, Smith C, Smith J, Smith J, Smitherman E, Soep J, Son M, Spence S, Spiegel L, Spitznagle J, Sran R, Srinivasalu H, Stapp H, Steigerwald K, Rakovchik YS, Stern S, Stevens A, Stevens B, Stevenson R, Stewart K, Stingl C, Stokes J, Stoll M, Stringer E, Sule S, Sumner J, Sundel R, Sutter M, Syed R, Syverson G, Szymanski A, Taber S, Tal R, Tambralli A, Taneja A, Tanner T, Tapani S, Tarshish G, Tarvin S, Tate L, Taxter A, Taylor J, Terry M, Tesher M, Thatayatikom A, Thomas B, Tiffany K, Ting T, Tipp A, Toib D, Torok K, Toruner C, Tory H, Toth M, Tse S, Tubwell V, Twilt M, Uriguen S, Valcarcel T, Van Mater H, Vannoy L, Varghese C, Vasquez N, Vazzana K, Vehe R, Veiga K, Velez J, Verbsky J, Vilar G, Volpe N, von Scheven E, Vora S, Wagner J, Wagner‐Weiner L, Wahezi D, Waite H, Walker J, Walters H, Muskardin TW, Waqar L, Waterfield M, Watson M, Watts A, Weiser P, Weiss J, Weiss P, Wershba E, White A, Williams C, Wise A, Woo J, Woolnough L, Wright T, Wu E, Yalcindag A, Yee M, Yen E, Yeung R, Yomogida K, Yu Q, Zapata R, Zartoshti A, Zeft A, Zeft R, Zhang Y, Zhao Y, Zhu A, Zic C. Childhood-Onset Lupus Nephritis in the Childhood Arthritis and Rheumatology Research Alliance Registry: Short-Term Kidney Status and Variation in Care. Arthritis Care Res (Hoboken) 2023; 75:1553-1562. [PMID: 36775844 PMCID: PMC10500561 DOI: 10.1002/acr.25002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 11/23/2021] [Revised: 07/14/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022]
Abstract
OBJECTIVE The goal was to characterize short-term kidney status and describe variation in early care utilization in a multicenter cohort of patients with childhood-onset systemic lupus erythematosus (cSLE) and nephritis. METHODS We analyzed previously collected prospective data from North American patients with cSLE with kidney biopsy-proven nephritis enrolled in the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Registry from March 2017 through December 2019. We determined the proportion of patients with abnormal kidney status at the most recent registry visit and applied generalized linear mixed models to identify associated factors. We also calculated frequency of medication use, both during induction and ever recorded. RESULTS We identified 222 patients with kidney biopsy-proven nephritis, with 64% class III/IV nephritis on initial biopsy. At the most recent registry visit at median (interquartile range) of 17 (8-29) months from initial kidney biopsy, 58 of 106 patients (55%) with available data had abnormal kidney status. This finding was associated with male sex (odds ratio [OR] 3.88, 95% confidence interval [95% CI] 1.21-12.46) and age at cSLE diagnosis (OR 1.23, 95% CI 1.01-1.49). Patients with class IV nephritis were more likely than class III to receive cyclophosphamide and rituximab during induction. There was substantial variation in mycophenolate, cyclophosphamide, and rituximab ever use patterns across rheumatology centers. CONCLUSION In this cohort with predominately class III/IV nephritis, male sex and older age at cSLE diagnosis were associated with abnormal short-term kidney status. We also observed substantial variation in contemporary medication use for pediatric lupus nephritis between pediatric rheumatology centers. Additional studies are needed to better understand the impact of this variation on long-term kidney outcomes.
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Lange M, Kramer S, Voll C, Corbacioglu S. Sturz vom Wickeltisch. Monatsschr Kinderheilkd 2023. [DOI: 10.1007/s00112-023-01712-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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Hahn T, Daymont C, Beukelman T, Groh B, Hays K, Bingham CA, Scalzi L, Abel N, Abulaban K, Adams A, Adams M, Agbayani R, Aiello J, Akoghlanian S, Alejandro C, Allenspach E, Alperin R, Alpizar M, Amarilyo G, Ambler W, Anderson E, Ardoin S, Armendariz S, Baker E, Balboni I, Balevic S, Ballenger L, Ballinger S, Balmuri N, Barbar-Smiley F, Barillas-Arias L, Basiaga M, Baszis K, Becker M, Bell-Brunson H, Beltz E, Benham H, Benseler S, Bernal W, Beukelman T, Bigley T, Binstadt B, Black C, Blakley M, Bohnsack J, Boland J, Boneparth A, Bowman S, Bracaglia C, Brooks E, Brothers M, Brown A, Brunner H, Buckley M, Buckley M, Bukulmez H, Bullock D, Cameron B, Canna S, Cannon L, Carper P, Cartwright V, Cassidy E, Cerracchio L, Chalom E, Chang J, Chang-Hoftman A, Chauhan V, Chira P, Chinn T, Chundru K, Clairman H, Co D, Confair A, Conlon H, Connor R, Cooper A, Cooper J, Cooper S, Correll C, Corvalan R, Costanzo D, Cron R, Curiel-Duran L, Curington T, Curry M, Dalrymple A, Davis A, Davis C, Davis C, Davis T, De Benedetti F, De Ranieri D, Dean J, Dedeoglu F, DeGuzman M, Delnay N, Dempsey V, DeSantis E, Dickson T, Dingle J, Donaldson B, Dorsey E, Dover S, Dowling J, Drew J, Driest K, Du Q, Duarte K, Durkee D, Duverger E, Dvergsten J, Eberhard A, Eckert M, Ede K, Edelheit B, Edens C, Edens C, Edgerly Y, Elder M, Ervin B, Fadrhonc S, Failing C, Fair D, Falcon M, Favier L, Federici S, Feldman B, Fennell J, Ferguson I, Ferguson P, Ferreira B, Ferrucho R, Fields K, Finkel T, Fitzgerald M, Fleming C, Flynn O, Fogel L, Fox E, Fox M, Franco L, Freeman M, Fritz K, Froese S, Fuhlbrigge R, Fuller J, George N, Gerhold K, Gerstbacher D, Gilbert M, Gillispie-Taylor M, Giverc E, Godiwala C, Goh I, Goheer H, Goldsmith D, Gotschlich E, Gotte A, Gottlieb B, Gracia C, Graham T, Grevich S, Griffin T, Griswold J, Grom A, Guevara M, Guittar P, Guzman M, Hager M, Hahn T, Halyabar O, Hammelev E, Hance M, Hanson A, Harel L, Haro S, Harris J, Harry O, Hartigan E, Hausmann J, Hay A, Hayward K, Heiart J, Hekl K, Henderson L, Henrickson M, Hersh A, Hickey K, Hill P, Hillyer S, Hiraki L, Hiskey M, Hobday P, Hoffart C, Holland M, Hollander M, Hong S, Horwitz M, Hsu J, Huber A, Huggins J, Hui-Yuen J, Hung C, Huntington J, Huttenlocher A, Ibarra M, Imundo L, Inman C, Insalaco A, Jackson A, Jackson S, James K, Janow G, Jaquith J, Jared S, Johnson N, Jones J, Jones J, Jones J, Jones K, Jones S, Joshi S, Jung L, Justice C, Justiniano A, Karan N, Kaufman K, Kemp A, Kessler E, Khalsa U, Kienzle B, Kim S, Kimura Y, Kingsbury D, Kitcharoensakkul M, Klausmeier T, Klein K, Klein-Gitelman M, Kompelien B, Kosikowski A, Kovalick L, Kracker J, Kramer S, Kremer C, Lai J, Lam J, Lang B, Lapidus S, Lapin B, Lasky A, Latham D, Lawson E, Laxer R, Lee P, Lee P, Lee T, Lentini L, Lerman M, Levy D, Li S, Lieberman S, Lim L, Lin C, Ling N, Lingis M, Lo M, Lovell D, Lowman D, Luca N, Lvovich S, Madison C, Madison J, Manzoni SM, Malla B, Maller J, Malloy M, Mannion M, Manos C, Marques L, Martyniuk A, Mason T, Mathus S, McAllister L, McCarthy K, McConnell K, McCormick E, McCurdy D, Stokes PMC, McGuire S, McHale I, McMonagle A, McMullen-Jackson C, Meidan E, Mellins E, Mendoza E, Mercado R, Merritt A, Michalowski L, Miettunen P, Miller M, Milojevic D, Mirizio E, Misajon E, Mitchell M, Modica R, Mohan S, Moore K, Moorthy L, Morgan S, Dewitt EM, Moss C, Moussa T, Mruk V, Murphy A, Muscal E, Nadler R, Nahal B, Nanda K, Nasah N, Nassi L, Nativ S, Natter M, Neely J, Nelson B, Newhall L, Ng L, Nicholas J, Nicolai R, Nigrovic P, Nocton J, Nolan B, Oberle E, Obispo B, O’Brien B, O’Brien T, Okeke O, Oliver M, Olson J, O’Neil K, Onel K, Orandi A, Orlando M, Osei-Onomah S, Oz R, Pagano E, Paller A, Pan N, Panupattanapong S, Pardeo M, Paredes J, Parsons A, Patel J, Pentakota K, Pepmueller P, Pfeiffer T, Phillippi K, Marafon DP, Phillippi K, Ponder L, Pooni R, Prahalad S, Pratt S, Protopapas S, Puplava B, Quach J, Quinlan-Waters M, Rabinovich C, Radhakrishna S, Rafko J, Raisian J, Rakestraw A, Ramirez C, Ramsay E, Ramsey S, Randell R, Reed A, Reed A, Reed A, Reid H, Remmel K, Repp A, Reyes A, Richmond A, Riebschleger M, Ringold S, Riordan M, Riskalla M, Ritter M, Rivas-Chacon R, Robinson A, Rodela E, Rodriquez M, Rojas K, Ronis T, Rosenkranz M, Rosolowski B, Rothermel H, Rothman D, Roth-Wojcicki E, Rouster-Stevens K, Rubinstein T, Ruth N, Saad N, Sabbagh S, Sacco E, Sadun R, Sandborg C, Sanni A, Santiago L, Sarkissian A, Savani S, Scalzi L, Schanberg L, Scharnhorst S, Schikler K, Schlefman A, Schmeling H, Schmidt K, Schmitt E, Schneider R, Schollaert-Fitch K, Schulert G, Seay T, Seper C, Shalen J, Sheets R, Shelly A, Shenoi S, Shergill K, Shirley J, Shishov M, Shivers C, Silverman E, Singer N, Sivaraman V, Sletten J, Smith A, Smith C, Smith J, Smith J, Smitherman E, Soep J, Son M, Spence S, Spiegel L, Spitznagle J, Sran R, Srinivasalu H, Stapp H, Steigerwald K, Rakovchik YS, Stern S, Stevens A, Stevens B, Stevenson R, Stewart K, Stingl C, Stokes J, Stoll M, Stringer E, Sule S, Sumner J, Sundel R, Sutter M, Syed R, Syverson G, Szymanski A, Taber S, Tal R, Tambralli A, Taneja A, Tanner T, Tapani S, Tarshish G, Tarvin S, Tate L, Taxter A, Taylor J, Terry M, Tesher M, Thatayatikom A, Thomas B, Tiffany K, Ting T, Tipp A, Toib D, Torok K, Toruner C, Tory H, Toth M, Tse S, Tubwell V, Twilt M, Uriguen S, Valcarcel T, Van Mater H, Vannoy L, Varghese C, Vasquez N, Vazzana K, Vehe R, Veiga K, Velez J, Verbsky J, Vilar G, Volpe N, von Scheven E, Vora S, Wagner J, Wagner-Weiner L, Wahezi D, Waite H, Walker J, Walters H, Muskardin TW, Waqar L, Waterfield M, Watson M, Watts A, Weiser P, Weiss J, Weiss P, Wershba E, White A, Williams C, Wise A, Woo J, Woolnough L, Wright T, Wu E, Yalcindag A, Yee M, Yen E, Yeung R, Yomogida K, Yu Q, Zapata R, Zartoshti A, Zeft A, Zeft R, Zhang Y, Zhao Y, Zhu A, Zic C. Intraarticular steroids as DMARD-sparing agents for juvenile idiopathic arthritis flares: Analysis of the Childhood Arthritis and Rheumatology Research Alliance Registry. Pediatr Rheumatol Online J 2022; 20:107. [PMID: 36434731 PMCID: PMC9701017 DOI: 10.1186/s12969-022-00770-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/08/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Children with juvenile idiopathic arthritis (JIA) who achieve a drug free remission often experience a flare of their disease requiring either intraarticular steroids (IAS) or systemic treatment with disease modifying anti-rheumatic drugs (DMARDs). IAS offer an opportunity to recapture disease control and avoid exposure to side effects from systemic immunosuppression. We examined a cohort of patients treated with IAS after drug free remission and report the probability of restarting systemic treatment within 12 months. METHODS We analyzed a cohort of patients from the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Registry who received IAS for a flare after a period of drug free remission. Historical factors and clinical characteristics and of the patients including data obtained at the time of treatment were analyzed. RESULTS We identified 46 patients who met the inclusion criteria. Of those with follow up data available 49% had restarted systemic treatment 6 months after IAS injection and 70% had restarted systemic treatment at 12 months. The proportion of patients with prior use of a biologic DMARD was the only factor that differed between patients who restarted systemic treatment those who did not, both at 6 months (79% vs 35%, p < 0.01) and 12 months (81% vs 33%, p < 0.05). CONCLUSION While IAS are an option for all patients who flare after drug free remission, it may not prevent the need to restart systemic treatment. Prior use of a biologic DMARD may predict lack of success for IAS. Those who previously received methotrexate only, on the other hand, are excellent candidates for IAS.
