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Hopf TA, Green AG, Schubert B, Mersmann S, Schärfe CPI, Ingraham JB, Toth-Petroczy A, Brock K, Riesselman AJ, Palmedo P, Kang C, Sheridan R, Draizen EJ, Dallago C, Sander C, Marks DS. The EVcouplings Python framework for coevolutionary sequence analysis. Bioinformatics 2020; 35:1582-1584. [PMID: 30304492 PMCID: PMC6499242 DOI: 10.1093/bioinformatics/bty862] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/06/2018] [Accepted: 10/08/2018] [Indexed: 01/03/2023] Open
Abstract
SUMMARY Coevolutionary sequence analysis has become a commonly used technique for de novo prediction of the structure and function of proteins, RNA, and protein complexes. We present the EVcouplings framework, a fully integrated open-source application and Python package for coevolutionary analysis. The framework enables generation of sequence alignments, calculation and evaluation of evolutionary couplings (ECs), and de novo prediction of structure and mutation effects. The combination of an easy to use, flexible command line interface and an underlying modular Python package makes the full power of coevolutionary analyses available to entry-level and advanced users. AVAILABILITY AND IMPLEMENTATION https://github.com/debbiemarkslab/evcouplings.
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Affiliation(s)
- Thomas A Hopf
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Anna G Green
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Benjamin Schubert
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA.,cBio Center, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sophia Mersmann
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Charlotta P I Schärfe
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Center for Bioinformatics, University of Tübingen, Tübingen, Germany.,Applied Bioinformatics, Department of Computer Science, Tübingen, Germany
| | - John B Ingraham
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Kelly Brock
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Adam J Riesselman
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Perry Palmedo
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
| | - Chan Kang
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Robert Sheridan
- Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eli J Draizen
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Christian Dallago
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA.,Department of Informatics, Technische Universität München, Garching, Germany
| | - Chris Sander
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.,cBio Center, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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Papi A, Dokic D, Tzimas W, Mészáros I, Olech-Cudzik A, Koroknai Z, McAulay K, Mersmann S, Dalvi PS, Overend T. Fluticasone propionate/formoterol for COPD management: a randomized controlled trial. Int J Chron Obstruct Pulmon Dis 2017; 12:1961-1971. [PMID: 28740376 PMCID: PMC5505160 DOI: 10.2147/copd.s136527] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
PURPOSE To evaluate fluticasone propionate/formoterol (FP/FORM) in COPD. PATIENTS AND METHODS COPD patients with forced expiratory volume in 1 s (FEV1) ≤50% predicted and ≥1 moderate/severe COPD exacerbation in the last 12 months were randomized to FP/FORM 500/20 or 250/10 µg bid, or formoterol (FORM) 12 µg bid for 52 weeks. The primary outcome was the annualized rate of moderate/severe COPD exacerbations. RESULTS In total, 1,765 patients were randomized. There were fewer discontinuations with FP/FORM 500/20 µg (20.6%) and 250/10 µg (24.0%) compared with FORM (26.1%). None of the two FP/FORM doses reduced the moderate/severe exacerbation rate versus FORM (rate ratios [RR]: 0.93; P≤0.402). There was a trend toward a lower moderate/severe exacerbation rate with FP/FORM 500/20 µg versus FORM in patients with ≥2 exacerbations in the preceding year (RR: 0.79; P=0.084). Pre- and post-dose FEV1 and forced vital capacity were greater with FP/FORM 500/20 µg versus FORM (P≤0.039). There was a trend toward a lower EXAcerbations of Chronic pulmonary disease Tool (EXACT) exacerbation rate with FP/FORM 500/20 µg versus FORM (RR: 0.87; P=0.077). There were more St George's Respiratory Questionnaire for COPD (SGRQ-C) responders with FP/FORM 500/20 µg than FORM (odds ratios [OR] at weeks 6, 23 and 52 ≥1.28; P≤0.054). EXACT-respiratory symptoms total and breathlessness scores were lower with both FP/FORM 500/20 µg and 250/10 µg versus FORM (P≤0.066). Acute β2-agonist-induced effects and 24-hour Holter findings were similar for all treatments. Mean 24-hour urinary cortisol was similarly reduced with both FP/FORM doses. Radiologically confirmed pneumonia was seen in 2.4%, 3.2% and 1.5% of FP/FORM 500/20 µg, FP/FORM 250/10 µg and FORM-treated patients, respectively. Adverse events were otherwise similar across treatment groups. CONCLUSION FP/FORM did not reduce exacerbation rates versus FORM. Numerical benefits were observed with FP/FORM 500/20 µg versus FORM for secondary variables, including lung function, EXACT exacerbations, SGRQ-C and EXACT-respiratory symptoms total and breathlessness scores. Few efficacy differences were evident between FP/FORM 250/10 µg and FORM. Pneumonia was more frequent in FP/FORM-treated patients, although the absolute difference was low. Adverse events were otherwise similar between treatments.
