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Jaeger-Honz S, Klein K, Schreiber F. Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data. J Cheminform 2024; 16:28. [PMID: 38475907 DOI: 10.1186/s13321-024-00822-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/02/2024] [Indexed: 03/14/2024] Open
Abstract
Computational methods such as molecular docking or molecular dynamics (MD) simulations have been developed to simulate and explore the interactions between biomolecules. However, the interactions obtained using these methods are difficult to analyse and evaluate. Interaction fingerprints (IFPs) have been proposed to derive interactions from static 3D coordinates and transform them into 1D bit vectors. More recently, the concept has been applied to derive IFPs from MD simulations, which adds a layer of complexity by adding the temporal motion and dynamics of a system. As a result, many IFPs are obtained from one MD simulation, resulting in a large number of individual IFPs that are difficult to analyse compared to IFPs derived from static 3D structures. Scientific contribution: We introduce a new method to systematically aggregate IFPs derived from MD simulation data. In addition, we propose visualisations to effectively analyse and compare IFPs derived from MD simulation data to account for the temporal evolution of interactions and to compare IFPs across different MD simulations. This has been implemented as a freely available Python library and can therefore be easily adopted by other researchers and to different MD simulation datasets.
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Affiliation(s)
- Sabrina Jaeger-Honz
- Department of Computer and Information Science, University of Konstanz, Universitätsstrasse 10, 78464, Constance, Germany.
| | - Karsten Klein
- Department of Computer and Information Science, University of Konstanz, Universitätsstrasse 10, 78464, Constance, Germany
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Universitätsstrasse 10, 78464, Constance, Germany
- Faculty of Information Technology, Monash University, Clayton, VIC, 3800, Australia
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Niarakis A, Ostaszewski M, Mazein A, Kuperstein I, Kutmon M, Gillespie ME, Funahashi A, Acencio ML, Hemedan A, Aichem M, Klein K, Czauderna T, Burtscher F, Yamada TG, Hiki Y, Hiroi NF, Hu F, Pham N, Ehrhart F, Willighagen EL, Valdeolivas A, Dugourd A, Messina F, Esteban-Medina M, Peña-Chilet M, Rian K, Soliman S, Aghamiri SS, Puniya BL, Naldi A, Helikar T, Singh V, Fernández MF, Bermudez V, Tsirvouli E, Montagud A, Noël V, Ponce-de-Leon M, Maier D, Bauch A, Gyori BM, Bachman JA, Luna A, Piñero J, Furlong LI, Balaur I, Rougny A, Jarosz Y, Overall RW, Phair R, Perfetto L, Matthews L, Rex DAB, Orlic-Milacic M, Gomez LCM, De Meulder B, Ravel JM, Jassal B, Satagopam V, Wu G, Golebiewski M, Gawron P, Calzone L, Beckmann JS, Evelo CT, D’Eustachio P, Schreiber F, Saez-Rodriguez J, Dopazo J, Kuiper M, Valencia A, Wolkenhauer O, Kitano H, Barillot E, Auffray C, Balling R, Schneider R. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Front Immunol 2024; 14:1282859. [PMID: 38414974 PMCID: PMC10897000 DOI: 10.3389/fimmu.2023.1282859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/22/2023] [Indexed: 02/29/2024] Open
Abstract
Introduction The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Methods Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors. Results Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. Discussion The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.
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Affiliation(s)
- Anna Niarakis
- Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alexander Mazein
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Inna Kuperstein
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Martina Kutmon
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
| | - Marc E. Gillespie
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- St. John’s University, Queens, NY, United States
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Marcio Luis Acencio
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ahmed Hemedan
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Michael Aichem
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Karsten Klein
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Tobias Czauderna
- Faculty of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Felicia Burtscher
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Takahiro G. Yamada
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Yusuke Hiki
- Center for Biosciences and Informatics, Graduate School of Fundamental Science and Technology, Keio University, Kanagawa, Japan
| | - Noriko F. Hiroi
- Faculty of Creative Engineering, Kanagawa Institute of Technology, Kanagawa, Japan
- Keio University School of Medicine, Tokyo, Japan
| | - Finterly Hu
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Nhung Pham
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Friederike Ehrhart
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Egon L. Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Alberto Valdeolivas
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Aurelien Dugourd
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Francesco Messina
- Department of Epidemiology, Preclinical Research and Advanced Diagnostic, National Institute for Infectious Diseases’ Lazzaro Spallanzani’ - IRCCS, Rome, Italy
| | - Marina Esteban-Medina
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain
| | - Maria Peña-Chilet
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Seville, Spain
| | - Kinza Rian
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
| | - Sylvain Soliman
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France
| | - Sara Sadat Aghamiri
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Bhanwar Lal Puniya
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Aurélien Naldi
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Vidisha Singh
- Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France
| | | | - Viviam Bermudez
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Eirini Tsirvouli
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arnau Montagud
- Barcelona Supercomputing Center (BSC.), Barcelona, Spain
| | - Vincent Noël
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | | | | | - Benjamin M. Gyori
- Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States
| | - John A. Bachman
- Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States
| | - Augustin Luna
- Computational Biology Branch, National Library of Medicine, Bethesda, MD, United States
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States
| | - Janet Piñero
- Medbioinformatics Solutions SL, Barcelona, Spain
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Laura I. Furlong
- Medbioinformatics Solutions SL, Barcelona, Spain
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Irina Balaur
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Adrien Rougny
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo, Japan
- Com. Bio Big Data Open Innovation Lab. (CBBD-OIL), AIST, Aomi, Tokyo, Japan
| | - Yohan Jarosz
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rupert W. Overall
- Institute for Biology, Humboldt University of Berlin, Berlin, Germany
| | - Robert Phair
- Integrative Bioinformatics, Inc., Mountain View, CA, United States
| | - Livia Perfetto
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Lisa Matthews
- Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States
| | | | | | - Luis Cristobal Monraz Gomez
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | - Jean Marie Ravel
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Bijay Jassal
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Venkata Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Guanming Wu
- Oregon Health Sciences University, Portland, OR, United States
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Piotr Gawron
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laurence Calzone
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | - Chris T. Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Peter D’Eustachio
- Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Faculty of Information Technology, Monash University, Clayton, Victoria, VIC, Australia
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Joaquin Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Seville, Spain
- FPS/ELIXIR-es, Hospital Virgen del Rocío, Sevilla, Spain
| | - Martin Kuiper
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC.), Barcelona, Spain
- I.C.R.E.A., Pg. Lluís Companys 23, Barcelona, Spain
| | - Olaf Wolkenhauer
- Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany
- Leibniz Institute for Food Systems Biology, at the Technical University Munich, Munich, Germany
| | | | - Emmanuel Barillot
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | - Rudi Balling
- Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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Staab S, Cardénas A, Peixoto RS, Schreiber F, Voolstra CR. Coracle-a machine learning framework to identify bacteria associated with continuous variables. Bioinformatics 2024; 40:btad749. [PMID: 38123508 PMCID: PMC10766586 DOI: 10.1093/bioinformatics/btad749] [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: 08/10/2023] [Revised: 11/06/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023] Open
Abstract
SUMMARY We present Coracle, an artificial intelligence (AI) framework that can identify associations between bacterial communities and continuous variables. Coracle uses an ensemble approach of prominent feature selection methods and machine learning (ML) models to identify features, i.e. bacteria, associated with a continuous variable, e.g. host thermal tolerance. The results are aggregated into a score that incorporates the performances of the different ML models and the respective feature importance, while also considering the robustness of feature selection. Additionally, regression coefficients provide first insights into the direction of the association. We show the utility of Coracle by analyzing associations between bacterial composition data (i.e. 16S rRNA Amplicon Sequence Variants, ASVs) and coral thermal tolerance (i.e. standardized short-term heat stress-derived diagnostics). This analysis identified high-scoring bacterial taxa that were previously found associated with coral thermal tolerance. Coracle scales with feature number and performs well with hundreds to thousands of features, corresponding to the typical size of current datasets. Coracle performs best if run at a higher taxonomic level first (e.g. order or family) to identify groups of interest that can subsequently be run at the ASV level. AVAILABILITY AND IMPLEMENTATION Coracle can be accessed via a dedicated web server that allows free and simple access: http://www.micportal.org/coracle/index. The underlying code is open-source and available via GitHub https://github.com/SebastianStaab/coracle.git.