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Affiliation(s)
- Timothy Hahn
- Department of Pediatrics, Penn State Children's Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA, 17033-0855, USA.
| | - Carrie Daymont
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
| | - Timothy Beukelman
- grid.265892.20000000106344187Department of Pediatrics, University of Alabama at Birmingham, CPPN G10, 1600 7th Ave South, Birmingham, AL 35233 USA
| | - Brandt Groh
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
| | | | - Catherine April Bingham
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
| | - Lisabeth Scalzi
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
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Spindler K, Callesen L, Andersen R, Pallisgaard N, Kramer S, Schlander S, Rafaelsen S, Boysen A, Jensen L, Jakobsen A, Hansen T. P-174 OPTIMISE: Optimization of treatment selection and follow-up in oligometastatic colorectal cancer – a ctDNA-guided phase II randomized approach with a run-in feasibility part. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Singh SB, Miesel L, Kramer S, Xu L, Li F, Lan J, Lipari P, Polishook JD, Liu G, Liang L, Flattery AM. Nocathiacin, Thiazomycin, and Polar Analogs Are Highly Effective Agents against Toxigenic Clostridioides difficile. J Nat Prod 2022; 85:1141-1146. [PMID: 35380836 DOI: 10.1021/acs.jnatprod.2c00093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Clostridioides difficile is a commensal Gram-positive gut bacterium that causes C. difficile-associated diarrhea. Currently available antibacterial therapeutic treatment options are effective except for the repeated recurrences significantly burdening the health care system and causing mortality. The development of new therapeutic modalities including new effective antibiotics with a low rate of recurrence has been unpredictive and exceedingly challenging, requiring continued profiling of many new classes of antibiotics. Nocathiacins and thiazomycins are a class of thiazolyl peptides exhibiting potent and selective broad-spectrum Gram-positive activity including activity against the anaerobe C. difficile. These compounds showed MIC values of 0.015-0.06 μg/mL against C. difficile with more than 100-200-fold selectivity versus commensurate Gram-negative Bacteroides fragilis. Nocathiacin I and one of its analogs exhibited potent in vivo efficacy in the gold-standard hamster model of C. difficile infection, providing 100% protection in this lethal model at 6.25 mg/kg orally twice daily. The efficacy was corroborated by robust reduction of cecum C. difficile burden and proportionate exposure of the compounds in the cecum contents without any systemic absorption. In this paper, details of the results of in vitro, in vivo, pharmacodynamics, and pharmacokinetic studies have been described.
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Affiliation(s)
- Sheo B Singh
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Lynn Miesel
- Antibacterial Discovery, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Susanne Kramer
- In Vivo Pharmacology, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Libo Xu
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Fangbio Li
- Pharmacokinetics, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Jing Lan
- Pharmacokinetics, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Phillip Lipari
- In Vivo Pharmacology, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Jon D Polishook
- In Vivo Pharmacology, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Gongjie Liu
- In Vivo Pharmacology, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Lianzhu Liang
- In Vivo Pharmacology, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Amy M Flattery
- In Vivo Pharmacology, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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Soulsby WD, Balmuri N, Cooley V, Gerber LM, Lawson E, Goodman S, Onel K, Mehta B, Abel N, Abulaban K, Adams A, Adams M, Agbayani R, Aiello J, Akoghlanian S, Alejandro C, Allenspach E, Alperin R, Alpizar M, Amarilyo G, Ambler W, Anderson E, Ardoin S, Armendariz S, Baker E, Balboni I, Balevic S, Ballenger L, Ballinger S, Balmuri N, Barbar-Smiley F, Barillas-Arias L, Basiaga M, Baszis K, Becker M, Bell-Brunson H, Beltz E, Benham H, Benseler S, Bernal W, Beukelman T, Bigley T, Binstadt B, Black C, Blakley M, Bohnsack J, Boland J, Boneparth A, Bowman S, Bracaglia C, Brooks E, Brothers M, Brown A, Brunner H, Buckley M, Buckley M, Bukulmez H, Bullock D, Cameron B, Canna S, Cannon L, Carper P, Cartwright V, Cassidy E, Cerracchio L, Chalom E, Chang J, Chang-Hoftman A, Chauhan V, Chira P, Chinn T, Chundru K, Clairman H, Co D, Confair A, Conlon H, Connor R, Cooper A, Cooper J, Cooper S, Correll C, Corvalan R, Costanzo D, Cron R, Curiel-Duran L, Curington T, Curry M, Dalrymple A, Davis A, Davis C, Davis C, Davis T, De Benedetti F, De Ranieri D, Dean J, Dedeoglu F, DeGuzman M, Delnay N, Dempsey V, DeSantis E, Dickson T, Dingle J, Donaldson B, Dorsey E, Dover S, Dowling J, Drew J, Driest K, Du Q, Duarte K, Durkee D, Duverger E, Dvergsten J, Eberhard A, Eckert M, Ede K, Edelheit B, Edens C, Edens C, Edgerly Y, Elder M, Ervin B, Fadrhonc S, Failing C, Fair D, Falcon M, Favier L, Federici S, Feldman B, Fennell J, Ferguson I, Ferguson P, Ferreira B, Ferrucho R, Fields K, Finkel T, Fitzgerald M, Fleming C, Flynn O, Fogel L, Fox E, Fox M, Franco L, Freeman M, Fritz K, Froese S, Fuhlbrigge R, Fuller J, George N, Gerhold K, Gerstbacher D, Gilbert M, Gillispie-Taylor M, Giverc E, Godiwala C, Goh I, Goheer H, Goldsmith D, Gotschlich E, Gotte A, Gottlieb B, Gracia C, Graham T, Grevich S, Griffin T, Griswold J, Grom A, Guevara M, Guittar P, Guzman M, Hager M, Hahn T, Halyabar O, Hammelev E, Hance M, Hanson A, Harel L, Haro S, Harris J, Harry O, Hartigan E, Hausmann J, Hay A, Hayward K, Heiart J, Hekl K, Henderson L, Henrickson M, Hersh A, Hickey K, Hill P, Hillyer S, Hiraki L, Hiskey M, Hobday P, Hoffart C, Holland M, Hollander M, Hong S, Horwitz M, Hsu J, Huber A, Huggins J, Hui-Yuen J, Hung C, Huntington J, Huttenlocher A, Ibarra M, Imundo L, Inman C, Insalaco A, Jackson A, Jackson S, James K, Janow G, Jaquith J, Jared S, Johnson N, Jones J, Jones J, Jones J, Jones K, Jones S, Joshi S, Jung L, Justice C, Justiniano A, Karan N, Kaufman K, Kemp A, Kessler E, Khalsa U, Kienzle B, Kim S, Kimura Y, Kingsbury D, Kitcharoensakkul M, Klausmeier T, Klein K, Klein-Gitelman M, Kompelien B, Kosikowski A, Kovalick L, Kracker J, Kramer S, Kremer C, Lai J, Lam J, Lang B, Lapidus S, Lapin B, Lasky A, Latham D, Lawson E, Laxer R, Lee P, Lee P, Lee T, Lentini L, Lerman M, Levy D, Li S, Lieberman S, Lim L, Lin C, Ling N, Lingis M, Lo M, Lovell D, Lowman D, Luca N, Lvovich S, Madison C, Madison J, Manzoni SM, Malla B, Maller J, Malloy M, Mannion M, Manos C, Marques L, Martyniuk A, Mason T, Mathus S, McAllister L, McCarthy K, McConnell K, McCormick E, McCurdy D, Stokes PMC, McGuire S, McHale I, McMonagle A, McMullen-Jackson C, Meidan E, Mellins E, Mendoza E, Mercado R, Merritt A, Michalowski L, Miettunen P, Miller M, Milojevic D, Mirizio E, Misajon E, Mitchell M, Modica R, Mohan S, Moore K, Moorthy L, Morgan S, Dewitt EM, Moss C, Moussa T, Mruk V, Murphy A, Muscal E, Nadler R, Nahal B, Nanda K, Nasah N, Nassi L, Nativ S, Natter M, Neely J, Nelson B, Newhall L, Ng L, Nicholas J, Nicolai R, Nigrovic P, Nocton J, Nolan B, Oberle E, Obispo B, O’Brien B, O’Brien T, Okeke O, Oliver M, Olson J, O’Neil K, Onel K, Orandi A, Orlando M, Osei-Onomah S, Oz R, Pagano E, Paller A, Pan N, Panupattanapong S, Pardeo M, Paredes J, Parsons A, Patel J, Pentakota K, Pepmueller P, Pfeiffer T, Phillippi K, Marafon DP, Phillippi K, Ponder L, Pooni R, Prahalad S, Pratt S, Protopapas S, Puplava B, Quach J, Quinlan-Waters M, Rabinovich C, Radhakrishna S, Rafko J, Raisian J, Rakestraw A, Ramirez C, Ramsay E, Ramsey S, Randell R, Reed A, Reed A, Reed A, Reid H, Remmel K, Repp A, Reyes A, Richmond A, Riebschleger M, Ringold S, Riordan M, Riskalla M, Ritter M, Rivas-Chacon R, Robinson A, Rodela E, Rodriquez M, Rojas K, Ronis T, Rosenkranz M, Rosolowski B, Rothermel H, Rothman D, Roth-Wojcicki E, Rouster-Stevens K, Rubinstein T, Ruth N, Saad N, Sabbagh S, Sacco E, Sadun R, Sandborg C, Sanni A, Santiago L, Sarkissian A, Savani S, Scalzi L, Schanberg L, Scharnhorst S, Schikler K, Schlefman A, Schmeling H, Schmidt K, Schmitt E, Schneider R, Schollaert-Fitch K, Schulert G, Seay T, Seper C, Shalen J, Sheets R, Shelly A, Shenoi S, Shergill K, Shirley J, Shishov M, Shivers C, Silverman E, Singer N, Sivaraman V, Sletten J, Smith A, Smith C, Smith J, Smith J, Smitherman E, Soep J, Son M, Spence S, Spiegel L, Spitznagle J, Sran R, Srinivasalu H, Stapp H, Steigerwald K, Rakovchik YS, Stern S, Stevens A, Stevens B, Stevenson R, Stewart K, Stingl C, Stokes J, Stoll M, Stringer E, Sule S, Sumner J, Sundel R, Sutter M, Syed R, Syverson G, Szymanski A, Taber S, Tal R, Tambralli A, Taneja A, Tanner T, Tapani S, Tarshish G, Tarvin S, Tate L, Taxter A, Taylor J, Terry M, Tesher M, Thatayatikom A, Thomas B, Tiffany K, Ting T, Tipp A, Toib D, Torok K, Toruner C, Tory H, Toth M, Tse S, Tubwell V, Twilt M, Uriguen S, Valcarcel T, Van Mater H, Vannoy L, Varghese C, Vasquez N, Vazzana K, Vehe R, Veiga K, Velez J, Verbsky J, Vilar G, Volpe N, von Scheven E, Vora S, Wagner J, Wagner-Weiner L, Wahezi D, Waite H, Walker J, Walters H, Muskardin TW, Waqar L, Waterfield M, Watson M, Watts A, Weiser P, Weiss J, Weiss P, Wershba E, White A, Williams C, Wise A, Woo J, Woolnough L, Wright T, Wu E, Yalcindag A, Yee M, Yen E, Yeung R, Yomogida K, Yu Q, Zapata R, Zartoshti A, Zeft A, Zeft R, Zhang Y, Zhao Y, Zhu A, Zic C. Social determinants of health influence disease activity and functional disability in Polyarticular Juvenile Idiopathic Arthritis. Pediatr Rheumatol Online J 2022; 20:18. [PMID: 35255941 PMCID: PMC8903717 DOI: 10.1186/s12969-022-00676-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/07/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Social determinants of health (SDH) greatly influence outcomes during the first year of treatment in rheumatoid arthritis, a disease similar to polyarticular juvenile idiopathic arthritis (pJIA). We investigated the correlation of community poverty level and other SDH with the persistence of moderate to severe disease activity and functional disability over the first year of treatment in pJIA patients enrolled in the Childhood Arthritis and Rheumatology Research Alliance Registry. METHODS In this cohort study, unadjusted and adjusted generalized linear mixed effects models analyzed the effect of community poverty and other SDH on disease activity, using the clinical Juvenile Arthritis Disease Activity Score-10, and disability, using the Child Health Assessment Questionnaire, measured at baseline, 6, and 12 months. RESULTS One thousand six hundred eighty-four patients were identified. High community poverty (≥20% living below the federal poverty level) was associated with increased odds of functional disability (OR 1.82, 95% CI 1.28-2.60) but was not statistically significant after adjustment (aOR 1.23, 95% CI 0.81-1.86) and was not associated with increased disease activity. Non-white race/ethnicity was associated with higher disease activity (aOR 2.48, 95% CI: 1.41-4.36). Lower self-reported household income was associated with higher disease activity and persistent functional disability. Public insurance (aOR 1.56, 95% CI 1.06-2.29) and low family education (aOR 1.89, 95% CI 1.14-3.12) was associated with persistent functional disability. CONCLUSION High community poverty level was associated with persistent functional disability in unadjusted analysis but not with persistent moderate to high disease activity. Race/ethnicity and other SDH were associated with persistent disease activity and functional disability.