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Affiliation(s)
- A Papi
- Department of Internal and CardioRespiratory Medicine, Reseach Center on Asthma and COPD, University of Ferrara, Ferrara, Italy
| | - D Dokic
- Clinic of Pulmology and Allergy, Clinical Centre, Medical Faculty, Ss. Cyril and Methodius University, Skopje, Macedonia
| | - W Tzimas
- Pneumologische Praxis, München, Germany
| | - I Mészáros
- Coral Szakorvosi Centrum, Budapest, Hungary
| | - A Olech-Cudzik
- Ostrowieckie Centrum Medyczne Spółka, Ostrowiec Swietokrzyski, Poland
| | - Z Koroknai
- PAREXEL International, Global Medical Services, Budapest, Hungary
| | - K McAulay
- Medical Operations, Mundipharma Research Limited, Cambridge, UK
| | - S Mersmann
- Biostatistics and Clinical Data Science, Mundipharma Research GmbH & Co. KG, Limburg, Germany
| | - PS Dalvi
- Medical Science - Respiratory, Mundipharma Research Limited, Cambridge, UK
| | - T Overend
- Medical Science - Respiratory, Mundipharma Research Limited, Cambridge, UK
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Abstract
Guard cells regulate plant gas exchange and transpiration by modulation of stomatal aperture upon integrating external cues like photosynthetic effective illumination, CO2 levels and water availability and internal signals like abscisic acid (ABA). Being pores, stomata constitute a natural entry site for potentially harmful microbes. To prevent microbial invasion, stomata close upon perception of microbe-associated molecular patterns (MAMPs), and this represents an important layer of active immunity at the preinvasive level. The signaling pathways leading to stomatal closure triggered by biotic and abiotic stresses employ several common components, such as reactive oxygen species, calcium, kinases, and hormones, suggesting considerable intersection between MAMP- and ABA-induced stomatal closures, which we will discuss in this review.
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Kunert J, Mersmann S. A-Optimal Designs for Treatment-Control Comparisons in Microarray Experiments with Random Block Effects. Journal of Statistical Theory and Practice 2011. [DOI: 10.1080/15598608.2011.10412051] [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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Beck J, Procopio G, Bajetta E, Keilholz U, Negrier S, Szczylik C, Bokemeyer C, Bracarda S, Richel DJ, Staehler M, Strauss UP, Mersmann S, Burock K, Escudier B. Final results of the European Advanced Renal Cell Carcinoma Sorafenib (EU-ARCCS) expanded-access study: a large open-label study in diverse community settings. Ann Oncol 2011; 22:1812-23. [PMID: 21324953 DOI: 10.1093/annonc/mdq651] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The European Advanced Renal Cell Carcinoma Sorafenib (EU-ARCCS) expanded-access study provided sorafenib to advanced renal cell carcinoma (RCC) patients in whom previous systemic therapy had failed. The study assessed the safety and use of sorafenib for the treatment of advanced RCC in a large community-based patient population across 11 countries in Europe. PATIENTS AND METHODS EU-ARCCS was a single-arm, open-label trial of sorafenib in advanced RCC patients. End points included safety, time to progression, progression-free survival (PFS), and disease control rate (DCR). Subgroup analyses included age, Eastern Cooperative Oncology Group performance status, histology, prior therapy, and number and sites of metastases. RESULTS About 1159 advanced RCC patients were enrolled. Most patients (94%) experienced drug-related adverse events (AEs) of any grade, with the most common grade ≥3 AEs including hand-foot skin reaction (13%), diarrhea (7%), fatigue (7%), hypertension (6%), and rash/desquamation (5%). The incidence of AEs in the subgroups was similar to that in the overall population. Median PFS was 6.6 months; DCR at ≥8 and ≥12 weeks was 85% and 78%, respectively. CONCLUSIONS The sorafenib safety profile in European community-based practice settings was similar to that reported in clinical trials. The heterogeneous advanced RCC patient population in EU-ARCCS permitted assessment of sorafenib in important subpopulations of advanced RCC patients.