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Affiliation(s)
- Sebastian Staab
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Anny Cardénas
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
- Department of Biology, American University, Washington, DC, 20016, USA
| | - Raquel S Peixoto
- Computational Biology Research Center (CBRC) and Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz 78457, Germany
- Faculty of Information Technology, Monash University, 3168, Australia
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Feyer SP, Pinaud B, Kobourov S, Brich N, Krone M, Kerren A, Behrisch M, Schreiber F, Klein K. 2D, 2.5D, or 3D? An Exploratory Study on Multilayer Network Visualisations in Virtual Reality. IEEE Trans Vis Comput Graph 2024; 30:469-479. [PMID: 37883262 DOI: 10.1109/tvcg.2023.3327402] [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] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Relational information between different types of entities is often modelled by a multilayer network (MLN) - a network with subnetworks represented by layers. The layers of an MLN can be arranged in different ways in a visual representation, however, the impact of the arrangement on the readability of the network is an open question. Therefore, we studied this impact for several commonly occurring tasks related to MLN analysis. Additionally, layer arrangements with a dimensionality beyond 2D, which are common in this scenario, motivate the use of stereoscopic displays. We ran a human subject study utilising a Virtual Reality headset to evaluate 2D, 2.5D, and 3D layer arrangements. The study employs six analysis tasks that cover the spectrum of an MLN task taxonomy, from path finding and pattern identification to comparisons between and across layers. We found no clear overall winner. However, we explore the task-to-arrangement space and derive empirical-based recommendations on the effective use of 2D, 2.5D, and 3D layer arrangements for MLNs.
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Landesberger V, Grenzebach K, Schreiber F, Nowak D, Gröger M, Oppel E, Schaub B, French LE, Kutzora S, Quartucci C, Herr C, Heinze S. Conception and pilot testing of a self-management health application for patients with pollen-related allergic rhinitis and allergic asthma-the APOLLO app. Sci Rep 2023; 13:21568. [PMID: 38057347 PMCID: PMC10700582 DOI: 10.1038/s41598-023-48540-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023] Open
Abstract
It has been shown that pollen information services are an important self-management tool for patients with pollen-related allergic rhinitis (AR) and allergic asthma (AA). This study aimed to design an online application for patients with AR and AA, which supports patients to better manage their disease as well as to evaluate the app and present the first results of the pilot study. The pollen data were obtained from the electronic pollen information network of Bavaria, Germany. Participants were asked to fill in their allergy-related complaints in the app over a 60-day period. Subsequently, the app was evaluated. Indices and diagrams visualized the participants' individual complaints as well as the daily pollen concentration in the air. In order to motivate participants to complete the app on a daily basis, we used elements of gamification. Two thirds of the participants (N = 46) reported feeling better informed about pollen counts and their allergy when using the app. The app's simple and comprehensible design was rated positively. More than 80% of the participants would recommend the app to their family and friends. The app can be a tool for patients with AR and AA to better understand their disease.
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Affiliation(s)
- V Landesberger
- Bavarian Health and Food Safety Authority, Munich/Oberschleißheim/Erlangen, Germany
| | - K Grenzebach
- Bavarian Health and Food Safety Authority, Munich/Oberschleißheim/Erlangen, Germany
| | - F Schreiber
- Bavarian Health and Food Safety Authority, Munich/Oberschleißheim/Erlangen, Germany
| | - D Nowak
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Pneumology Center (CPC) Munich, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - M Gröger
- Department of Otorhinolaryngology, University Hospital, LMU Munich, Munich, Germany
| | - E Oppel
- Department of Dermatology and Allergy, University Hospital, LMU Munich, Munich, Germany
| | - B Schaub
- LMU Munich, University Children's Hospital, Munich, Germany
- Member of the German Center of Lung Research (DZL), Munich, Germany
| | - L E French
- Department of Dermatology and Allergy, University Hospital, LMU Munich, Munich, Germany
| | - S Kutzora
- Bavarian Health and Food Safety Authority, Munich/Oberschleißheim/Erlangen, Germany.
| | - C Quartucci
- Bavarian Health and Food Safety Authority, Munich/Oberschleißheim/Erlangen, Germany
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Pneumology Center (CPC) Munich, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - C Herr
- Bavarian Health and Food Safety Authority, Munich/Oberschleißheim/Erlangen, Germany
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Pneumology Center (CPC) Munich, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - S Heinze
- Bavarian Health and Food Safety Authority, Munich/Oberschleißheim/Erlangen, Germany
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Pneumology Center (CPC) Munich, Member of the German Center of Lung Research (DZL), Munich, Germany
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Zhang Y, Klein K, Schreiber F, Safi K. Beyond the horizon: immersive developments for animal ecology research. Vis Comput Ind Biomed Art 2023; 6:11. [PMID: 37338732 DOI: 10.1186/s42492-023-00138-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/19/2023] [Indexed: 06/21/2023] Open
Abstract
More diverse data on animal ecology are now available. This "data deluge" presents challenges for both biologists and computer scientists; however, it also creates opportunities to improve analysis and answer more holistic research questions. We aim to increase awareness of the current opportunity for interdisciplinary research between animal ecology researchers and computer scientists. Immersive analytics (IA) is an emerging research field in which investigations are performed into how immersive technologies, such as large display walls and virtual reality and augmented reality devices, can be used to improve data analysis, outcomes, and communication. These investigations have the potential to reduce the analysis effort and widen the range of questions that can be addressed. We propose that biologists and computer scientists combine their efforts to lay the foundation for IA in animal ecology research. We discuss the potential and the challenges and outline a path toward a structured approach. We imagine that a joint effort would combine the strengths and expertise of both communities, leading to a well-defined research agenda and design space, practical guidelines, robust and reusable software frameworks, reduced analysis effort, and better comparability of results.
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Affiliation(s)
- Ying Zhang
- Department of Computer and Information Science, University of Konstanz, Konstanz, 78464, Germany.
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, 78315, Germany.
| | - Karsten Klein
- Department of Computer and Information Science, University of Konstanz, Konstanz, 78464, Germany
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, 78464, Germany
- Faculty of Information Technologies, Monash University, Melbourne, VIC, 3145, Australia
| | - Kamran Safi
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, 78315, Germany
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König M, Gleeson P, Golebiewski M, Gorochowski TE, Hucka M, Keating SM, Myers CJ, Nickerson DP, Sommer B, Waltemath D, Schreiber F. Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022. J Integr Bioinform 2023; 20:jib-2023-0004. [PMID: 36989443 PMCID: PMC10063176 DOI: 10.1515/jib-2023-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2022 special issue presents three updates to the standards: CellML 2.0.1, SBML Level 3 Package: Spatial Processes, Version 1, Release 1, and Synthetic Biology Open Language (SBOL) Version 3.1.0. This document can also be used to identify the latest specifications for all COMBINE standards. In addition, this editorial provides a brief overview of the COMBINE 2022 meeting in Berlin.
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Affiliation(s)
- Matthias König
- Institute for Biology, Institute for Theoretical Biology, Humboldt-University Berlin, Berlin, Germany
| | | | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | | | | | | | - Chris J Myers
- Department of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, Boulder, USA
| | - David P Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | | | - Dagmar Waltemath
- Medical Informatics Laboratory, University Medicine Greifswald, Greifswald, Germany
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Faculty of Information Technology, Monash University, Clayton, Australia
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Kern M, Jaeger-Honz S, Schreiber F, Sommer B. APL@voro-interactive visualization and analysis of cell membrane simulations. Bioinformatics 2023; 39:7031239. [PMID: 36752505 PMCID: PMC9969824 DOI: 10.1093/bioinformatics/btad083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/11/2022] [Accepted: 02/07/2023] [Indexed: 02/09/2023] Open
Abstract
SUMMARY Molecular dynamics (MD) simulations of cell membranes allow for a better understanding of complex processes such as changing membrane dynamics, lipid rafts and the incorporation/passing of macromolecules into/through membranes. To explore and understand cell membrane compositions, dynamics and processes, visual analytics can help to interpret MD simulation data. APL@Voro is a software for the interactive visualization and analysis of cell membrane simulations. Here, we present the new APL@Voro, which has been continuously developed since its initial release in 2013. We discuss newly implemented algorithms, methodologies and features, such as the interactive comparison of related simulations and methods to assign lipids to either the upper or lower leaflet. AVAILABILITY AND IMPLEMENTATION The current open-source version of APL@Voro can be downloaded from http://aplvoro.com.