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Affiliation(s)
- William Daniel Soulsby
- University of California, San Francisco, 550 16th Street, 4th Floor, Box #0632, San Francisco, CA, 94158, USA.
| | - Nayimisha Balmuri
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Victoria Cooley
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Linda M. Gerber
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Erica Lawson
- grid.266102.10000 0001 2297 6811University of California, San Francisco, 550 16th Street, 4th Floor, Box #0632, San Francisco, CA 94158 USA
| | - Susan Goodman
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Karen Onel
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Bella Mehta
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
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Achiam MP, Nordsmark M, Ladekarl M, Olsen A, Loft A, Garbyal RS, Larsen MH, Ainsworth AP, Kristensen TS, Dikinis S, Kjær DW, Bæksgaard L, Siemsen M, Nielsen MB, Schlander S, Kramer S, Katballe N, Kruhlikava I, Tabaksblat E, Fisker RV, Mortensen PB, Holtved E, Eckardt J, Detlefsen S, Naujokaite G, Lütken CD. Clinically decisive (dis)agreement in multidisciplinary team assessment of esophageal squamous cell carcinoma; a prospective, national, multicenter study. Acta Oncol 2021; 60:1091-1099. [PMID: 34313177 DOI: 10.1080/0284186x.2021.1937308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Decisions regarding tumor staging, operability, resectability, and treatment strategy in patients with esophageal cancer are made at multidisciplinary team (MDT) conferences. We aimed to assess interobserver agreement from four national MDT conferences and whether this would have a clinical impact. METHODS A total of 20 patients with esophageal cancer were included across all four upper gastrointestinal (GI) cancer centers. Fully anonymized patient data were distributed among the MDT conferences which decided on TNM category, resectability, operability, curability, and treatment strategy blinded to each other's decisions. The interobserver agreement was expressed as both the raw observer agreement and with Krippendorff's α values. Finally, a case-by-case evaluation was performed to determine if disagreement would have had a clinical impact. RESULTS A total of 80 MDT evaluations were available for analysis. A moderate to near-perfect observer agreement of 79.2%, 55.8%, and 82.5% for TNM category was observed, respectively. Substantial agreement for resectability and moderate agreement for curability were found. However, an only fair agreement was observed for the operability category. The treatment strategies had a slight agreement which corresponded to disagreement having a clinical impact in 12 patients. CONCLUSIONS Esophageal cancer MDT conferences had an acceptable interobserver agreement on resectability and TM categories; however, the operability assessment had a high level of disagreement. Consequently, the agreement on treatment strategy was reduced with a potential clinical impact. In future MDT conferences, emphasis should be on prioritizing the relevant information being readily available (operability, T & M categories) to minimize the risk of disagreement in the assessments and treatment strategies, and thus, delayed or suboptimal treatment.
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Affiliation(s)
- Michael Patrick Achiam
- Department of Surgical Gastroenterology, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
| | - M. Nordsmark
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - M. Ladekarl
- Department of Oncology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - A. Olsen
- Department of Surgical Gastroenterology, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
| | - A. Loft
- Department of Clinical Physiology, Nuclear Medicine and PET, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
| | - Rajendra Singh Garbyal
- Department of Pathology, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
| | - M. H. Larsen
- Department of Surgical Gastroenterology, Odense University Hospital, Odense, Denmark
| | - A. P. Ainsworth
- Department of Surgical Gastroenterology, Odense University Hospital, Odense, Denmark
| | - T. S. Kristensen
- Department of Radiology, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
| | - S. Dikinis
- Department of Surgical Gastroenterology, Aalborg University Hospital, Aalborg, Denmark
| | - D. W. Kjær
- Department of Surgery, Esophagogastric Section, Aarhus University Hospital, Aarhus, Denmark
| | - L. Bæksgaard
- Department of Oncology, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
| | - M. Siemsen
- Department of Cardiothoracic Surgery, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
| | - M. B. Nielsen
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - S. Schlander
- Department of Radiology, Aarhus University Hospital, Aarhus, Denmark
| | - S. Kramer
- Department of Nuclear Medicine and PET-Centre, Aarhus University Hospital, Aarhus, Denmark
| | - N. Katballe
- Department of Heart, Lung, and Vascular Surgery, Aarhus University Hospital, Aarhus, Denmark
| | - I. Kruhlikava
- Department of Surgery, Esophagogastric Section, Aarhus University Hospital, Aarhus, Denmark
| | - E. Tabaksblat
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - R. V. Fisker
- Department of Nuclear Medicine, Aalborg University Hospital, Aalborg, Denmark
| | - P. B. Mortensen
- Department of Surgical Gastroenterology, Aalborg University Hospital, Aalborg, Denmark
| | - E. Holtved
- Department of Oncology, Odense University Hospital, Odense, Denmark
| | - J. Eckardt
- Department of Cardiac, Thoracic, and Vascular Surgery, Odense University Hospital, Odense, Denmark
| | - S. Detlefsen
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - G. Naujokaite
- Department of Nuclear Medicine, Aalborg University Hospital, Aalborg, Denmark
- Department of Radiology, Aalborg University Hospital, Aalborg, Denmark
| | - C. D. Lütken
- Department of Surgical Gastroenterology, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
- Department of Radiology, Aalborg University Hospital, Aalborg, Denmark
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Castañeda Londoño PA, Banholzer N, Bannermann B, Kramer S. Is mRNA decapping by ApaH like phosphatases present in eukaryotes beyond the Kinetoplastida? BMC Ecol Evol 2021; 21:131. [PMID: 34162332 PMCID: PMC8220851 DOI: 10.1186/s12862-021-01858-x] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/10/2021] [Indexed: 11/20/2022] Open
Abstract
Background ApaH like phosphatases (ALPHs) originate from the bacterial ApaH protein and have been identified in all eukaryotic super-groups. Only two of these proteins have been functionally characterised. We have shown that the ApaH like phosphatase ALPH1 from the Kinetoplastid Trypanosoma brucei is the mRNA decapping enzyme of the parasite. In eukaryotes, Dcp2 is the major mRNA decapping enzyme and mRNA decapping by ALPHs is unprecedented, but the bacterial ApaH protein was recently found decapping non-conventional caps of bacterial mRNAs. These findings prompted us to explore whether mRNA decapping by ALPHs is restricted to Kinetoplastida or could be more widespread among eukaryotes. Results We screened 827 eukaryotic proteomes with a newly developed Python-based algorithm for the presence of ALPHs and used the data to characterize the phylogenetic distribution, conserved features, additional domains and predicted intracellular localisation of this protein family. For most organisms, we found ALPH proteins to be either absent (495/827 organisms) or to have non-cytoplasmic localisation predictions (73% of all ALPHs), excluding a function in mRNA decapping. Although, non-cytoplasmic ALPH proteins had in vitro mRNA decapping activity. Only 71 non-Kinetoplastida have ALPH proteins with predicted cytoplasmic localisations. However, in contrast to Kinetoplastida, these organisms also possess a homologue of Dcp2 and in contrast to ALPH1 of Kinetoplastida, these ALPH proteins are very short and consist of the catalytic domain only. Conclusions ALPH was present in the last common ancestor of eukaryotes, but most eukaryotes have either lost the enzyme, or use it exclusively outside the cytoplasm. The acceptance of mRNA as a substrate indicates that ALPHs, like bacterial ApaH, have a wide substrate range: the need to protect mRNAs from unregulated degradation is one possible explanation for the selection against the presence of cytoplasmic ALPH proteins in most eukaryotes. Kinetoplastida succeeded to exploit ALPH as their only or major mRNA decapping enzyme. 71 eukaryotic organisms outside the Kinetoplastid lineage have short ALPH proteins with cytoplasmic localisation predictions: whether these proteins are used as decapping enzymes in addition to Dcp2 or else have adapted to not accept mRNAs as a substrate, remains to be explored. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01858-x.
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Affiliation(s)
| | - Nicole Banholzer
- Zell- Und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
| | | | - Susanne Kramer
- Zell- Und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany.
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Aarts K, De Witte E, Kramer S, Iannone D, Destrebecq F, Di Luca M. European brain research area: The operational level. Eur Psychiatry 2021. [PMCID: PMC9471873 DOI: 10.1192/j.eurpsy.2021.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Brain research in Europe is a rapidly evolving field, and increasingly at the forefront of science. Although considerable amounts of knowledge and innovative approaches have been generated, the translation into new health interventions is hindered by excessive fragmentation. Effective and efficient collaboration and cooperation among the various initiatives are often identified as a key success factor to achieve brain research full impact. EBRA fully responds to these needs by bringing together the various stakeholders and major brain research initiatives, at European level and beyond. EBRA creates the conditions for real and effective cross fertilisation, dialogue, building consensus and exploiting research potential. On the operational level, EBRA facilitates the emergence of research projects in specific areas in active clusters. A cluster is understood as a research community that can be directed towards basic research, clinical research and/or methodological approaches under a common topic and disease area within brain research. EBRA support clusters to: 1. Consolidate or expand further the research community expand their community, 2. Engage with policy makers and other relevant stakeholders, 3. Build consensus on various issues (research priorities, research roadmap, data sharing, etc.), 4. Promote links with existing research infrastructures, 5. Increase the visibility of the research community through communication and dissemination activities, 6. Coordinate the development of position/consensus papers, white papers, guidelines, meeting reports and/or other cluster outcomes. EBRA currently has 6 existing clusters: EPICLUSTER, Prevention of Severe Mental Disorders (PSMD)-cluster, TRISOMY21-cluster, BRAINFOOD-cluster., PREMOS-cluster and ECIB-cluster.
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Di Luca M, De Witte E, Aarts K, Kramer S, Iannone D, Destrebecq F. European brain research area: The strategic level. Eur Psychiatry 2021. [PMCID: PMC9471743 DOI: 10.1192/j.eurpsy.2021.171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Brain research in Europe is a rapidly evolving field, and increasingly at the forefront of science. Although considerable amounts of knowledge and innovative approaches have been generated, the translation into new health interventions is hindered by excessive fragmentation. Effective and efficient collaboration and cooperation among the various initiatives are often identified as a key success factor to achieve brain research full impact. EBRA fully responds to these needs by bringing together the various stakeholders and major brain research initiatives, at European level and beyond. EBRA creates the conditions for real and effective cross fertilisation, dialogue, building consensus and exploiting research potential. At the strategic level, EBRA acts by fostering alignment and better coordination of research strategies across European and global brain initiatives. Therefore, an overview of the scale and scope of brain research activities funded in the EU framework programme and the funding initiatives of JPND, NEURON and HBP has been created. The results of the mapping exercise then underpinned the development of a Shared European Brain Research Agenda (SEBRA). The SEBRA focuses on research opportunities and research gaps to be addressed in the field, and priorities for action in the short- and long-term. It integrates pre-existing documents as well as expert (i.e., researchers, neurologists/psychiatrists, patient representatives) input that has been collected through surveys and in a dedicated expert workshop. The SEBRA will be used to provide recommendations on future areas for excellent, innovative, and translational research comprising those for maximized cooperation, reduced overlap, and fragmentation.