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Affiliation(s)
- J Beck
- Johannes Gutenberg University Medical Center, Mainz, Germany
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Mersmann S, Bourdais G, Rietz S, Robatzek S. Ethylene signaling regulates accumulation of the FLS2 receptor and is required for the oxidative burst contributing to plant immunity. Plant Physiol 2010; 154:391-400. [PMID: 20592040 PMCID: PMC2938167 DOI: 10.1104/pp.110.154567] [Citation(s) in RCA: 247] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 06/28/2010] [Indexed: 05/18/2023]
Abstract
Reactive oxygen species (ROS) are potent signal molecules rapidly generated in response to stress. Detection of pathogen-associated molecular patterns induces a transient apoplastic ROS through the function of the NADPH respiratory burst oxidase homologs D (RbohD). However, little is known about the regulation of pathogen-associated molecular pattern-elicited ROS or its role in plant immunity. We investigated ROS production triggered by bacterial flagellin (flg22) in Arabidopsis (Arabidopsis thaliana). The oxidative burst was diminished in ethylene-insensitive mutants. Flagellin Sensitive2 (FLS2) accumulation was reduced in etr1 and ein2, indicating a requirement of ethylene signaling for FLS2 expression. Multiplication of virulent bacteria was enhanced in Arabidopsis lines displaying altered ROS production at early but not late stages of infection, suggesting an impairment of preinvasive immunity. Stomatal closure, a mechanism used to reduce bacterial entry into plant tissues, was abolished in etr1, ein2, and rbohD mutants. These results point to the importance of flg22-triggered ROS at an early stage of the plant immune response.
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Wrzaczek M, Brosché M, Salojärvi J, Kangasjärvi S, Idänheimo N, Mersmann S, Robatzek S, Karpiński S, Karpińska B, Kangasjärvi J. Transcriptional regulation of the CRK/DUF26 group of receptor-like protein kinases by ozone and plant hormones in Arabidopsis. BMC Plant Biol 2010; 10:95. [PMID: 20500828 PMCID: PMC3095361 DOI: 10.1186/1471-2229-10-95] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Accepted: 05/25/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plant Receptor-like/Pelle kinases (RLK) are a group of conserved signalling components that regulate developmental programs and responses to biotic and abiotic stresses. One of the largest RLK groups is formed by the Domain of Unknown Function 26 (DUF26) RLKs, also called Cysteine-rich Receptor-like Kinases (CRKs), which have been suggested to play important roles in the regulation of pathogen defence and programmed cell death. Despite the vast number of RLKs present in plants, however, only a few of them have been functionally characterized. RESULTS We examined the transcriptional regulation of all Arabidopsis CRKs by ozone (O3), high light and pathogen/elicitor treatment - conditions known to induce the production of reactive oxygen species (ROS) in various subcellular compartments. Several CRKs were transcriptionally induced by exposure to O3 but not by light stress. O3 induces an extracellular oxidative burst, whilst light stress leads to ROS production in chloroplasts. Analysis of publicly available microarray data revealed that the transcriptional responses of the CRKs to O3 were very similar to responses to microbes or pathogen-associated molecular patterns (PAMPs). Several mutants altered in hormone biosynthesis or signalling showed changes in basal and O3-induced transcriptional responses. CONCLUSIONS Combining expression analysis from multiple treatments with mutants altered in hormone biosynthesis or signalling suggest a model in which O3 and salicylic acid (SA) activate separate signaling pathways that exhibit negative crosstalk. Although O3 is classified as an abiotic stress to plants, transcriptional profiling of CRKs showed strong similarities between the O3 and biotic stress responses.