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Affiliation(s)
- Martin Kern
- Department of Computer and Information Science, University of Konstanz, Konstanz 76484, Germany
| | - Sabrina Jaeger-Honz
- Department of Computer and Information Science, University of Konstanz, Konstanz 76484, Germany
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz 76484, Germany.,Faculty of Information Technology, Monash University, Clayton, VIC 3800, Australia
| | - Bjorn Sommer
- Royal College of Art, School of Design, London SW7 2EU, UK
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9
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Aichem M, Klein K, Czauderna T, Garkov D, Zhao J, Li J, Schreiber F. Towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual reality. J Integr Bioinform 2022; 19:jib-2022-0034. [PMID: 36215728 PMCID: PMC9800044 DOI: 10.1515/jib-2022-0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/06/2022] [Indexed: 01/09/2023] Open
Abstract
Biomolecular networks, including genome-scale metabolic models (GSMMs), assemble the knowledge regarding the biological processes that happen inside specific organisms in a way that allows for analysis, simulation, and exploration. With the increasing availability of genome annotations and the development of powerful reconstruction tools, biomolecular networks continue to grow ever larger. While visual exploration can facilitate the understanding of such networks, the network sizes represent a major challenge for current visualisation systems. Building on promising results from the area of immersive analytics, which among others deals with the potential of immersive visualisation for data analysis, we present a concept for a hybrid user interface that combines a classical desktop environment with a virtual reality environment for the visual exploration of large biomolecular networks and corresponding data. We present system requirements and design considerations, describe a resulting concept, an envisioned technical realisation, and a systems biology usage scenario. Finally, we discuss remaining challenges.
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Affiliation(s)
- Michael Aichem
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Karsten Klein
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Tobias Czauderna
- Faculty of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Dimitar Garkov
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Jinxin Zhao
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Jian Li
- Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Faculty of Information Technology, Monash University, Melbourne, Australia
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10
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Joos L, Jaeger-Honz S, Schreiber F, Keim DA, Klein K. Visual Comparison of Networks in VR. IEEE Trans Vis Comput Graph 2022; 28:3651-3661. [PMID: 36048995 DOI: 10.1109/tvcg.2022.3203001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Networks are an important means for the representation and analysis of data in a variety of research and application areas. While there are many efficient methods to create layouts for networks to support their visual analysis, approaches for the comparison of networks are still underexplored. Especially when it comes to the comparison of weighted networks, which is an important task in several areas, such as biology and biomedicine, there is a lack of efficient visualization approaches. With the availability of affordable high-quality virtual reality (VR) devices, such as head-mounted displays (HMDs), the research field of immersive analytics emerged and showed great potential for using the new technology for visual data exploration. However, the use of immersive technology for the comparison of networks is still underexplored. With this work, we explore how weighted networks can be visually compared in an immersive VR environment and investigate how visual representations can benefit from the extended 3D design space. For this purpose, we develop different encodings for 3D node-link diagrams supporting the visualization of two networks within a single representation and evaluate them in a pilot user study. We incorporate the results into a more extensive user study comparing node-link representations with matrix representations encoding two networks simultaneously. The data and tasks designed for our experiments are similar to those occurring in real-world scenarios. Our evaluation shows significantly better results for the node-link representations, which is contrary to comparable 2D experiments and indicates a high potential for using VR for the visual comparison of networks.
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11
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Jiang X, Han M, Tran K, Patil NA, Ma W, Roberts KD, Xiao M, Sommer B, Schreiber F, Wang L, Velkov T, Li J. An Intelligent Strategy with All-Atom Molecular Dynamics Simulations for the Design of Lipopeptides against Multidrug-Resistant Pseudomonas aeruginosa. J Med Chem 2022; 65:10001-10013. [PMID: 35786900 DOI: 10.1021/acs.jmedchem.2c00657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Multidrug-resistant Gram-negative bacteria seriously threaten modern medicine due to the lack of efficacious therapeutic options. Their outer membrane (OM) is an essential protective fortress to exclude many antibiotics. Unfortunately, current structural biology methods are not able to resolve the membrane structure and it is difficult to examine the specific interaction between the OM and small molecules. These limitations hinder mechanistic understanding of antibiotic penetration through the OM and antibiotic discovery. Here, we developed biologically relevant OM models by quantitatively determining membrane lipidomics of Pseudomonas aeruginosa and elucidated how lipopolysaccharide modifications and OM vesicles mediated resistance to polymyxins. Supported by chemical biology and pharmacological assays, our multiscale molecular dynamics simulations provide an intelligent platform to quantify the membrane-penetrating thermodynamics of peptides and predict their antimicrobial activity. Through experimental validations with our in-house polymyxin analogue library, our computational strategy may have significant potential in accelerating the discovery of lipopeptides against bacterial "superbugs".
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Affiliation(s)
- Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Meiling Han
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Kevin Tran
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Nitin A Patil
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Wendong Ma
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Kade D Roberts
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Min Xiao
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Bjorn Sommer
- Department of Computer and Information Science, University of Konstanz, Konstanz 78457, Germany
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz 78457, Germany
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Tony Velkov
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne 3010, Australia
| | - Jian Li
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
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12
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Schreiber F, Czauderna T. Design considerations for representing systems biology information with the Systems Biology Graphical Notation. J Integr Bioinform 2022; 19:jib-2022-0024. [PMID: 35786424 PMCID: PMC9377698 DOI: 10.1515/jib-2022-0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022] Open
Abstract
Visual representations are commonly used to explore, analyse, and communicate information and knowledge in systems biology and beyond. Such visualisations not only need to be accurate but should also be aesthetically pleasing and informative. Using the example of the Systems Biology Graphical Notation (SBGN) we will investigate design considerations for graphically presenting information from systems biology, in particular regarding the use of glyphs for types of information, the style of graph layout for network representation, and the concept of bricks for visual network creation.
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Affiliation(s)
- Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.,Faculty of Information Technology, Monash University, Clayton, Australia
| | - Tobias Czauderna
- Faculty of Information Technology, Monash University, Clayton, Australia.,Faculty of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
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13
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Niarakis A, Waltemath D, Glazier J, Schreiber F, Keating SM, Nickerson D, Chaouiya C, Siegel A, Noël V, Hermjakob H, Helikar T, Soliman S, Calzone L. Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. Brief Bioinform 2022; 23:6603929. [PMID: 35671510 PMCID: PMC9294410 DOI: 10.1093/bib/bbac212] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/20/2022] [Accepted: 05/06/2022] [Indexed: 11/14/2022] Open
Abstract
Computational models are often employed in systems biology to study the dynamic behaviours of complex systems. With the rise in the number of computational models, finding ways to improve the reusability of these models and their ability to reproduce virtual experiments becomes critical. Correct and effective model annotation in community-supported and standardised formats is necessary for this improvement. Here, we present recent efforts toward a common framework for annotated, accessible, reproducible and interoperable computational models in biology, and discuss key challenges of the field.
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Affiliation(s)
- Anna Niarakis
- Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France.,Lifeware Group, Inria, Saclay-île de France, 91120 Palaiseau, France
| | - Dagmar Waltemath
- Department of Medical Informatics, University Medicine Greifswald, Greifswald, Germany
| | - James Glazier
- Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.,Faculty of Information Technology, Monash University, Clayton, Australia
| | | | - David Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | | | - Anne Siegel
- Univ Rennes, CNRS, Inria - IRISA lab. Rennes
| | - Vincent Noël
- Institut Curie, PSL Research University, Paris, France.,INSERM, U900, Paris, France.,MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Henning Hermjakob
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Sylvain Soliman
- Lifeware Group, Inria, Saclay-île de France, 91120 Palaiseau, France
| | - Laurence Calzone
- Institut Curie, PSL Research University, Paris, France.,INSERM, U900, Paris, France.,MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
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14
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Pfister M, Frantsev R, Schreiber F, Garz C, Perosa V, Assmann A, Düzel E, Butryn M, Glanz W, Vielhaber S, Schreiber S, John A. P 25 CSF biomarkers in CAA compared to AD. Clin Neurophysiol 2022. [DOI: 10.1016/j.clinph.2022.01.056] [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: 11/03/2022]
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15
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Empting E, Klopotek M, Hinderhofer A, Schreiber F, Oettel M. Erratum: Lattice gas study of thin-film growth scenarios and transitions between them: Role of substrate [Phys. Rev. E 103, 023302 (2021)]. Phys Rev E 2022; 105:049901. [PMID: 35590687 DOI: 10.1103/physreve.105.049901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 06/15/2023]
Abstract
This corrects the article DOI: 10.1103/PhysRevE.103.023302.