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Kramer S, Meyer-Natus E, Stigloher C, Thoma H, Schnaufer A, Engstler M. Parallel monitoring of RNA abundance, localization and compactness with correlative single molecule FISH on LR White embedded samples. Nucleic Acids Res 2021; 49:e14. [PMID: 33275141 PMCID: PMC7897490 DOI: 10.1093/nar/gkaa1142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/16/2020] [Accepted: 11/17/2020] [Indexed: 01/19/2023] Open
Abstract
Single mRNA molecules are frequently detected by single molecule fluorescence in situ hybridization (smFISH) using branched DNA technology. While providing strong and background-reduced signals, the method is inefficient in detecting mRNAs within dense structures, in monitoring mRNA compactness and in quantifying abundant mRNAs. To overcome these limitations, we have hybridized slices of high pressure frozen, freeze-substituted and LR White embedded cells (LR White smFISH). mRNA detection is physically restricted to the surface of the resin. This enables single molecule detection of RNAs with accuracy comparable to RNA sequencing, irrespective of their abundance, while at the same time providing spatial information on RNA localization that can be complemented with immunofluorescence and electron microscopy, as well as array tomography. Moreover, LR White embedding restricts the number of available probe pair recognition sites for each mRNA to a small subset. As a consequence, differences in signal intensities between RNA populations reflect differences in RNA structures, and we show that the method can be employed to determine mRNA compactness. We apply the method to answer some outstanding questions related to trans-splicing, RNA granules and mitochondrial RNA editing in single-cellular trypanosomes and we show an example of differential gene expression in the metazoan Caenorhabditis elegans.
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Affiliation(s)
- Susanne Kramer
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
| | | | - Christian Stigloher
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany.,Imaging Core Facility, Biozentrum, Universität Würzburg, Würzburg, Germany
| | - Hanna Thoma
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
| | - Achim Schnaufer
- Institute for Immunology & Infection Research, University of Edinburgh, Edinburgh, UK
| | - Markus Engstler
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
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Nyeng TB, Møller DS, Farr K, Kramer S, Khalil AA, Grau C, Hoffmann L. A comparison of two methods for segmentation of functional volumes in radiotherapy planning of lung cancer patients. Acta Oncol 2021; 60:353-360. [PMID: 33522851 DOI: 10.1080/0284186x.2021.1877811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
BACKGROUND In radiotherapy (RT) of lung cancer, dose to functional lung (FL) volumes segmented with two different methods (perfusion SPECT (Q-SPECT) and 4D-CT (4D) ventilation (V)) have been shown to correlate with the incidence of radiation pneumonitis (RP). This study aims to compare the FL volumes identified by both methods. MATERIAL AND METHODS Thirty lung cancer patients had a 4D and Q-SPECT prior to treatment. Seventeen of these patients also had a ventilation SPECT (V-SPECT). FL sub-volumes were segmented automatically, using cut-off values. The volumes were compared in terms of overlap fraction (OF) relative to the minimal volume, and intersection fraction (IF) of the FL volume relative to the total lung volume (VLung). RESULTS Cut-off values suggested in literature for Q-SPECT and 4D-V resulted in volumes differing in size by a median 18% [6%;31%], and a median OF and IF of 0.48 [0.23;0.70] and 0.09 [0.02;0.25], respectively. Segmenting volumes of comparable size of about 1/3 of VLung (FL-m(1/3), m = method) resulted in a median OF and IF of 0.43 [0.23;0.58] and 0.12 [0.06;0.19], respectively. Twenty-five patients (83%) had a reasonable overlap between FL-Q(1/3) and FL-4D-V(1/3) volumes, with OF values above 0.33. IF increased significantly (p = .036) compared to using fixed cut-off values. Similarly, volumes of comparable size of about 1/3 VLung were produced for V-SPECT, and FL-Q(1/3), FL-V(1/3), and FL-4D-V(1/3) were compared. The overlaps and intersections of FL-V(1/3) with FL-Q(1/3) volumes were significantly (p<.001) larger than the corresponding overlaps and intersections of FL-Q(1/3) with FL-4D(1/3) and FL-V(1/3) with FL-4D(1/3). CONCLUSION The Q-SPECT and 4D-V methods do not segment entirely the same FL volumes. A reasonable overlap of the volumes along with the findings of other studies that both correlate to RP incidence, suggests that a combination of both volumes, e.g. using the IF, may be useful in RT treatment planning.
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Affiliation(s)
- T. B. Nyeng
- Department of Oncology, Section for Medical Physics, Aarhus University Hospital, Aarhus, Denmark
| | - D. S. Møller
- Department of Oncology, Section for Medical Physics, Aarhus University Hospital, Aarhus, Denmark
| | - K. Farr
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - S. Kramer
- Department of Nuclear Medicine & PET-Centre, Aarhus University Hospital, Aarhus, Denmark
| | - A. A. Khalil
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - C. Grau
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - L. Hoffmann
- Department of Oncology, Section for Medical Physics, Aarhus University Hospital, Aarhus, Denmark
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Stöver T, Dazert S, Plontke SK, Kramer S, Ambrosch P, Arens C, Betz C, Beutner D, Bohr C, Bruchhage KL, Canis M, Dietz A, Guntinas-Lichius O, Hagen R, Hosemann W, Iro H, Klussmann JP, Knopf A, Lang S, Leinung M, Lenarz T, Löwenheim H, Matthias C, Mlynski R, Olze H, Park J, Plinkert P, Radeloff A, Rotter N, Rudack C, Bozzato A, Schipper J, Schrader M, Schuler PJ, Strieth S, Stuck BA, Volkenstein S, Westhofen M, Wolf G, Wollenberg B, Zahnert T, Zenk J, Hoffmann TK. [Effects of the SARS-CoV‑2 pandemic on the otolaryngology university hospitals in the field of research, student teaching and specialist training]. HNO 2021; 69:633-641. [PMID: 33502578 PMCID: PMC7839289 DOI: 10.1007/s00106-021-01001-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 11/26/2022]
Abstract
Hintergrund Ab Frühjahr 2020 kam es zur weltweiten Verbreitung von SARS-CoV‑2 mit der heute als erste Welle der Pandemie bezeichneten Phase ab März 2020. Diese resultierte an vielen Kliniken in Umstrukturierungen und Ressourcenverschiebungen. Ziel unserer Arbeit war die Erfassung der Auswirkungen der Pandemie auf die universitäre Hals-Nasen-Ohren(HNO)-Heilkunde für die Forschung, Lehre und Weiterbildung. Material und Methoden Die Direktorinnen und Direktoren der 39 Universitäts-HNO-Kliniken in Deutschland wurden mithilfe einer strukturierten Online-Befragung zu den Auswirkungen der Pandemie im Zeitraum von März bis April 2020 auf die Forschung, Lehre und die Weiterbildung befragt. Ergebnisse Alle 39 Direktorinnen und Direktoren beteiligten sich an der Umfrage. Hiervon gaben 74,4 % (29/39) an, dass es zu einer Verschlechterung ihrer Forschungstätigkeit infolge der Pandemie gekommen sei. Von 61,5 % (24/39) wurde berichtet, dass pandemiebezogene Forschungsaspekte aufgegriffen wurden. Von allen Kliniken wurde eine Einschränkung der Präsenzlehre berichtet und 97,5 % (38/39) führten neue digitale Lehrformate ein. Im Beobachtungszeitraum sahen 74,4 % der Klinikdirektoren die Weiterbildung der Assistenten nicht gefährdet. Schlussfolgerung Die Ergebnisse geben einen Einblick in die heterogenen Auswirkungen der Pandemie. Die kurzfristige Bearbeitung pandemiebezogener Forschungsthemen und die Einführung innovativer digitaler Konzepte für die studentische Lehre belegt eindrücklich das große innovative Potenzial und die schnelle Reaktionsfähigkeit der HNO-Universitätskliniken, um auch während der Pandemie ihre Aufgaben in der Forschung, Lehre und Weiterbildung bestmöglich zu erfüllen.
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Affiliation(s)
- T Stöver
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Frankfurt a.M., Frankfurt a.M., Deutschland.
| | - S Dazert
- Klinik für Hals-Nasen-Ohrenheilkunde, Ruhr-Universität-Bochum, St. Elisabeth-Hospital, Bochum, Deutschland
| | - S K Plontke
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Halle/S., Halle/S., Deutschland
| | - S Kramer
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Frankfurt a.M., Frankfurt a.M., Deutschland
| | - P Ambrosch
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Kiel, Kiel, Deutschland
| | - C Arens
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Magdeburg, Magdeburg, Deutschland
| | - C Betz
- Klinik und Poliklinik für Hals‑, Nasen- und Ohrenheilkunde, Universitätsklinikum Hamburg Eppendorf, Hamburg, Deutschland
| | - D Beutner
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Göttingen, Göttingen, Deutschland
| | - C Bohr
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Regensburg, Regensburg, Deutschland
| | - K-L Bruchhage
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Lübeck, Lübeck, Deutschland
| | - M Canis
- Klinik und Poliklinik für Hals-Nasen-Ohrenheilkunde, Klinikum der Universität München, LMU München, München, Deutschland
| | - A Dietz
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Leipzig, Leipzig, Deutschland
| | - O Guntinas-Lichius
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Jena, Jena, Deutschland
| | - R Hagen
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Würzburg, Würzburg, Deutschland
| | - W Hosemann
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Greifswald, Greifswald, Deutschland
- Helios Hanseklinikum Stralsund, Stralsund, Deutschland
| | - H Iro
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Erlangen, Erlangen, Deutschland
| | - J P Klussmann
- Klinik für Hals-Nasen-Ohrenheilkunde, Uniklinik Köln und Medizinische Fakultät, Universität zu Köln, Köln, Deutschland
| | - A Knopf
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Freiburg, Freiburg, Deutschland
| | - S Lang
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Essen, Essen, Deutschland
| | - M Leinung
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Frankfurt a.M., Frankfurt a.M., Deutschland
| | - T Lenarz
- Klinik für Hals-Nasen-Ohrenheilkunde, Medizinische Hochschule Hannover, Hannover, Deutschland
| | - H Löwenheim
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Tübingen, Tübingen, Deutschland
| | - C Matthias
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Mainz, Mainz, Deutschland
| | - R Mlynski
- Klinik und Poliklinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie "Otto Körner", Universitätsmedizin Rostock, Rostock, Deutschland
| | - H Olze
- Klinik für Hals-Nasen-Ohrenheilkunde, Charité - Universitätsmedizin Berlin, Berlin, Deutschland
| | - J Park
- Klinik für Hals-Nasen-Ohrenheilkunde, Universität Witten/Herdecke, Witten/Herdecke, Deutschland
| | - P Plinkert
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - A Radeloff
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Oldenburg, Oldenburg, Deutschland
| | - N Rotter
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Mannheim, Mannheim, Deutschland
| | - C Rudack
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Münster, Münster, Deutschland
| | - A Bozzato
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum des Saarlandes, Saarlandes, Deutschland
| | - J Schipper
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Düsseldorf, Düsseldorf, Deutschland
| | - M Schrader
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Minden, Minden, Deutschland
| | - P J Schuler
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Ulm, Ulm, Deutschland
| | - S Strieth
- Klinik und Poliklinik für Hals-Nasen-Ohren-Heilkunde, Universitätsklinikum Bonn, Bonn, Deutschland
| | - B A Stuck
- Klinik für Hals‑, Nasen- und Ohrenheilkunde, Universitätsklinikum Gießen und Marburg GmbH, Standort Marburg, Philipps-Universität Marburg, Marburg, Deutschland
| | - S Volkenstein
- Klinik für Hals-Nasen-Ohrenheilkunde, Ruhr-Universität-Bochum, St. Elisabeth-Hospital, Bochum, Deutschland
| | - M Westhofen
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Aachen, Aachen, Deutschland
| | - G Wolf
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen, Justus-Liebig-Universität, Gießen, Deutschland
- Evangelisches Krankenhaus Düsseldorf, Düsseldorf, Deutschland
| | - B Wollenberg
- Klinik für Hals-Nasen-Ohrenheilkunde, Klinikum rechts der Isar der Technischen Universität München, München, Deutschland
| | - T Zahnert
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Dresden, Dresden, Deutschland
| | - J Zenk
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Augsburg, Augsburg, Deutschland
| | - T K Hoffmann
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Ulm, Ulm, Deutschland
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Stöver T, Dazert S, Hoffmann TK, Plontke SK, Ambrosch P, Arens C, Betz C, Beutner D, Bohr C, Bruchhage KL, Canis M, Dietz A, Guntinas-Lichius O, Hagen R, Hosemann W, Iro H, Klussmann JP, Knopf A, Kramer S, Lang S, Leinung M, Lenarz T, Löwenheim H, Matthias C, Mlynski R, Olze H, Park J, Plinkert P, Radeloff A, Rotter N, Rudack C, Bozzato A, Schipper J, Schrader M, Strieth S, Stuck BA, Volkenstein S, Westhofen M, Wolf G, Wollenberg B, Zahnert T, Zenk J. [Effects of the SARS-CoV-2 pandemic on the otorhinolaryngology university hospitals in the field of medical care]. Laryngorhinootologie 2020; 99:694-706. [PMID: 32767296 PMCID: PMC7645814 DOI: 10.1055/a-1232-4911] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Since December 2019, the SARS-CoV-2 virus has been rapidly spreading worldwide. In Germany, an exponential increase in the number of infections was registered at the beginning of March 2020 and led to a call of the Ministry of Health to create more capacity for intensive medical treatment in hospitals. The aim of the present study was to determine the effects of the SARS-CoV-2 pandemic on Oto-Rhino-Laryngology (ORL) university hospitals regarding patient care. MATERIALS AND METHODS An online survey was sent out to all chairmen of the 39 ORL university hospitals in Germany. The answers to the questions referred to the defined period from March 15th to April 15th 2020 and were carried out using the online survey tool "SurveyMonkey". 87 questions focused on general information, health care, and structural effects in the respective institution. RESULTS All chairmen of the 39 university hospitals in Germany participated in the survey. The collected data prove the considerable impact on organizational, structural and medical aspects of patient care. For example, the surveyed clinics reported a decrease in outpatient cases by 73.8 % to 26.2 ± 14.2 % and in surgical treatments by 65.9 % to 34.1 ± 13.9 %. In contrast, emergency treatment remained unchanged or even increased in 80 % of the facilities and surgical treatment of emergency patients remained unchanged or even increased in more than 90 %. Emergency outpatient and surgical treatment of patients was provided throughout the pandemic in all facilities. In total, about 35 000 outpatients and about 12 000 surgical cases were postponed. As a result of the acute structural changes, the potential danger of falling below current treatment standards was seen in individual areas of patient care. DISCUSSION The assessment of the impact of the SARS-CoV-2 pandemic is heterogeneous. The majority of the chairmen are critically aware of the risk of falling below current medical treatment standards or guidelines. In the phase of an exponential increase in the number of infections, significant changes in treatment processes had to be accepted for understandable reasons. However, with the currently significantly reduced number of infections, falling below treatment standards and guidelines should not be allowed to remain constant and tolerated. SUMMARY This study shows a differentiated picture with regard to the effects of the SARS-CoV-2 pandemic on outpatient, inpatient and operative patient care at the ORL university hospitals in Germany and illustrates the importance of these institutions for ensuring patient care during this critical phase.