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Affiliation(s)
- Michael Wrzaczek
- Plant Biology Division, Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Mikael Brosché
- Plant Biology Division, Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Jarkko Salojärvi
- Plant Biology Division, Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | | | - Niina Idänheimo
- Plant Biology Division, Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Sophia Mersmann
- Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, DE-50829 Cologne, Germany
| | - Silke Robatzek
- Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, DE-50829 Cologne, Germany
- The Sainsbury Laboratories, Norwich Research Park, Colney Lane, NR4 7UH, Norwich, UK
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding and Plant Biotechnology, Warsaw University of Life Sciences, Nowoursynowska st. 159, PL 02-776, Warsaw, Poland
| | - Barbara Karpińska
- Department of Life Sciences, Södertörn University College, SE-141 89 Huddinge, Sweden
| | - Jaakko Kangasjärvi
- Plant Biology Division, Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
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Beck J, Procopio I, Negrier S, Keilholz D, Sczylik C, Bokemeyer C, Strauss U, Burock K, Mersmann S, Escudier B. 7137 Final analysis of a large open-label, noncomparative, phase 3 study of sorafenib in European patients with advanced RCC (EU-ARCCS). EJC Suppl 2009. [DOI: 10.1016/s1359-6349(09)71470-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Göhre V, Spallek T, Häweker H, Mersmann S, Mentzel T, Boller T, de Torres M, Mansfield JW, Robatzek S. Plant pattern-recognition receptor FLS2 is directed for degradation by the bacterial ubiquitin ligase AvrPtoB. Curr Biol 2009; 18:1824-32. [PMID: 19062288 DOI: 10.1016/j.cub.2008.10.063] [Citation(s) in RCA: 298] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 10/24/2008] [Accepted: 10/28/2008] [Indexed: 01/09/2023]
Abstract
BACKGROUND An important layer of active defense in plant immunity is the detection of pathogen-associated molecular patterns (PAMPs) mediated by cell-surface receptors. For the establishment of disease, pathogens depend on the ability to overcome PAMP perception and disable plant signaling pathways activated in response to PAMPs. Pattern recognition receptors (PRRs) are therefore prime targets for pathogen effectors. FLS2, its coreceptor BAK1, and EFR encode receptor-like kinases that play a role in immunity against bacterial pathogens. RESULTS Here, we report that virulence of Pseudomonas syringae pv tomato DC3000 (PtoDC3000) in Arabidopsis is enhanced through the action of its effector AvrPtoB, which promotes degradation of FLS2. We show that AvrPtoB, through its N terminus, associates with FLS2 and BAK1, of which interaction with FLS2 is enhanced by flg22 activation. In vitro, AvrPtoB is active as an E3 ligase to catalyze polyubiquitination of the kinase domain of FLS2, a process confirmed in planta. Full enhancement of PtoDC3000 virulence appears to require the E3 ligase activity of AvrPtoB. CONCLUSIONS AvrPtoB, initially identified through its activation of hypersensitive resistance in tomato cultivars expressing the Pto kinase, is composed of at least two functional domains: the N terminus is responsible for interaction with Pto, and the C terminus carries an E3 ligase activity. Based on our findings, we propose that both domains of AvrPtoB act together to support the virulence of PtoDC3000 in Arabidopsis through their ability to eliminate FLS2 from the cell periphery, and probably also other PAMP sensors that are constitutively expressed or induced after pathogen challenge.
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Affiliation(s)
- Vera Göhre
- Max-Planck-Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Cologne, Germany
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Beck J, Procopio G, Verzoni E, Négrier S, Keilholz U, Szczylik C, Mersmann S, Burock K, Huber C, Escudier BJ. Large open-label, non-comparative, clinical experience trial of the multi-targeted kinase inhibitor sorafenib in European patients with advanced RCC. J Clin Oncol 2008. [DOI: 10.1200/jco.2008.26.15_suppl.16021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Beck J, Bajetta E, Escudier B, Negrier S, Keilholz U, Szczylik C, Mersmann S, Burock K, Erlandsson F, Huber C. 4506 ORAL A large open-label, non-comparative, phase III study of the multi-targeted kinase inhibitor sorafenib in European patients with advanced renal cell carcinoma. EJC Suppl 2007. [DOI: 10.1016/s1359-6349(07)71137-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Mross K, Steinbild S, Baas F, Reil M, Buss P, Mersmann S, Voliotis D, Schwartz B, Brendel E. Drug-drug interaction pharmacokinetic study with the Raf kinase inhibitor (RKI) BAY 43-9006 administered in combination with irinotecan (CPT-11) in patients with solid tumors. Int J Clin Pharmacol Ther 2003; 41:618-9. [PMID: 14692719 DOI: 10.5414/cpp41618] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- K Mross
- Tumor Biology Center, Albert-Ludwigs-University Freiburg, Germany.
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