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16
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Bienroth D, Nim HT, Garkov D, Klein K, Jaeger-Honz S, Ramialison M, Schreiber F. Spatially resolved transcriptomics in immersive environments. Vis Comput Ind Biomed Art 2022; 5:2. [PMID: 35001220 PMCID: PMC8743310 DOI: 10.1186/s42492-021-00098-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/24/2021] [Indexed: 12/13/2022] Open
Abstract
Spatially resolved transcriptomics is an emerging class of high-throughput technologies that enable biologists to systematically investigate the expression of genes along with spatial information. Upon data acquisition, one major hurdle is the subsequent interpretation and visualization of the datasets acquired. To address this challenge, VR-Cardiomics is presented, which is a novel data visualization system with interactive functionalities designed to help biologists interpret spatially resolved transcriptomic datasets. By implementing the system in two separate immersive environments, fish tank virtual reality (FTVR) and head-mounted display virtual reality (HMD-VR), biologists can interact with the data in novel ways not previously possible, such as visually exploring the gene expression patterns of an organ, and comparing genes based on their 3D expression profiles. Further, a biologist-driven use-case is presented, in which immersive environments facilitate biologists to explore and compare the heart expression profiles of different genes.
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Affiliation(s)
- Denis Bienroth
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.,Cell Biology, Murdoch Children's Research Institute, Parkville, Melbourne, VIC, Australia
| | - Hieu T Nim
- Cell Biology, Murdoch Children's Research Institute, Parkville, Melbourne, VIC, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Melbourne, VIC, Australia.,Systems Biology Institute Australia, Clayton, Melbourne, VIC, Australia
| | - Dimitar Garkov
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Karsten Klein
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Sabrina Jaeger-Honz
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Mirana Ramialison
- Cell Biology, Murdoch Children's Research Institute, Parkville, Melbourne, VIC, Australia. .,Australian Regenerative Medicine Institute, Monash University, Clayton, Melbourne, VIC, Australia. .,Systems Biology Institute Australia, Clayton, Melbourne, VIC, Australia.
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany. .,Faculty of Information Technologies, Monash University, Melbourne, Australia.
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17
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Jaeger-Honz S, Nitschke J, Altaner S, Klein K, Dietrich DR, Schreiber F. Investigation of microcystin conformation and binding towards PPP1 by molecular dynamics simulation. Chem Biol Interact 2022; 351:109766. [PMID: 34861245 DOI: 10.1016/j.cbi.2021.109766] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 11/30/2022]
Abstract
Microcystins (MC) are a group of structurally similar cyanotoxins with currently 279 described structural variants. Human exposure is frequent by consumption of contaminated water, food or food supplements. MC can result in serious intoxications, commensurate with ensuing pathology in various organs or in rare cases even mortality. The current WHO risk assessment primarily considers MC-LR, while all other structural variants are treated as equivalent to MC-LR, despite that current data strongly suggest that MC-LR is not the most toxic MC, and toxicity can be very different for MC congeners. To investigate and analyse binding and conformation of different MC congeners, we applied for the first time Molecular Dynamics (MD) simulation to four MC congeners (MC-LR, MC-LF, [Enantio-Adda5]MC-LF, [β-D-Asp3,Dhb7]MC-RR). We could show that ser/thr protein phosphatase 1 is stable in all MD simulations and that MC-LR backbone adopts to a second conformation in solvent MD simulation, which was previously unknown. We could also show that MC congeners can adopt to different backbone conformation when simulated in solvent or in complex with ser/thr protein phosphatase 1 and differ in their binding behaviour. Our findings suggest that MD Simulation of different MC congeners aid in understanding structural differences and binding of this group of structurally similar cyanotoxins.
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Affiliation(s)
- Sabrina Jaeger-Honz
- Department of Computer and Information Science, University of Konstanz, Germany
| | - Jahn Nitschke
- Department of Biology, University of Konstanz, Germany
| | | | - Karsten Klein
- Department of Computer and Information Science, University of Konstanz, Germany
| | | | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Germany; Faculty of Information Technology, Monash University, Australia.
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18
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Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff-Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Willighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R. COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol 2021; 17:e10851. [PMID: 34939300 PMCID: PMC8696085 DOI: 10.15252/msb.202110851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/19/2022] Open
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19
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Klein K, Garkov D, Rütschlin S, Böttcher T, Schreiber F. Corrigendum to: QSDB—a graphical Quorum Sensing Database. Database (Oxford) 2021; 2021:6444194. [PMID: 34849665 PMCID: PMC8641760 DOI: 10.1093/database/baab071] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Karsten Klein
- Department of Information and Computer Science, University of Konstanz, Universitätsstraße 10, Konstanz, Baden-Württemberg 78464, Germany
| | - Dimitar Garkov
- Department of Information and Computer Science, University of Konstanz, Universitätsstraße 10, Konstanz, Baden-Württemberg 78464, Germany
| | - Sina Rütschlin
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, Universitätsstraße 10, Konstanz, Baden-Württemberg 78464, Germany
| | - Thomas Böttcher
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, Universitätsstraße 10, Konstanz, Baden-Württemberg 78464, Germany
- Institute of Biological Chemistry and Centre for Microbiology and Environmental Systems Science, University of Vienna, UZAII, Althanstraße 14, Vienna 1090, Austria
| | - Falk Schreiber
- Department of Information and Computer Science, University of Konstanz, Universitätsstraße 10, Konstanz, Baden-Württemberg 78464, Germany
- Department of Information Technology, Monash University, 20 Research Way, Melbourne, VIC 3800, Australia
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20
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Schreiber F, Gleeson P, Golebiewski M, Gorochowski TE, Hucka M, Keating SM, König M, Myers CJ, Nickerson DP, Sommer B, Waltemath D. Specifications of standards in systems and synthetic biology: status and developments in 2021. J Integr Bioinform 2021; 18:jib-2021-0026. [PMID: 34674411 PMCID: PMC8573232 DOI: 10.1515/jib-2021-0026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2021 special issue presents four updates of standards: Synthetic Biology Open Language Visual Version 2.3, Synthetic Biology Open Language Visual Version 3.0, Simulation Experiment Description Markup Language Level 1 Version 4, and OMEX Metadata specification Version 1.2. This document can also be consulted to identify the latest specifications of all COMBINE standards.
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Affiliation(s)
- Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Faculty of Information Technology, Monash University, Clayton, Australia
| | | | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | | | | | | | - Matthias König
- Institute for Theoretical Biology, Humboldt-University Berlin, Berlin, Germany
| | - Chris J. Myers
- Department of Electrical, Computer, and Energy Eng., University of Colorado Boulder, Boulder, USA
| | - David P. Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
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21
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Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta‐Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic‐Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel J, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban‐Medina M, Peña‐Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez‐Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol 2021; 17:e10387. [PMID: 34664389 PMCID: PMC8524328 DOI: 10.15252/msb.202110387] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022] Open
Abstract
We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.