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Affiliation(s)
- T Stöver
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Frankfurt a. M
| | - S Dazert
- Klinik für Hals-Nasen-Ohrenheilkunde, Ruhr-Universität-Bochum, St. Elisabeth-Hospital
| | - T K Hoffmann
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Ulm
| | - S K Plontke
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Halle/S
| | - P Ambrosch
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Kiel
| | - C Arens
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Magdeburg
| | - C Betz
- Klinik und Poliklinik für Hals-, Nasen- und Ohrenheilkunde, Universitätsklinikum Hamburg Eppendorf
| | - D Beutner
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Göttingen
| | - C Bohr
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Regensburg
| | - K-L Bruchhage
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Lübeck
| | - M Canis
- Klinik und Poliklinik für Hals-Nasen-Ohrenheilkunde, Klinikum der Universität München, LMU München
| | - A Dietz
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Leipzig
| | | | - R Hagen
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Würzburg
| | - W Hosemann
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Greifswald
| | - H Iro
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Erlangen
| | - J-P Klussmann
- Klinik für Hals-Nasen-Ohrenheilkunde, Uniklinik Köln und Medizinische Fakultät, Universität zu Köln
| | - A Knopf
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Freiburg
| | - S Kramer
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Frankfurt a. M
| | - S Lang
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Essen
| | - M Leinung
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Frankfurt a. M
| | - T Lenarz
- Klinik für Hals-Nasen-Ohrenheilkunde, Medizinische Hochschule Hannover
| | - H Löwenheim
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Tübingen
| | - C Matthias
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Mainz
| | - R Mlynski
- Klinik und Poliklinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie "Otto Körner", Universitätsmedizin Rostock
| | - H Olze
- Klinik für Hals-Nasen-Ohrenheilkunde, Charité Berlin
| | - J Park
- Klinik für Hals-Nasen-Ohrenheilkunde, Universität Witten/Herdecke
| | - P Plinkert
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Heidelberg
| | - A Radeloff
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Oldenburg
| | - N Rotter
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Mannheim
| | - C Rudack
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Münster
| | - A Bozzato
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum des Saarlandes
| | - J Schipper
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Düsseldorf
| | - M Schrader
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Minden
| | - S Strieth
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Bonn
| | - B A Stuck
- Klinik für Hals-, Nasen- und Ohrenheilkunde, Universitätsklinikum Gießen und Marburg GmbH, Standort Marburg, Philipps-Universität Marburg
| | - S Volkenstein
- Klinik für Hals-Nasen-Ohrenheilkunde, Ruhr-Universität-Bochum, St. Elisabeth-Hospital
| | - M Westhofen
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Aachen
| | - G Wolf
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen, Justus-Liebig-Universität, Gießen
| | - B Wollenberg
- Klinik für Hals-Nasen-Ohrenheilkunde, Klinikum rechts der Isar der Technischen Universität München
| | - T Zahnert
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Dresden
| | - J Zenk
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinikum Augsburg
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Goos C, Dejung M, Wehman AM, M-Natus E, Schmidt J, Sunter J, Engstler M, Butter F, Kramer S. Trypanosomes can initiate nuclear export co-transcriptionally. Nucleic Acids Res 2019; 47:266-282. [PMID: 30418648 PMCID: PMC6326799 DOI: 10.1093/nar/gky1136] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 06/18/2018] [Accepted: 10/25/2018] [Indexed: 02/03/2023] Open
Abstract
The nuclear envelope serves as important messenger RNA (mRNA) surveillance system. In yeast and human, several control systems act in parallel to prevent nuclear export of unprocessed mRNAs. Trypanosomes lack homologues to most of the involved proteins and their nuclear mRNA metabolism is non-conventional exemplified by polycistronic transcription and mRNA processing by trans-splicing. We here visualized nuclear export in trypanosomes by intra- and intermolecular multi-colour single molecule FISH. We found that, in striking contrast to other eukaryotes, the initiation of nuclear export requires neither the completion of transcription nor splicing. Nevertheless, we show that unspliced mRNAs are mostly prevented from reaching the nucleus-distant cytoplasm and instead accumulate at the nuclear periphery in cytoplasmic nuclear periphery granules (NPGs). Further characterization of NPGs by electron microscopy and proteomics revealed that the granules are located at the cytoplasmic site of the nuclear pores and contain most cytoplasmic RNA-binding proteins but none of the major translation initiation factors, consistent with a function in preventing faulty mRNAs from reaching translation. Our data indicate that trypanosomes regulate the completion of nuclear export, rather than the initiation. Nuclear export control remains poorly understood, in any organism, and the described way of control may not be restricted to trypanosomes.
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Affiliation(s)
- Carina Goos
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Mario Dejung
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Ann M Wehman
- Rudolf Virchow Center, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Elisabeth M-Natus
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Johannes Schmidt
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jack Sunter
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Susanne Kramer
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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17
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Kramer S, McLennan AG. The complex enzymology of mRNA decapping: Enzymes of four classes cleave pyrophosphate bonds. Wiley Interdiscip Rev RNA 2019; 10:e1511. [PMID: 30345629 DOI: 10.1002/wrna.1511] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 12/16/2022]
Abstract
The 5' ends of most RNAs are chemically modified to enable protection from nucleases. In bacteria, this is often achieved by keeping the triphosphate terminus originating from transcriptional initiation, while most eukaryotic mRNAs and small nuclear RNAs have a 5'→5' linked N7 -methyl guanosine (m7 G) cap added. Several other chemical modifications have been described at RNA 5' ends. Common to all modifications is the presence of at least one pyrophosphate bond. To enable RNA turnover, these chemical modifications at the RNA 5' end need to be reversible. Dependent on the direction of the RNA decay pathway (5'→3' or 3'→5'), some enzymes cleave the 5'→5' cap linkage of intact RNAs to initiate decay, while others act as scavengers and hydrolyse the cap element of the remnants of the 3'→5' decay pathway. In eukaryotes, there is also a cap quality control pathway. Most enzymes involved in the cleavage of the RNA 5' ends are pyrophosphohydrolases, with only a few having (additional) 5' triphosphonucleotide hydrolase activities. Despite the identity of their enzyme activities, the enzymes belong to four different enzyme classes. Nudix hydrolases decap intact RNAs as part of the 5'→3' decay pathway, DXO family members mainly degrade faulty RNAs, members of the histidine triad (HIT) family are scavenger proteins, while an ApaH-like phosphatase is the major mRNA decay enzyme of trypanosomes, whose RNAs have a unique cap structure. Many novel cap structures and decapping enzymes have only recently been discovered, indicating that we are only beginning to understand the mechanisms of RNA decapping. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
- Susanne Kramer
- Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Alexander G McLennan
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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Hava D, Tan L, Johnson P, Curran A, Perry J, Kramer S, Kane K, Bedwell P, Henderson D, Layton G, Singh K, Connor L, Singh D, Roach J. A PHASE 1/1B STUDY OF AN INHALED FORMULATION OF ITRACONAZOLE IN HEALTHY VOLUNTEERS AND ASTHMATICS. Ann Allergy Asthma Immunol 2018. [DOI: 10.1016/j.anai.2018.09.190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Exner T, Dokler J, Bachler D, Farcal L, Evelo C, Willighagen E, Jennen D, Jabocs M, Doganis P, Sarimveis H, Lynch I, Gkoutos G, Kramer S, Notredame C, Spjuth O, Jennings P, Dudgeon T, Bois F, Hardy B. OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in risk assessment. Toxicol Lett 2018. [DOI: 10.1016/j.toxlet.2018.06.617] [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: 10/28/2022]
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20
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Stratmann C, Baeumler P, Kramer S, Fleckenstein J, Irnich D. Acupuncture for Acute Herpes Zoster – Secondary Outcomes of a Randomized Controlled Non-inferiority Trial. J Acupunct Meridian Stud 2018. [DOI: 10.1016/j.jams.2018.08.181] [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: 10/28/2022] Open
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21
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Karvounis A, Baeumler P, Kramer S, Kolb F, Kutz D, Irnich D. Validation of the High-Resolution Electrical DermaScan (Hi-REDS) as a Tool for Measuring Electrical Skin Resistance over Acupuncture Points. J Acupunct Meridian Stud 2018. [DOI: 10.1016/j.jams.2018.08.204] [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: 10/28/2022] Open
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22
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Zoltner M, Krienitz N, Field MC, Kramer S. Comparative proteomics of the two T. brucei PABPs suggests that PABP2 controls bulk mRNA. PLoS Negl Trop Dis 2018; 12:e0006679. [PMID: 30040867 PMCID: PMC6075789 DOI: 10.1371/journal.pntd.0006679] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 08/03/2018] [Accepted: 07/10/2018] [Indexed: 01/17/2023] Open
Abstract
Poly(A)-binding proteins (PABPs) regulate mRNA fate by controlling stability and translation through interactions with both the poly(A) tail and eIF4F complex. Many organisms have several paralogs of PABPs and eIF4F complex components and it is likely that different eIF4F/PABP complex combinations regulate distinct sets of mRNAs. Trypanosomes have five eIF4G paralogs, six of eIF4E and two PABPs, PABP1 and PABP2. Under starvation, polysomes dissociate and the majority of mRNAs, most translation initiation factors and PABP2 reversibly localise to starvation stress granules. To understand this more broadly we identified a protein interaction cohort for both T. brucei PABPs by cryo-mill/affinity purification-mass spectrometry. PABP1 very specifically interacts with the previously identified interactors eIF4E4 and eIF4G3 and few others. In contrast PABP2 is promiscuous, with a larger set of interactors including most translation initiation factors and most prominently eIF4G1, with its two partners TbG1-IP and TbG1-IP2. Only RBP23 was specific to PABP1, whilst 14 RNA-binding proteins were exclusively immunoprecipitated with PABP2. Significantly, PABP1 and associated proteins are largely excluded from starvation stress granules, but PABP2 and most interactors translocate to granules on starvation. We suggest that PABP1 regulates a small subpopulation of mainly small-sized mRNAs, as it interacts with a small and distinct set of proteins unable to enter the dominant pathway into starvation stress granules and localises preferentially to a subfraction of small polysomes. By contrast PABP2 likely regulates bulk mRNA translation, as it interacts with a wide range of proteins, enters stress granules and distributes over the full range of polysomes.
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Affiliation(s)
- Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Nina Krienitz
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Susanne Kramer
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
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Reusche N, Beineke A, Urhausen C, Beyerbach M, Schmicke M, Kramer S, Günzel-Apel A. Proliferative and apoptotic changes in the healthy canine endometrium and in cystic endometrial hyperplasia. Theriogenology 2018; 114:14-24. [DOI: 10.1016/j.theriogenology.2018.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 03/02/2018] [Accepted: 03/13/2018] [Indexed: 10/17/2022]
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Bannerman BP, Kramer S, Dorrell RG, Carrington M. Multispecies reconstructions uncover widespread conservation, and lineage-specific elaborations in eukaryotic mRNA metabolism. PLoS One 2018; 13:e0192633. [PMID: 29561870 PMCID: PMC5862402 DOI: 10.1371/journal.pone.0192633] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/26/2018] [Indexed: 12/01/2022] Open
Abstract
The degree of conservation and evolution of cytoplasmic mRNA metabolism pathways across the eukaryotes remains incompletely resolved. In this study, we describe a comprehensive genome and transcriptome-wide analysis of proteins involved in mRNA maturation, translation, and mRNA decay across representative organisms from the six eukaryotic super-groups. We demonstrate that eukaryotes share common pathways for mRNA metabolism that were almost certainly present in the last eukaryotic common ancestor, and show for the first time a correlation between intron density and a selective absence of some Exon Junction Complex (EJC) components in eukaryotes. In addition, we identify pathways that have diversified in individual lineages, with a specific focus on the unique gene gains and losses in members of the Excavata and SAR groups that contribute to their unique gene expression pathways compared to other organisms.
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Affiliation(s)
| | - Susanne Kramer
- Biozentrum, Lehrstuhl für Zell-und Entwicklungsbiologie, Universität Würzburg, Am Hubland, Würzburg, Germany
| | - Richard G. Dorrell
- Institute of Biology, École Normale Supérieure, PSL Research University, Paris, France
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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Koch S, Stegherr A, Mörgeli R, Kramer S, Toubekis E, Lichtner G, von Dincklage F, Spies C. Electroencephalogram dynamics in children during different levels of anaesthetic depth. Clin Neurophysiol 2017; 128:2014-2021. [DOI: 10.1016/j.clinph.2017.07.417] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/18/2017] [Accepted: 07/24/2017] [Indexed: 10/19/2022]
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26
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Kramer S. Simultaneous detection of mRNA transcription and decay intermediates by dual colour single mRNA FISH on subcellular resolution. Nucleic Acids Res 2017; 45:e49. [PMID: 27940558 PMCID: PMC5397161 DOI: 10.1093/nar/gkw1245] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 11/28/2016] [Indexed: 02/06/2023] Open
Abstract
The detection of mRNAs undergoing transcription or decay is challenging, because both processes are fast. However, the relative proportion of an mRNA in synthesis or decay increases with mRNA size and decreases with mRNA half-life. Based on this rationale, I have exploited a 22 200 nucleotide-long, short-lived endogenous mRNA as a reporter for mRNA metabolism in trypanosomes. The extreme 5΄ and 3΄ ends were labeled with red- and green-fluorescent Affymetrix® single mRNA FISH probes, respectively. In the resulting fluorescence images, yellow spots represent intact mRNAs; red spots are mRNAs in transcription or 3΄-5΄ decay, and green spots are mRNAs in 5΄-3΄ degradation. Most red spots were nuclear and insensitive to transcriptional inhibition and thus likely transcription intermediates. Most green spots were cytoplasmic, confirming that the majority of cytoplasmic decay in trypanosomes is 5΄-3΄. The system showed the expected changes at inhibition of transcription or translation and RNAi depletion of the trypanosome homologue to the 5΄-3΄ exoribonuclease Xrn1. The method allows to monitor changes in mRNA metabolism both on cellular and on population/tissue wide levels, but also to study the subcellular localization of mRNA transcription and decay pathways. I show that the system is applicable to mammalian cells.
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Affiliation(s)
- Susanne Kramer
- Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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27
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Haack M, Kramer S, Seidel G, Nickel S, Kofahl C, Dierks ML. Wer besucht eine Selbsthilfegruppe – und warum? Ergebnisse aus der SHILD-Studie. Das Gesundheitswesen 2017. [DOI: 10.1055/s-0037-1605778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- M Haack
- Medizinische Hochschule Hannover, Institut für Epidemiologie, Sozialmedizin und Gesundheitssystemforschung, Hannover
| | - S Kramer
- Medizinische Hochschule Hannover, Institut für Epidemiologie, Sozialmedizin und Gesundheitssystemforschung, Hannover
| | - G Seidel
- Medizinische Hochschule Hannover, Institut für Epidemiologie, Sozialmedizin und Gesundheitssystemforschung, Hannover
| | - S Nickel
- Universitätsklinikum Hamburg-Eppendorf, Institut für Medizinische Soziologie, Hamburg
| | - C Kofahl
- Universitätsklinikum Hamburg-Eppendorf, Institut für Medizinische Soziologie, Hamburg
| | - ML Dierks
- Medizinische Hochschule Hannover, Institut für Epidemiologie, Sozialmedizin und Gesundheitssystemforschung, Hannover
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28
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Kramer S, Haack M, Seidel G, Dierks ML. Befragung von Männern mit Prostatakrebs auf Basis der Daten des Epidemiologischen Krebsregisters Niedersachen. Das Gesundheitswesen 2017. [DOI: 10.1055/s-0037-1605974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- S Kramer
- Medizinische Hochschule Hannover, Institut für Epidemiologie, Sozialmedizin und Gesundheitssystemforschung, Hannover
| | - M Haack
- Medizinische Hochschule Hannover, Institut für Epidemiologie, Sozialmedizin und Gesundheitssystemforschung, Hannover
| | - G Seidel
- Medizinische Hochschule Hannover, Institut für Epidemiologie, Sozialmedizin und Gesundheitssystemforschung, Hannover
| | - ML Dierks
- Medizinische Hochschule Hannover, Institut für Epidemiologie, Sozialmedizin und Gesundheitssystemforschung, Hannover
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29
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Neumann J, Soerensen N, Ruebsamen N, Ojeda F, Renne T, Qaderi V, Teltrop E, Kramer S, Quantius L, Zeller T, Karakas M, Blankenberg S, Westermann D. 257Discrimination of Patients with Type 2 Myocardial Infarction. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx501.257] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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30
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Abstract
Trypanosoma brucei is a protozoan flagellate that is transmitted by tsetse flies into the mammalian bloodstream. The parasite has a huge impact on human health both directly by causing African sleeping sickness and indirectly, by infecting domestic cattle. The biology of trypanosomes involves some highly unusual, nuclear-localised processes. These include polycistronic transcription without classical promoters initiated from regions defined by histone variants, trans-splicing of all transcripts to the exon of a spliced leader RNA, transcription of some very abundant proteins by RNA polymerase I and antigenic variation, a switch in expression of the cell surface protein variants that allows the parasite to resist the immune system of its mammalian host. Here, we provide the nuclear proteome of procyclic Trypanosoma brucei, the stage that resides within the tsetse fly midgut. We have performed quantitative label-free mass spectrometry to score 764 significantly nuclear enriched proteins in comparison to whole cell lysates. A comparison with proteomes of several experimentally characterised nuclear and non-nuclear structures and pathways confirmed the high quality of the dataset: the proteome contains about 80% of all nuclear proteins and less than 2% false positives. Using motif enrichment, we found the amino acid sequence KRxR present in a large number of nuclear proteins. KRxR is a sub-motif of a classical eukaryotic monopartite nuclear localisation signal and could be responsible for nuclear localization of proteins in Kinetoplastida species. As a proof of principle, we have confirmed the nuclear localisation of six proteins with previously unknown localisation by expressing eYFP fusion proteins. While proteome data of several T. brucei organelles have been published, our nuclear proteome closes an important gap in knowledge to study trypanosome biology, in particular nuclear-related processes.
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Affiliation(s)
- Carina Goos
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Mario Dejung
- Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz, Germany
| | - Christian J. Janzen
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz, Germany
- * E-mail: (SK); (FB)
| | - Susanne Kramer
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
- * E-mail: (SK); (FB)
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Abstract
5’-3’ decay is the major mRNA decay pathway in many eukaryotes, including trypanosomes. After deadenylation, mRNAs are decapped by the nudix hydrolase DCP2 of the decapping complex and finally degraded by the 5’-3’ exoribonuclease. Uniquely, trypanosomes lack homologues to all subunits of the decapping complex, while deadenylation and 5’-3’ degradation are conserved. Here, I show that the parasites use an ApaH-like phosphatase (ALPH1) as their major mRNA decapping enzyme. The protein was recently identified as a novel trypanosome stress granule protein and as involved in mRNA binding. A fraction of ALPH1 co-localises exclusively with the trypanosome 5’-3’ exoribonuclease XRNA to a special granule at the posterior pole of the cell, indicating a connection between the two enzymes. RNAi depletion of ALPH1 is lethal and causes a massive increase in total mRNAs that are deadenylated, but have not yet started 5’-3’ decay. These data suggest that ALPH1 acts downstream of deadenylation and upstream of mRNA degradation, consistent with a function in mRNA decapping. In vitro experiments show that recombinant, N-terminally truncated ALHP1 protein, but not a catalytically inactive mutant, sensitises the capped trypanosome spliced leader RNA to yeast Xrn1, but only if an RNA 5’ polyphosphatase is included. This indicates that the decapping mechanism of ALPH1 differs from the decapping mechanism of Dcp2 by leaving more than one phosphate group at the mRNA’s 5’ end. This is the first reported function of a eukaryotic ApaH-like phosphatase, a bacterial-derived class of enzymes present in all phylogenetic super-groups of the eukaryotic kingdom. The substrates of eukaryotic ApaH-like phosphatases are unknown. However, the substrate of the related bacterial enzyme ApaH, diadenosine tetraphosphate, is highly reminiscent of a eukaryotic mRNA cap. Eukaryotic mRNAs are stabilised by a 5’ cap and one important step in mRNA decay is the removal of this cap by the nudix domain protein Dcp2 of the decapping complex. The decapping complex is highly conserved throughout eukaryotes, with the exception of trypanosomes that lack the entire complex. Here, I show that trypanosomes have evolved to use an ApaH-like phosphatase instead of a nudix domain protein as their major decapping enzyme. This work closes an important gap in the knowledge of trypanosome mRNA metabolism. Moreover, this is the first reported function of an ApaH-like phosphatase, a bacterial derived class of enzymes that are widespread throughout eukaryotes.
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Affiliation(s)
- Susanne Kramer
- Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
- * E-mail:
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Zimmermann H, Subota I, Batram C, Kramer S, Janzen CJ, Jones NG, Engstler M. A quorum sensing-independent path to stumpy development in Trypanosoma brucei. PLoS Pathog 2017; 13:e1006324. [PMID: 28394929 PMCID: PMC5398725 DOI: 10.1371/journal.ppat.1006324] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/20/2017] [Accepted: 03/29/2017] [Indexed: 11/19/2022] Open
Abstract
For persistent infections of the mammalian host, African trypanosomes limit their population size by quorum sensing of the parasite-excreted stumpy induction factor (SIF), which induces development to the tsetse-infective stumpy stage. We found that besides this cell density-dependent mechanism, there exists a second path to the stumpy stage that is linked to antigenic variation, the main instrument of parasite virulence. The expression of a second variant surface glycoprotein (VSG) leads to transcriptional attenuation of the VSG expression site (ES) and immediate development to tsetse fly infective stumpy parasites. This path is independent of SIF and solely controlled by the transcriptional status of the ES. In pleomorphic trypanosomes varying degrees of ES-attenuation result in phenotypic plasticity. While full ES-attenuation causes irreversible stumpy development, milder attenuation may open a time window for rescuing an unsuccessful antigenic switch, a scenario that so far has not been considered as important for parasite survival.
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Affiliation(s)
- Henriette Zimmermann
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Ines Subota
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Christopher Batram
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Susanne Kramer
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Christian J. Janzen
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Nicola G. Jones
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
- * E-mail:
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Kramer S, Dibbern D, Moll J, Huenninghaus M, Koller R, Krueger D, Marhan S, Urich T, Wubet T, Bonkowski M, Buscot F, Lueders T, Kandeler E. Resource Partitioning between Bacteria, Fungi, and Protists in the Detritusphere of an Agricultural Soil. Front Microbiol 2016; 7:1524. [PMID: 27725815 PMCID: PMC5035733 DOI: 10.3389/fmicb.2016.01524] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [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: 06/29/2016] [Accepted: 09/12/2016] [Indexed: 01/31/2023] Open
Abstract
The flow of plant-derived carbon in soil is a key component of global carbon cycling. Conceptual models of trophic carbon fluxes in soil have assumed separate bacterial and fungal energy channels in the detritusphere, controlled by both substrate complexity and recalcitrance. However, detailed understanding of the key populations involved and niche-partitioning between them is limited. Here, a microcosm experiment was performed to trace the flow of detritusphere C from substrate analogs (glucose, cellulose) and plant biomass amendments (maize leaves, roots) in an agricultural soil. Carbon flow was traced by rRNA stable isotope probing and amplicon sequencing across three microbial kingdoms. Distinct lineages within the Actinobacteria, Bacteroidetes, Gammaproteobacteria, Basidiomycota, Ascomycota as well as Peronosporomycetes were identified as important primary substrate consumers. A dynamic succession of primary consumers was observed especially in the cellulose treatments, but also in plant amendments over time. While intra-kingdom niche partitioning was clearly observed, distinct bacterial and fungal energy channels were not apparent. Furthermore, while the diversity of primary substrate consumers did not notably increase with substrate complexity, consumer succession and secondary trophic links to bacterivorous and fungivorous microbes resulted in increased food web complexity in the more recalcitrant substrates. This suggests that rather than substrate-defined energy channels, consumer succession as well as intra- and inter-kingdom cross-feeding should be considered as mechanisms supporting food web complexity in the detritusphere.