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Affiliation(s)
- Marek Ostaszewski
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Anna Niarakis
- Université Paris‐SaclayLaboratoire Européen de Recherche pour la Polyarthrite rhumatoïde ‐ GenhotelUniv EvryEvryFrance
- Lifeware GroupInria Saclay‐Ile de FrancePalaiseauFrance
| | - Alexander Mazein
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Inna Kuperstein
- Institut CuriePSL Research UniversityParisFrance
- INSERMParisFrance
- MINES ParisTechPSL Research UniversityParisFrance
| | - Robert Phair
- Integrative Bioinformatics, Inc.Mountain ViewCAUSA
| | - Aurelio Orta‐Resendiz
- Institut PasteurUniversité de Paris, Unité HIVInflammation et PersistanceParisFrance
- Bio Sorbonne Paris CitéUniversité de ParisParisFrance
| | - Vidisha Singh
- Université Paris‐SaclayLaboratoire Européen de Recherche pour la Polyarthrite rhumatoïde ‐ GenhotelUniv EvryEvryFrance
| | - Sara Sadat Aghamiri
- Inserm‐ Institut national de la santé et de la recherche médicaleParisFrance
| | - Marcio Luis Acencio
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Andreas Ruepp
- Institute of Experimental Genetics (IEG)Helmholtz Zentrum München‐German Research Center for Environmental Health (GmbH)NeuherbergGermany
| | - Gisela Fobo
- Institute of Experimental Genetics (IEG)Helmholtz Zentrum München‐German Research Center for Environmental Health (GmbH)NeuherbergGermany
| | - Corinna Montrone
- Institute of Experimental Genetics (IEG)Helmholtz Zentrum München‐German Research Center for Environmental Health (GmbH)NeuherbergGermany
| | - Barbara Brauner
- Institute of Experimental Genetics (IEG)Helmholtz Zentrum München‐German Research Center for Environmental Health (GmbH)NeuherbergGermany
| | - Goar Frishman
- Institute of Experimental Genetics (IEG)Helmholtz Zentrum München‐German Research Center for Environmental Health (GmbH)NeuherbergGermany
| | - Luis Cristóbal Monraz Gómez
- Institut CuriePSL Research UniversityParisFrance
- INSERMParisFrance
- MINES ParisTechPSL Research UniversityParisFrance
| | - Julia Somers
- Department of Molecular and Medical GeneticsOregon Health & Sciences UniversityPortlandORUSA
| | - Matti Hoch
- Department of Systems Biology and BioinformaticsUniversity of RostockRostockGermany
| | | | - Julia Scheel
- Department of Systems Biology and BioinformaticsUniversity of RostockRostockGermany
| | - Hanna Borlinghaus
- Department of Computer and Information ScienceUniversity of KonstanzKonstanzGermany
| | - Tobias Czauderna
- Faculty of Information TechnologyDepartment of Human‐Centred ComputingMonash UniversityClaytonVic.Australia
| | - Falk Schreiber
- Department of Computer and Information ScienceUniversity of KonstanzKonstanzGermany
- Faculty of Information TechnologyDepartment of Human‐Centred ComputingMonash UniversityClaytonVic.Australia
| | | | | | - Akira Funahashi
- Department of Biosciences and InformaticsKeio UniversityYokohamaJapan
| | - Yusuke Hiki
- Department of Biosciences and InformaticsKeio UniversityYokohamaJapan
| | - Noriko Hiroi
- Graduate School of Media and GovernanceResearch Institute at SFCKeio UniversityKanagawaJapan
| | - Takahiro G Yamada
- Department of Biosciences and InformaticsKeio UniversityYokohamaJapan
| | - Andreas Dräger
- Computational Systems Biology of Infections and Antimicrobial‐Resistant PathogensInstitute for Bioinformatics and Medical Informatics (IBMI)University of TübingenTübingenGermany
- Department of Computer ScienceUniversity of TübingenTübingenGermany
- German Center for Infection Research (DZIF), partner siteTübingenGermany
| | - Alina Renz
- Computational Systems Biology of Infections and Antimicrobial‐Resistant PathogensInstitute for Bioinformatics and Medical Informatics (IBMI)University of TübingenTübingenGermany
- Department of Computer ScienceUniversity of TübingenTübingenGermany
| | - Muhammad Naveez
- Department of Systems Biology and BioinformaticsUniversity of RostockRostockGermany
- Institute of Applied Computer SystemsRiga Technical UniversityRigaLatvia
| | - Zsolt Bocskei
- Sanofi R&DTranslational SciencesChilly‐MazarinFrance
| | - Francesco Messina
- Dipartimento di Epidemiologia Ricerca Pre‐Clinica e Diagnostica AvanzataNational Institute for Infectious Diseases 'Lazzaro Spallanzani' I.R.C.C.S.RomeItaly
- COVID‐19 INMI Network Medicine for IDs Study GroupNational Institute for Infectious Diseases 'Lazzaro Spallanzani' I.R.C.C.SRomeItaly
| | - Daniela Börnigen
- Bioinformatics Core FacilityUniversitätsklinikum Hamburg‐EppendorfHamburgGermany
| | - Liam Fergusson
- Royal (Dick) School of Veterinary MedicineThe University of EdinburghEdinburghUK
| | - Marta Conti
- Faculty of Mathematics and Natural SciencesUniversity of BonnBonnGermany
| | - Marius Rameil
- Faculty of Mathematics and Natural SciencesUniversity of BonnBonnGermany
| | - Vanessa Nakonecnij
- Faculty of Mathematics and Natural SciencesUniversity of BonnBonnGermany
| | - Jakob Vanhoefer
- Faculty of Mathematics and Natural SciencesUniversity of BonnBonnGermany
| | - Leonard Schmiester
- Faculty of Mathematics and Natural SciencesUniversity of BonnBonnGermany
- Center for MathematicsChair of Mathematical Modeling of Biological SystemsTechnische Universität MünchenGarchingGermany
| | - Muying Wang
- Department of Chemical and Petroleum EngineeringUniversity of PittsburghPittsburghPAUSA
| | - Emily E Ackerman
- Department of Chemical and Petroleum EngineeringUniversity of PittsburghPittsburghPAUSA
| | - Jason E Shoemaker
- Department of Chemical and Petroleum EngineeringUniversity of PittsburghPittsburghPAUSA
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghPAUSA
| | | | | | | | | | | | - Kristina Hanspers
- Institute of Data Science and BiotechnologyGladstone InstitutesSan FranciscoCAUSA
| | - Martina Kutmon
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
- Maastricht Centre for Systems Biology (MaCSBio)Maastricht UniversityMaastrichtThe Netherlands
| | - Susan Coort
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
| | - Lars Eijssen
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
- Maastricht University Medical CentreMaastrichtThe Netherlands
| | - Friederike Ehrhart
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
- Maastricht University Medical CentreMaastrichtThe Netherlands
| | | | - Denise Slenter
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
| | - Marvin Martens
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
| | - Nhung Pham
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
| | - Robin Haw
- MaRS CentreOntario Institute for Cancer ResearchTorontoONCanada
| | - Bijay Jassal
- MaRS CentreOntario Institute for Cancer ResearchTorontoONCanada
| | | | | | - Andrea Senff Ribeiro
- MaRS CentreOntario Institute for Cancer ResearchTorontoONCanada
- Universidade Federal do ParanáCuritibaBrasil
| | - Karen Rothfels
- MaRS CentreOntario Institute for Cancer ResearchTorontoONCanada
| | | | - Ralf Stephan
- MaRS CentreOntario Institute for Cancer ResearchTorontoONCanada
| | - Cristoffer Sevilla
- European Bioinformatics Institute (EMBL‐EBI)European Molecular Biology LaboratoryHinxton, CambridgeshireUK
| | - Thawfeek Varusai
- European Bioinformatics Institute (EMBL‐EBI)European Molecular Biology LaboratoryHinxton, CambridgeshireUK
| | - Jean‐Marie Ravel
- INSERM UMR_S 1256Nutrition, Genetics, and Environmental Risk Exposure (NGERE)Faculty of Medicine of NancyUniversity of LorraineNancyFrance
- Laboratoire de génétique médicaleCHRU NancyNancyFrance
| | - Rupsha Fraser
- Queen's Medical Research InstituteThe University of EdinburghEdinburghUK
| | - Vera Ortseifen
- Senior Research Group in Genome Research of Industrial MicroorganismsCenter for BiotechnologyBielefeld UniversityBielefeldGermany
| | - Silvia Marchesi
- Department of Surgical ScienceUppsala UniversityUppsalaSweden
| | - Piotr Gawron
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
- Institute of Computing SciencePoznan University of TechnologyPoznanPoland
| | - Ewa Smula
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Laurent Heirendt
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Venkata Satagopam
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Guanming Wu
- Department of Medical Informatics and Clinical EpidemiologyOregon Health & Science UniversityPortlandORUSA
| | - Anders Riutta
- Institute of Data Science and BiotechnologyGladstone InstitutesSan FranciscoCAUSA
| | | | - Stuart Owen
- Department of Computer ScienceThe University of ManchesterManchesterUK
| | - Carole Goble
- Department of Computer ScienceThe University of ManchesterManchesterUK
| | - Xiaoming Hu
- Heidelberg Institute for Theoretical Studies (HITS)HeidelbergGermany
| | - Rupert W Overall
- German Center for Neurodegenerative Diseases (DZNE) DresdenDresdenGermany
- Center for Regenerative Therapies Dresden (CRTD)Technische Universität DresdenDresdenGermany
- Institute for BiologyHumboldt University of BerlinBerlinGermany
| | | | | | - Benjamin M Gyori
- Harvard Medical SchoolLaboratory of Systems PharmacologyBostonMAUSA
| | - John A Bachman
- Harvard Medical SchoolLaboratory of Systems PharmacologyBostonMAUSA
| | - Carlos Vega
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Valentin Grouès
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | | | - Pablo Porras
- European Bioinformatics Institute (EMBL‐EBI)European Molecular Biology LaboratoryHinxton, CambridgeshireUK
| | - Luana Licata
- Department of BiologyUniversity of Rome Tor VergataRomeItaly
| | | | - Francesca Sacco
- Department of BiologyUniversity of Rome Tor VergataRomeItaly
| | | | | | | | - Denes Turei
- Institute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Augustin Luna
- cBio Center, Divisions of Biostatistics and Computational BiologyDepartment of Data SciencesDana‐Farber Cancer InstituteBostonMAUSA
- Department of Cell BiologyHarvard Medical SchoolBostonMAUSA
| | - Ozgun Babur
- Computer Science DepartmentUniversity of Massachusetts BostonBostonMAUSA
| | | | - Alberto Valdeolivas
- Institute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Marina Esteban‐Medina
- Clinical Bioinformatics AreaFundación Progreso y Salud (FPS)Hospital Virgen del RocioSevillaSpain
- Computational Systems Medicine GroupInstitute of Biomedicine of Seville (IBIS)Hospital Virgen del RocioSevillaSpain
| | - Maria Peña‐Chilet
- Clinical Bioinformatics AreaFundación Progreso y Salud (FPS)Hospital Virgen del RocioSevillaSpain
- Computational Systems Medicine GroupInstitute of Biomedicine of Seville (IBIS)Hospital Virgen del RocioSevillaSpain
- Bioinformatics in Rare Diseases (BiER)Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)FPS, Hospital Virgen del RocíoSevillaSpain
| | - Kinza Rian
- Clinical Bioinformatics AreaFundación Progreso y Salud (FPS)Hospital Virgen del RocioSevillaSpain
- Computational Systems Medicine GroupInstitute of Biomedicine of Seville (IBIS)Hospital Virgen del RocioSevillaSpain
| | - Tomáš Helikar
- Department of BiochemistryUniversity of Nebraska‐LincolnLincolnNEUSA
| | | | - Dezso Modos
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | - Agatha Treveil
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | - Marton Olbei
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | | | - Stephane Ballereau
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
| | - Aurélien Dugourd
- Institute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
- Institute of Experimental Medicine and Systems BiologyFaculty of Medicine, RWTHAachen UniversityAachenGermany
| | | | - Vincent Noël
- Institut CuriePSL Research UniversityParisFrance
- INSERMParisFrance
- MINES ParisTechPSL Research UniversityParisFrance
| | - Laurence Calzone
- Institut CuriePSL Research UniversityParisFrance
- INSERMParisFrance
- MINES ParisTechPSL Research UniversityParisFrance
| | - Chris Sander
- cBio Center, Divisions of Biostatistics and Computational BiologyDepartment of Data SciencesDana‐Farber Cancer InstituteBostonMAUSA
- Department of Cell BiologyHarvard Medical SchoolBostonMAUSA
| | - Emek Demir
- Department of Molecular and Medical GeneticsOregon Health & Sciences UniversityPortlandORUSA
| | | | - Tom C Freeman
- The Roslin InstituteUniversity of EdinburghEdinburghUK
| | - Franck Augé
- Sanofi R&DTranslational SciencesChilly‐MazarinFrance
| | | | - Jan Hasenauer
- Helmholtz Zentrum München – German Research Center for Environmental HealthInstitute of Computational BiologyNeuherbergGermany
- Interdisciplinary Research Unit Mathematics and Life SciencesUniversity of BonnBonnGermany
| | - Olaf Wolkenhauer
- Department of Systems Biology and BioinformaticsUniversity of RostockRostockGermany
| | - Egon L Wilighagen
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
| | - Alexander R Pico
- Institute of Data Science and BiotechnologyGladstone InstitutesSan FranciscoCAUSA
| | - Chris T Evelo
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
- Maastricht Centre for Systems Biology (MaCSBio)Maastricht UniversityMaastrichtThe Netherlands
| | - Marc E Gillespie
- MaRS CentreOntario Institute for Cancer ResearchTorontoONCanada
- St. John’s University College of Pharmacy and Health SciencesQueensNYUSA
| | - Lincoln D Stein
- MaRS CentreOntario Institute for Cancer ResearchTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Henning Hermjakob
- European Bioinformatics Institute (EMBL‐EBI)European Molecular Biology LaboratoryHinxton, CambridgeshireUK
| | | | | | - Joaquin Dopazo
- Clinical Bioinformatics AreaFundación Progreso y Salud (FPS)Hospital Virgen del RocioSevillaSpain
- Computational Systems Medicine GroupInstitute of Biomedicine of Seville (IBIS)Hospital Virgen del RocioSevillaSpain
- Bioinformatics in Rare Diseases (BiER)Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)FPS, Hospital Virgen del RocíoSevillaSpain
- FPS/ELIXIR‐esHospital Virgen del RocíoSevillaSpain
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC)BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| | - Hiroaki Kitano
- Systems Biology InstituteTokyoJapan
- Okinawa Institute of Science and Technology Graduate SchoolOkinawaJapan
| | - Emmanuel Barillot
- Institut CuriePSL Research UniversityParisFrance
- INSERMParisFrance
- MINES ParisTechPSL Research UniversityParisFrance
| | - Charles Auffray
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
| | - Rudi Balling
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Reinhard Schneider
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
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22
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Klein K, Garkov D, Rütschlin S, Böttcher T, Schreiber F. QSDB-a graphical Quorum Sensing Database. Database (Oxford) 2021; 2021:6375033. [PMID: 34559210 PMCID: PMC8604260 DOI: 10.1093/database/baab058] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 08/13/2021] [Accepted: 09/10/2021] [Indexed: 01/08/2023]
Abstract
The human microbiome is largely shaped by the chemical interactions of its microbial members, which includes cross-talk via shared signals or quenching of the signalling of other species. Quorum sensing is a process that allows microbes to coordinate their behaviour in dependence of their population density and to adjust gene expression accordingly. We present the Quorum Sensing Database (QSDB), a comprehensive database of all published sensing and quenching relations between organisms and signalling molecules of the human microbiome, as well as an interactive web interface that allows browsing the database, provides graphical depictions of sensing mechanisms as Systems Biology Graphical Notation diagrams and links to other databases. Database URL: QSDB (Quorum Sensing DataBase) is freely available via an interactive web interface and as a downloadable csv file at http://qsdb.org.