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Affiliation(s)
- Susanne Kramer
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart, Germany
| | - Dörte Dibbern
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health Neuherberg, Germany
| | - Julia Moll
- Department of Soil Ecology, Helmholtz Centre for Environmental Research Leipzig-HalleHalle, Germany; Institute of Biology, University of LeipzigLeipzig, Germany
| | - Maike Huenninghaus
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne Köln, Germany
| | - Robert Koller
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne Köln, Germany
| | - Dirk Krueger
- Department of Soil Ecology, Helmholtz Centre for Environmental Research Leipzig-Halle Halle, Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart, Germany
| | - Tim Urich
- Department of Bacterial Physiology, Institute for Microbiology, Ernst-Moritz-Arndt University of Greifswald Greifswald, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, Helmholtz Centre for Environmental Research Leipzig-HalleHalle, Germany; German Centre for Integrative Biodiversity Research (iDiv)Leipzig, Germany
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne Köln, Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz Centre for Environmental Research Leipzig-HalleHalle, Germany; Institute of Biology, University of LeipzigLeipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv)Leipzig, Germany
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health Neuherberg, Germany
| | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart, Germany
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Farr K, Khalil A, Møller D, Bluhme H, Kramer S, Morsing A, Grau C. OC-0381: Perfusion SPECT can quantify radiation-induced changes in the lung after IMRT for NSCLC. Radiother Oncol 2016. [DOI: 10.1016/s0167-8140(16)31630-9] [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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Guijarro D, Lebrin M, Lairez O, Bourin P, Piriou N, Pozzo J, Lande G, Berry M, Le Tourneau T, Cussac D, Sensebe L, Gross F, Lamirault G, Huynh A, Manrique A, Ruidavet J, Elbaz M, Trochu J, Parini A, Kramer S, Galinier M, Lemarchand P, Roncalli J. Intramyocardial transplantation of mesenchymal stromal cells for chronic myocardial ischemia and impaired left ventricular function: Results of the MESAMI 1 pilot trial. Int J Cardiol 2016; 209:258-65. [DOI: 10.1016/j.ijcard.2016.02.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 01/10/2016] [Accepted: 02/01/2016] [Indexed: 11/27/2022]
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Kramer S, Piper S, Estevez A, Carrington M. Polycistronic trypanosome mRNAs are a target for the exosome. Mol Biochem Parasitol 2016; 205:1-5. [PMID: 26946399 PMCID: PMC4850246 DOI: 10.1016/j.molbiopara.2016.02.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 02/03/2016] [Revised: 02/26/2016] [Accepted: 02/29/2016] [Indexed: 11/02/2022]
Abstract
Eukaryotic cells have several mRNA quality control checkpoints to avoid the production of aberrant proteins. Intron-containing mRNAs are actively degraded by the nuclear exosome, prevented from nuclear exit and, if these systems fail, degraded by the cytoplasmic NMD machinery. Trypanosomes have only two introns. However, they process mRNAs from long polycistronic precursors by trans-splicing and polycistronic mRNA molecules frequently arise from any missed splice site. Here, we show that RNAi depletion of the trypanosome exosome, but not of the cytoplasmic 5'-3' exoribonuclease XRNA or the NMD helicase UPF1, causes accumulation of oligocistronic mRNAs. We have also revisited the localization of the trypanosome exosome by expressing eYFP-fusion proteins of the exosome subunits RRP44 and RRP6. Both proteins are significantly enriched in the nucleus. Together with published data, our data suggest a major nuclear function of the trypanosome exosome in rRNA, snoRNA and mRNA quality control.
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Affiliation(s)
- Susanne Kramer
- Biozentrum, Julius-Maximilians Universität Würzburg, Am Hubland, 97074 Würzburg, Germany; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
| | - Sophie Piper
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Antonio Estevez
- Instituto de Parasitología y Biomedicina "López-Neyra", IPBL N-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento, s/n.18100 Armilla, Granada, Spain
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
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Friedrich M, Swords D, Altgassen C, Baum S, Kramer S. Alloplastic breast reconstruction after mastectomy. EUR J GYNAECOL ONCOL 2016; 37:622-626. [PMID: 29786998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The aim of reconstruction with expanders is to restore breast shape and volume as close as possible to the contralateral breast and to reconstruct the inframammary fold with adequate ptosis.
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Gundert-Remy U, Batke M, Bitsch A, Gütlein M, Kramer S, Partosch F, Seeland M. Optimization of curation of the dataset with data on repeated dose toxicity. Toxicol Lett 2015. [DOI: 10.1016/j.toxlet.2015.08.566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Seidel G, Haack M, Kramer S, Kofahl C, Werner S, Nickel S, dem Knesebeck OV, Dierks ML. Partizipative Forschung und Rekrutierungspfade in der Selbsthilfeforschung der SHILD-Studie. Gesundheitswesen 2015. [DOI: 10.1055/s-0035-1563131] [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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Pausch J, Kramer S, Scharroba A, Scheunemann N, Butenschoen O, Kandeler E, Marhan S, Riederer M, Scheu S, Kuzyakov Y, Ruess L. Small but active – pool size does not matter for carbon incorporation in below‐ground food webs. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12512] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Johanna Pausch
- Department of Soil Science of Temperate Ecosystems Georg August University Göttingen Büsgen‐Institute Büsgenweg 2 37077 Göttingen Germany
| | - Susanne Kramer
- Institute of Soil Science and Land Evaluation Soil Biology University of Hohenheim Emil‐Wolff‐Str. 27 70593 Stuttgart Germany
| | - Anika Scharroba
- Institute of Biology Ecology Group Humboldt‐Universität zu Berlin Philippstr. 13 10115 Berlin Germany
| | - Nicole Scheunemann
- J.F. Blumenbach Institute of Zoology and Anthropology Georg August University Göttingen Berliner Str. 28 37073 Göttingen Germany
| | - Olaf Butenschoen
- J.F. Blumenbach Institute of Zoology and Anthropology Georg August University Göttingen Berliner Str. 28 37073 Göttingen Germany
| | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation Soil Biology University of Hohenheim Emil‐Wolff‐Str. 27 70593 Stuttgart Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation Soil Biology University of Hohenheim Emil‐Wolff‐Str. 27 70593 Stuttgart Germany
| | - Michael Riederer
- Department of Micrometeorology BayCEER University of Bayreuth Universitätsstr. 30 95447 Bayreuth Germany
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology Georg August University Göttingen Berliner Str. 28 37073 Göttingen Germany
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems Georg August University Göttingen Büsgen‐Institute Büsgenweg 2 37077 Göttingen Germany
- Department of Agricultural Soil Science Georg August University Göttingen Büsgenweg 2 37077 Göttingen Germany
| | - Liliane Ruess
- Institute of Biology Ecology Group Humboldt‐Universität zu Berlin Philippstr. 13 10115 Berlin Germany
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Moll J, Goldmann K, Kramer S, Hempel S, Kandeler E, Marhan S, Ruess L, Krüger D, Buscot F. Resource Type and Availability Regulate Fungal Communities Along Arable Soil Profiles. Microb Ecol 2015; 70:390-399. [PMID: 25687125 DOI: 10.1007/s00248-015-0569-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 01/13/2015] [Indexed: 06/04/2023]
Abstract
Soil fungi play an essential role in the decomposition of plant-derived organic material entering soils. The quality and quantity of organic compounds vary seasonally as well as with soil depth. To elucidate how these resources affect fungal communities in an arable soil, a field experiment was set up with two plant species, maize and wheat. Resource availability was experimentally manipulated by maize litter input on one half of these maize and wheat plots after harvest in autumn. Fungal biomass was determined by ergosterol quantification, and community structure was investigated by fungal automated ribosomal intergenic spacer analysis (F-ARISA). An annual cycle was assessed across a depth gradient, distinguishing three soil habitats: the plough layer, rooted soil below the plough layer, and deeper root-free soil. Fungal communities appeared highly dynamic and varied according to soil depth and plant resources. In the plough layer, the availability of litter played a dominant role in shaping fungal communities, whereas in the rooted layer below, community structure and biomass mainly differed between plant species. This plant effect was also extended into the root-free soil at a depth of 70 cm. In winter, the availability of litter also affected fungal communities in deeper soil layers, suggesting vertical transport processes under fallow conditions. These distinct resource effects indicate diverse ecological niches along the soil profile, comprising specific fungal metacommunities. The recorded responses to both living plants and litter point to a central role of fungi in connecting primary production and decomposition within the plant-soil system.
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Affiliation(s)
- Julia Moll
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle, Germany,
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Fritz M, Vanselow J, Sauer N, Lamer S, Goos C, Siegel TN, Subota I, Schlosser A, Carrington M, Kramer S. Novel insights into RNP granules by employing the trypanosome's microtubule skeleton as a molecular sieve. Nucleic Acids Res 2015; 43:8013-32. [PMID: 26187993 PMCID: PMC4652759 DOI: 10.1093/nar/gkv731] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/07/2015] [Indexed: 02/07/2023] Open
Abstract
RNP granules are ribonucleoprotein assemblies that regulate the post-transcriptional fate of mRNAs in all eukaryotes. Their exact function remains poorly understood, one reason for this is that RNP granule purification has not yet been achieved. We have exploited a unique feature of trypanosomes to prepare a cellular fraction highly enriched in starvation stress granules. First, granules remain trapped within the cage-like, subpellicular microtubule array of the trypanosome cytoskeleton while soluble proteins are washed away. Second, the microtubules are depolymerized and the granules are released. RNA sequencing combined with single molecule mRNA FISH identified the short and highly abundant mRNAs encoding ribosomal mRNAs as being excluded from granules. By mass spectrometry we have identified 463 stress granule candidate proteins. For 17/49 proteins tested by eYFP tagging we have confirmed the localization to granules, including one phosphatase, one methyltransferase and two proteins with a function in trypanosome life-cycle regulation. The novel method presented here enables the unbiased identification of novel RNP granule components, paving the way towards an understanding of RNP granule function.
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Affiliation(s)
- Melanie Fritz
- Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jens Vanselow
- Rudolf Virchow Center, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Nadja Sauer
- Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Stephanie Lamer
- Rudolf Virchow Center, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Carina Goos
- Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - T Nicolai Siegel
- Research Center for Infectious Diseases, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Ines Subota
- Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Mark Carrington
- Department of Biochemistry, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Susanne Kramer
- Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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Blackwell K, Semiglazov V, Krasnozhon D, Davidenko I, Nelyubina L, Nakov R, Stiegler G, Singh P, Schwebig A, Kramer S, Harbeck N. Comparison of EP2006, a filgrastim biosimilar, to the reference: a phase III, randomized, double-blind clinical study in the prevention of severe neutropenia in patients with breast cancer receiving myelosuppressive chemotherapy. Ann Oncol 2015; 26:1948-1953. [PMID: 26122726 PMCID: PMC4551159 DOI: 10.1093/annonc/mdv281] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [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: 04/27/2015] [Accepted: 06/19/2015] [Indexed: 11/13/2022] Open
Abstract
This randomized, double-blind comparison demonstrates that biosimilar filgrastim (EP2006) and the US-licensed reference filgrastim are similar with no clinically meaningful differences regarding efficacy and safety in prevention of severe neutropenia. Biosimilar filgrastim could represent an important alternative to the reference product, potentially increasing access to filgrastim treatment. Background Biosimilars of filgrastim are in widespread clinical use in Europe. This phase III study compares biosimilar filgrastim (EP2006), with the US-licensed reference product, Neupogen®, in breast cancer patients receiving (neo)adjuvant myelosuppressive chemotherapy (TAC). Patients and methods A total of 218 patients receiving 5 µg/kg/day filgrastim over six chemotherapy cycles were randomized 1:1:1:1 into four arms. Two arms received only one product (nonalternating), biosimilar or reference, and two arms (alternating) received alternating treatments during each cycle (biosimilar then reference or vice versa). The primary end point was duration of severe neutropenia (DSN) during cycle 1. Results The baseline characteristics were balanced between the four treatment arms. Noninferiority of biosimilar versus the reference was demonstrated: DSN (days) in cycle 1 was 1.17 ± 1.11 (biosimilar, N = 101) and 1.20 ± 1.02 (reference, N = 103), 97.5% confidence interval lower boundary for the difference was −0.26 days (above the predefined limit of −1 day). No clinically meaningful differences were observed regarding any other efficacy parameter: incidence of febrile neutropenia (FN); hospitalization due to FN; incidence of infections; depth and time of absolute neutrophil count (ANC) nadir and time to ANC recovery during cycle 1 and across all cycles. The pattern and frequency of adverse events were similar across all treatments. Conclusion This study demonstrates that biosimilar and the reference filgrastim are similar with no clinically meaningful differences regarding efficacy and safety in prevention of severe neutropenia. Biosimilar filgrastim could represent an important alternative to the reference product, potentially benefiting public health by increasing access to filgrastim treatment. Study number NCT01519700.