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Affiliation(s)
- Karsten Klein
- Department of Information and Computer Science, University of Konstanz, Universitätsstraße 10, Konstanz, Baden-Württemberg 78464, Germany
| | - Dimitar Garkov
- Department of Information and Computer Science, University of Konstanz, Universitätsstraße 10, Konstanz, Baden-Württemberg 78464, Germany
| | - Sina Rütschlin
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, Universitätsstraße 10, Konstanz, Baden-Württemberg 78464, Germany
| | - Thomas Böttcher
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, Universitätsstraße 10, Konstanz, Baden-Württemberg 78464, Germany.,Faculty of Chemistry, Institute of Biological Chemistry and Centre for Microbiology and Environmental Systems Science, University of Vienna, UZAII, Althanstraße 14, Vienna 1090, Austria
| | - Falk Schreiber
- Department of Information and Computer Science, University of Konstanz, Universitätsstraße 10, Konstanz, Baden-Württemberg 78464, Germany.,Department of Information Technology, Monash University, 20 Research Way, Melbourne, Clayton, Victoria 3800, Australia
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23
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Jiang X, Patil NA, Azad MAK, Wickremasinghe H, Yu H, Zhao J, Zhang X, Li M, Gong B, Wan L, Ma W, Thompson PE, Yang K, Yuan B, Schreiber F, Wang L, Velkov T, Roberts KD, Li J. A novel chemical biology and computational approach to expedite the discovery of new-generation polymyxins against life-threatening Acinetobacter baumannii. Chem Sci 2021; 12:12211-12220. [PMID: 34667587 PMCID: PMC8457388 DOI: 10.1039/d1sc03460j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/12/2021] [Indexed: 01/20/2023] Open
Abstract
Multidrug-resistant Gram-negative bacteria represent a major medical challenge worldwide. New antibiotics are desperately required with 'old' polymyxins often being the only available therapeutic option. Here, we systematically investigated the structure-activity relationship (SAR) of polymyxins using a quantitative lipidomics-informed outer membrane (OM) model of Acinetobacter baumannii and a series of chemically synthesized polymyxin analogs. By integrating chemical biology and all-atom molecular dynamics simulations, we deciphered how each residue of the polymyxin molecule modulated its conformational folding and specific interactions with the bacterial OM. Importantly, a novel designed polymyxin analog FADDI-287 with predicted stronger OM penetration showed improved in vitro antibacterial activity. Collectively, our study provides a novel chemical biology and computational strategy to expedite the discovery of new-generation polymyxins against life-threatening Gram-negative 'superbugs'.
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Affiliation(s)
- Xukai Jiang
- National Glycoengineering Research Center, Shandong University Qingdao China
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Nitin A Patil
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Mohammad A K Azad
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Hasini Wickremasinghe
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Heidi Yu
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Jinxin Zhao
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Xinru Zhang
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Mengyao Li
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Bin Gong
- School of Software, Shandong University Jinan China
| | - Lin Wan
- School of Software, Shandong University Jinan China
| | - Wendong Ma
- Centre for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University Suzhou China
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Science, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University Melbourne Australia
| | - Kai Yang
- Centre for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University Suzhou China
| | - Bing Yuan
- Centre for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University Suzhou China
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz Konstanz Germany
- Faculty of Information Technology, Monash University Melbourne Australia
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University Qingdao China
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, University of Melbourne Melbourne Australia
| | - Kade D Roberts
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
| | - Jian Li
- Biomedicine Discovery Institute, Infection & Immunity Program, Monash University Melbourne Australia +61 3 9905 6450 +61 3 9903 9702
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24
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Kraus M, Klein K, Fuchs J, Keim D, Schreiber F, Sedlmair M, Rhyne TM. The Value of Immersive Visualization. IEEE Comput Graph Appl 2021; 41:125-132. [PMID: 34264822 DOI: 10.1109/mcg.2021.3075258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In recent years, research on immersive environments has experienced a new wave of interest, and immersive analytics has been established as a new research field. Every year, a vast amount of different techniques, applications, and user studies are published that focus on employing immersive environments for visualizing and analyzing data. Nevertheless, immersive analytics is still a relatively unexplored field that needs more basic research in many aspects and is still viewed with skepticism. Rightly so, because in our opinion, many researchers do not fully exploit the possibilities offered by immersive environments and, on the contrary, sometimes even overestimate the power of immersive visualizations. Although a growing body of papers has demonstrated individual advantages of immersive analytics for specific tasks and problems, the general benefit of using immersive environments for effective analytic tasks remains controversial. In this article, we reflect on when and how immersion may be appropriate for the analysis and present four guiding scenarios. We report on our experiences, discuss the landscape of assessment strategies, and point out the directions where we believe immersive visualizations have the greatest potential.
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25
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Jiang X, Yang K, Yuan B, Han M, Zhu Y, Roberts KD, Patil NA, Li J, Gong B, Hancock REW, Velkov T, Schreiber F, Wang L, Li J. Molecular dynamics simulations informed by membrane lipidomics reveal the structure-interaction relationship of polymyxins with the lipid A-based outer membrane of Acinetobacter baumannii. J Antimicrob Chemother 2021; 75:3534-3543. [PMID: 32911540 DOI: 10.1093/jac/dkaa376] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 08/04/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND MDR bacteria represent an urgent threat to human health globally. Polymyxins are a last-line therapy against life-threatening Gram-negative 'superbugs', including Acinetobacter baumannii. Polymyxins exert antimicrobial activity primarily via permeabilizing the bacterial outer membrane (OM); however, the mechanism of interaction between polymyxins and the OM remains unclear at the atomic level. METHODS We constructed a lipid A-based OM model of A. baumannii using quantitative membrane lipidomics data and employed all-atom molecular dynamics simulations with umbrella sampling techniques to elucidate the structure-interaction relationship and thermodynamics governing the penetration of polymyxins [B1 and E1 (i.e. colistin A) representing the two clinically used polymyxins] into the OM. RESULTS Polymyxin B1 and colistin A bound to the A. baumannii OM by the initial electrostatic interactions between the Dab residues of polymyxins and the phosphates of lipid A, competitively displacing the cations from the headgroup region of the OM. Both polymyxin B1 and colistin A formed a unique folded conformation upon approaching the hydrophobic centre of the OM, consistent with previous experimental observations. Polymyxin penetration induced reorientation of the headgroups of the OM lipids near the penetration site and caused local membrane disorganization, thereby significantly increasing membrane permeability and promoting the subsequent penetration of polymyxin molecules into the OM and periplasmic space. CONCLUSIONS The thermodynamics governing the penetration of polymyxins through the outer leaflet of the A. baumannii OM were examined and novel structure-interaction relationship information was obtained at the atomic and membrane level. Our findings will facilitate the discovery of novel polymyxins against MDR Gram-negative pathogens.
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Affiliation(s)
- Xukai Jiang
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Kai Yang
- Centre for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Bing Yuan
- Centre for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Meiling Han
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Yan Zhu
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Kade D Roberts
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Nitin A Patil
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Jingliang Li
- Institute for Frontier Materials, Deakin University, Geelong, Victoria, Australia
| | - Bin Gong
- School of Computer Science and Technology, Shandong University, Jinan, China
| | - Robert E W Hancock
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, University of Melbourne, Melbourne, Australia
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian Li
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
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Aichem M, Czauderna T, Zhu Y, Zhao J, Klapperstück M, Klein K, Li J, Schreiber F. Visual Exploration of Large Metabolic Models. Bioinformatics 2021; 37:4460-4468. [PMID: 33970212 DOI: 10.1093/bioinformatics/btab335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 03/01/2021] [Accepted: 04/30/2021] [Indexed: 01/09/2023] Open
Abstract
MOTIVATION Large metabolic models, including genome-scale metabolic models (GSMMs), are nowadays common in systems biology, biotechnology and pharmacology. They typically contain thousands of metabolites and reactions and therefore methods for their automatic visualisation and interactive exploration can facilitate a better understanding of these models. RESULTS We developed a novel method for the visual exploration of large metabolic models and implemented it in LMME (Large Metabolic Model Explorer), an add-on for the biological network analysis tool VANTED. The underlying idea of our method is to analyse a large model as follows. Starting from a decomposition into several subsystems, relationships between these subsystems are identified and an overview is computed and visualised. From this overview, detailed subviews may be constructed and visualised in order to explore subsystems and relationships in greater detail. Decompositions may either be predefined or computed, using built-in or self-implemented methods. Realised as add-on for VANTED, LMME is embedded in a domain-specific environment, allowing for further related analysis at any stage during the exploration. We describe the method, provide a use case, and discuss the strengths and weaknesses of different decomposition methods. AVAILABILITY The methods and algorithms presented here are implemented in LMME, an open-source add-on for VANTED. LMME can be downloaded from www.cls.uni-konstanz.de/software/lmme and VANTED can be downloaded from www.vanted.org. The source code of LMME is available from GitHub, at https://github.com/LSI-UniKonstanz/lmme.