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Affiliation(s)
| | - V Semiglazov
- 'Railway Clinical Hospital of OJSC "RZhD"', Non-State Healthcare Institution (NSHI), Saint Petersburg
| | - D Krasnozhon
- 'Leningrad Regional Oncological Dispensary' at the Surgery Department #2, State Healthcare Institution (SHI), Saint Petersburg
| | - I Davidenko
- 'Clinical Oncological Dispensary No. 1' of Healthcare Department of Krasnodar Territory, State Healthcare Institution (SHI), Krasnodar
| | - L Nelyubina
- Institution of the Russian Academy of Medical Sciences, 'Russian Oncology Research Center n.a. N.N. Blochin of RAMS', Moscow, Russia
| | | | | | | | | | | | - N Harbeck
- Breast Center, University of Munich, Munich, Germany
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Billinghurst BE, Bergstrom JC, Baribeau C, Batten T, Dallin L, May TE, Vogt JM, Wurtz WA, Warnock R, Bizzozero DA, Kramer S. Observation of Wakefields and Resonances in Coherent Synchrotron Radiation. Phys Rev Lett 2015; 114:204801. [PMID: 26047232 DOI: 10.1103/physrevlett.114.204801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Indexed: 06/04/2023]
Abstract
We report on high resolution measurements of resonances in the spectrum of coherent synchrotron radiation (CSR) at the Canadian Light Source (CLS). The resonances permeate the spectrum at wave number intervals of 0.074 cm(-1), and are highly stable under changes in the machine setup (energy, bucket filling pattern, CSR in bursting or continuous mode). Analogous resonances were predicted long ago in an idealized theory as eigenmodes of a smooth toroidal vacuum chamber driven by a bunched beam moving on a circular orbit. A corollary of peaks in the spectrum is the presence of pulses in the wakefield of the bunch at well-defined spatial intervals. Through experiments and further calculations we elucidate the resonance and wakefield mechanisms in the CLS vacuum chamber, which has a fluted form much different from a smooth torus. The wakefield is observed directly in the 30-110 GHz range by rf diodes, and indirectly by an interferometer in the THz range. The wake pulse sequence found by diodes is less regular than in the toroidal model, and depends on the point of observation, but is accounted for in a simulation of fields in the fluted chamber. Attention is paid to polarization of the observed fields, and possible coherence of fields produced in adjacent bending magnets. Low frequency wakefield production appears to be mainly local in a single bend, but multibend effects cannot be excluded entirely, and could play a role in high frequency resonances. New simulation techniques have been developed, which should be invaluable in further work.
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Affiliation(s)
- B E Billinghurst
- Canadian Light Source Inc., University of Saskatchewan, Saskatoon, Saskatchewan S7N 2V3, Canada
| | - J C Bergstrom
- Canadian Light Source Inc., University of Saskatchewan, Saskatoon, Saskatchewan S7N 2V3, Canada
| | - C Baribeau
- Canadian Light Source Inc., University of Saskatchewan, Saskatoon, Saskatchewan S7N 2V3, Canada
| | - T Batten
- Canadian Light Source Inc., University of Saskatchewan, Saskatoon, Saskatchewan S7N 2V3, Canada
| | - L Dallin
- Canadian Light Source Inc., University of Saskatchewan, Saskatoon, Saskatchewan S7N 2V3, Canada
| | - T E May
- Canadian Light Source Inc., University of Saskatchewan, Saskatoon, Saskatchewan S7N 2V3, Canada
| | - J M Vogt
- Canadian Light Source Inc., University of Saskatchewan, Saskatoon, Saskatchewan S7N 2V3, Canada
| | - W A Wurtz
- Canadian Light Source Inc., University of Saskatchewan, Saskatoon, Saskatchewan S7N 2V3, Canada
| | - R Warnock
- SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA and Department of Mathematics and Statistics, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - D A Bizzozero
- Department of Mathematics and Statistics, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - S Kramer
- Brookhaven National Laboratory, Upton, New York 11973, USA
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Prosnitz LR, Goldenberg IS, Harris JR, Hellman S, Danoff BF, Kramer S, Wallner PE, Brady LW. Radiotherapy for carcinoma of the breast instead of mastectomy. An update. Front Radiat Ther Oncol 2015; 17:69-75. [PMID: 6822356 DOI: 10.1159/000407279] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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46
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Farr K, Khalil A, Kramer S, Morsing A, Grau C. PO-0662: Role of SPECT in predicting the risk of lung toxicity after radiotherapy in lung cancer patients. a prospective study. Radiother Oncol 2015. [DOI: 10.1016/s0167-8140(15)40654-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Fleckenstein J, Kohls N, Evtouchenko E, Lehmeyer L, Kramer S, Lang P, Siebeck M, Mussack T, Hatz R, Heindl B, Conzen P, Rehm M, Czerner S, Zwißler B, Irnich D. No effect of the cyclooxygenase-2 inhibitor etoricoxib on pre-emptive and post-operative analgesia in visceral surgery: results of a randomized controlled trial. Eur J Pain 2015; 20:186-95. [DOI: 10.1002/ejp.699] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2015] [Indexed: 11/06/2022]
Affiliation(s)
- J. Fleckenstein
- Department of Anaesthesiology; University of Munich; Germany
| | - N. Kohls
- Division Integrative Health Promotion; University of Applied Sciences and Arts Coburg; Germany
- Brain, Mind & Healing Program; Samueli Institute; Alexandria USA
| | - E. Evtouchenko
- Department of Anaesthesiology; University of Munich; Germany
| | - L. Lehmeyer
- Department of Anaesthesiology; University of Munich; Germany
| | - S. Kramer
- Department of Anaesthesiology; University of Munich; Germany
| | - P.M. Lang
- Department of Anaesthesiology; University of Munich; Germany
| | - M. Siebeck
- Department of General, Visceral, Transplantation, Vascular and Thoracic Surgery; Ludwig Maximilians University; Munich Germany
| | - T. Mussack
- Department of General, Visceral, Transplantation, Vascular and Thoracic Surgery; Ludwig Maximilians University; Munich Germany
| | - R. Hatz
- Department of General, Visceral, Transplantation, Vascular and Thoracic Surgery; Ludwig Maximilians University; Munich Germany
| | - B. Heindl
- Department of Anaesthesiology; University of Munich; Germany
| | - P. Conzen
- Department of Anaesthesiology; University of Munich; Germany
| | - M. Rehm
- Department of Anaesthesiology; University of Munich; Germany
| | - S. Czerner
- Department of Anaesthesiology; University of Munich; Germany
| | - B. Zwißler
- Department of Anaesthesiology; University of Munich; Germany
| | - D. Irnich
- Department of Anaesthesiology; University of Munich; Germany
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48
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Vincendeau M, Göttesdorfer I, Schreml JMH, Wetie AGN, Mayer J, Greenwood AD, Helfer M, Kramer S, Seifarth W, Hadian K, Brack-Werner R, Leib-Mösch C. Modulation of human endogenous retrovirus (HERV) transcription during persistent and de novo HIV-1 infection. Retrovirology 2015; 12:27. [PMID: 25886562 PMCID: PMC4375885 DOI: 10.1186/s12977-015-0156-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [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: 06/05/2014] [Accepted: 03/05/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The human genome contains multiple LTR elements including human endogenous retroviruses (HERVs) that together account for approximately 8-9% of the genomic DNA. At least 40 different HERV groups have been assigned to three major HERV classes on the basis of their homologies to exogenous retroviruses. Although most HERVs are silenced by a variety of genetic and epigenetic mechanisms, they may be reactivated by environmental stimuli such as exogenous viruses and thus may contribute to pathogenic conditions. The objective of this study was to perform an in-depth analysis of the influence of HIV-1 infection on HERV activity in different cell types. RESULTS A retrovirus-specific microarray that covers major HERV groups from all three classes was used to analyze HERV transcription patterns in three persistently HIV-1 infected cell lines of different cellular origins and in their uninfected counterparts. All three persistently infected cell lines showed increased transcription of multiple class I and II HERV groups. Up-regulated transcription of five HERV taxa (HERV-E, HERV-T, HERV-K (HML-10) and two ERV9 subgroups) was confirmed by quantitative reverse transcriptase PCR analysis and could be reversed by knock-down of HIV-1 expression with HIV-1-specific siRNAs. Cells infected de novo by HIV-1 showed stronger transcriptional up-regulation of the HERV-K (HML-2) group than persistently infected cells of the same origin. Analysis of transcripts from individual members of this group revealed up-regulation of predominantly two proviral loci (ERVK-7 and ERVK-15) on chromosomes 1q22 and 7q34 in persistently infected KE37.1 cells, as well as in de novo HIV-1 infected LC5 cells, while only one single HML-2 locus (ERV-K6) on chromosome 7p22.1 was activated in persistently infected LC5 cells. CONCLUSIONS Our results demonstrate that HIV-1 can alter HERV transcription patterns of infected cells and indicate a correlation between activation of HERV elements and the level of HIV-1 production. Moreover, our results suggest that the effects of HIV-1 on HERV activity may be far more extensive and complex than anticipated from initial studies with clinical material.
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Affiliation(s)
- Michelle Vincendeau
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany. .,Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
| | - Ingmar Göttesdorfer
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
| | - Julia M H Schreml
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany.
| | - Armand G Ngounou Wetie
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
| | - Jens Mayer
- Department of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, University of Saarland, Homburg, Germany.
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.
| | - Markus Helfer
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
| | - Susanne Kramer
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
| | - Wolfgang Seifarth
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany.
| | - Kamyar Hadian
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany. .,Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
| | - Ruth Brack-Werner
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
| | - Christine Leib-Mösch
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany. .,Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany.
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49
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Harenberg J, Du S, Weiss C, Kramer S. C0313: Determination of Rivaroxaban, Apixaban and Dabigatran from Plasma Samples of Patients Using Citrate, EDTA and Prostaglandin-Citric Acid as Anticoagulant. Thromb Res 2014. [DOI: 10.1016/s0049-3848(14)50286-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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50
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Henning H, Masal C, Herr A, Wolf K, Urhausen C, Beineke A, Beyerbach M, Kramer S, Günzel-Apel AR. Effect of short-term scrotal hyperthermia on spermatological parameters, testicular blood flow and gonadal tissue in dogs. Reprod Domest Anim 2014; 49:145-57. [PMID: 24428565 DOI: 10.1111/rda.12244] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 08/30/2013] [Indexed: 11/29/2022]
Abstract
The objective was to assess the effect of a short-term scrotal hyperthermia in dogs on quantitative and qualitative ejaculate parameters, testicular blood flow and testicular and epididymal histology. After a control period, the scrotum of seven normospermic adult beagle dogs was insulated with a self-made suspensory for 48 h. Nine weeks later, two animals were castrated, while in five animals, scrotal hyperthermia was repeated. Dogs were castrated either 10 or 40 days thereafter. In each phase of scrotal insulation, average scrotal surface temperature increased by 3.0°C. Semen was collected twice weekly throughout the experiment. Total sperm count did not change after the first hyperthermia, but it slightly decreased after the second (p < 0.05). Profiles of sperm morphology and velocity parameters (CASA) rather indicated subtle physiological variations in sperm quality than effects of a local heat stress. Chromatin stability of ejaculated spermatozoa as indicated by SCSA remained constant throughout the experiment. Perfusion characteristics of the gonads, that is, systolic peak velocity, pulsatility and resistance index at the marginal location of the testicular artery, did not change due to hyperthermia (p > 0.05). Histological examination of excised testes and epididymides for apoptotic (TUNEL and activated caspase-3) and proliferating cells (Ki-67 antigen) indicated only marginal effects of scrotal insulation on tissue morphology. In conclusion, a mild short-term scrotal hyperthermia in dogs does not cause substantial changes in sperm quantity and quality. In contrast to other species, canine testes and epididymides may have a higher competence to compensate such thermal stress.
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Affiliation(s)
- H Henning
- Unit for Reproductive Medicine of Clinics, University of Veterinary Medicine Hannover, Hannover, Germany; Clinic for Pigs and Small Ruminants, University of Veterinary Medicine Hannover, Hannover, Germany
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