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Affiliation(s)
- Michael Aichem
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Tobias Czauderna
- Faculty of Information Technology, Monash University, Melbourne, Australia
| | - Yan Zhu
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Jinxin Zhao
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | | | - Karsten Klein
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Jian Li
- Biomedicine Discovery Institute, Infection & Immunity Program and Department of Microbiology, Monash University, Melbourne, Australia
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.,Faculty of Information Technology, Monash University, Melbourne, Australia
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27
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Empting E, Klopotek M, Hinderhofer A, Schreiber F, Oettel M. Lattice gas study of thin-film growth scenarios and transitions between them: Role of substrate. Phys Rev E 2021; 103:023302. [PMID: 33736115 DOI: 10.1103/physreve.103.023302] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/17/2021] [Indexed: 11/07/2022]
Abstract
Thin-film growth is investigated in two types of lattice gas models where substrate and film particles are different, expressed by unequal interaction energy parameters. The first is of solid-on-solid type, whereas the second additionally incorporates desorption, diffusion in the gas phase above the film and readsorption at the film (appropriate for growth in colloidal systems). In both models, the difference between particle-substrate and particle-particle interactions plays a central role for the evolution of the film morphology at intermediate times. The models exhibit a dynamic layering transition which occurs at generally lower substrate attraction strengths than the equilibrium layering transition. A second, flattening transition is found where initial island growth transforms to layer-by-layer growth at intermediate deposition times. Combined with the known roughening behavior in such models for very large deposition times, we present four global growth scenarios, charting out the possible types of roughness evolution.
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Affiliation(s)
- E Empting
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - M Klopotek
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - A Hinderhofer
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - F Schreiber
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - M Oettel
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
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28
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Duva G, Pithan L, Gerlach A, Janik A, Hinderhofer A, Schreiber F. Roughness evolution in strongly interacting donor:acceptor mixtures of molecular semiconductors. An in situ, real-time growth study using x-ray reflectivity. J Phys Condens Matter 2021; 33:115003. [PMID: 33285533 DOI: 10.1088/1361-648x/abd11c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The evolution of surface roughness in binary mixtures of the two molecular organic semiconductors (OSCs) diindenoperylene (DIP) as electron-donor and 1, 3, 4, 5, 7, 8-hexafluoro-tetracyano naphthoquinodimethane (F6TCNNQ) as electron-acceptor is studied. We co-deposit DIP and F6TCNNQ in vacuum with varying relative molar content while keeping a molar excess of DIP in order to produce phase-heterogeneous mixtures. The excess DIP phase segregates in pristine crystallites, whereas the remaining mixed phase is constituted by DIP:F6TCNNQ co-crystallites. We calculate the surface roughness as function of film thickness by modelling x-ray reflectivity data acquired in situ and in real-time during film growth. To model the experimental data, two distinct approaches, namely the kinematic approximation and the Parratt formalism, are applied. A comparative study of surface roughness evolution as function of DIP:F6TCNNQ mixing ratio is carried out implementing the Trofimov growth model within the kinematic approximation. Depending on the thickness regime, mixing ratio-specific trends are identified and discussed. To explain them, a growth mechanism for binary heterogeneous mixtures of strongly interacting OSCs is proposed.
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Affiliation(s)
- G Duva
- University of Tübingen, Institute for Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - L Pithan
- ESRF - The European Synchrotron, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - A Gerlach
- University of Tübingen, Institute for Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - A Janik
- University of Tübingen, Institute for Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - A Hinderhofer
- University of Tübingen, Institute for Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - F Schreiber
- University of Tübingen, Institute for Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Center for Light-Matter Interactions, Sensors and Analytics (LISA+), Auf der Morgenstelle 15, 72076 Tübingen, Germany
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29
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Zhao J, Zhu Y, Han J, Lin YW, Aichem M, Wang J, Chen K, Velkov T, Schreiber F, Li J. Genome-Scale Metabolic Modeling Reveals Metabolic Alterations of Multidrug-Resistant Acinetobacter baumannii in a Murine Bloodstream Infection Model. Microorganisms 2020; 8:microorganisms8111793. [PMID: 33207684 PMCID: PMC7696501 DOI: 10.3390/microorganisms8111793] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 01/22/2023] Open
Abstract
Multidrug-resistant (MDR) Acinetobacter baumannii is a critical threat to human health globally. We constructed a genome-scale metabolic model iAB5075 for the hypervirulent, MDR A. baumannii strain AB5075. Predictions of nutrient utilization and gene essentiality were validated using Biolog assay and a transposon mutant library. In vivo transcriptomics data were integrated with iAB5075 to elucidate bacterial metabolic responses to the host environment. iAB5075 contains 1530 metabolites, 2229 reactions, and 1015 genes, and demonstrated high accuracies in predicting nutrient utilization and gene essentiality. At 4 h post-infection, a total of 146 metabolic fluxes were increased and 52 were decreased compared to 2 h post-infection; these included enhanced fluxes through peptidoglycan and lipopolysaccharide biosynthesis, tricarboxylic cycle, gluconeogenesis, nucleotide and fatty acid biosynthesis, and altered fluxes in amino acid metabolism. These flux changes indicate that the induced central metabolism, energy production, and cell membrane biogenesis played key roles in establishing and enhancing A. baumannii bloodstream infection. This study is the first to employ genome-scale metabolic modeling to investigate A. baumannii infection in vivo. Our findings provide important mechanistic insights into the adaption of A. baumannii to the host environment and thus will contribute to the development of new therapeutic agents against this problematic pathogen.
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Affiliation(s)
- Jinxin Zhao
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (J.Z.); (Y.-W.L.); (J.W.); (K.C.)
| | - Yan Zhu
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (J.Z.); (Y.-W.L.); (J.W.); (K.C.)
- Correspondence: (Y.Z.); (J.L.); Tel.: +61-3-99029178 (Y.Z.); +61-3-99039172 (J.L.); Fax: +61-3-99056450 (J.L.)
| | - Jiru Han
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
| | - Yu-Wei Lin
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (J.Z.); (Y.-W.L.); (J.W.); (K.C.)
| | - Michael Aichem
- Department of Computer and Information Science, University of Konstanz, 78457 Konstanz, Germany; (M.A.); (F.S.)
| | - Jiping Wang
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (J.Z.); (Y.-W.L.); (J.W.); (K.C.)
| | - Ke Chen
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (J.Z.); (Y.-W.L.); (J.W.); (K.C.)
| | - Tony Velkov
- Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, VIC 3010, Australia;
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, 78457 Konstanz, Germany; (M.A.); (F.S.)
| | - Jian Li
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (J.Z.); (Y.-W.L.); (J.W.); (K.C.)
- Correspondence: (Y.Z.); (J.L.); Tel.: +61-3-99029178 (Y.Z.); +61-3-99039172 (J.L.); Fax: +61-3-99056450 (J.L.)
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30
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Jiang X, Yang K, Han ML, Yuan B, Li J, Gong B, Velkov T, Schreiber F, Wang L, Li J. Outer Membranes of Polymyxin-Resistant Acinetobacter baumannii with Phosphoethanolamine-Modified Lipid A and Lipopolysaccharide Loss Display Different Atomic-Scale Interactions with Polymyxins. ACS Infect Dis 2020; 6:2698-2708. [PMID: 32871077 DOI: 10.1021/acsinfecdis.0c00330] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Resistance to the last-line polymyxins is increasingly reported in multidrug-resistant Gram-negative pathogens, including Acinetobacter baumannii, which develops resistance via either lipid A modification (e.g., with phosphoethanolamine [pEtN]) or even lipopolysaccharide (LPS) loss in the outer membrane (OM). Considering these two different mechanisms, quantitative membrane lipidomics data were utilized to develop three OM models representing polymyxin-susceptible and -resistant A. baumannii strains. Through all-atom molecular simulations with enhanced sampling techniques, the effect of lipid A-pEtN modification and LPS loss on the action of colistin (i.e., polymyxin E) was examined for the first time, with a focus on the dynamics and energetics of colistin penetration into these OMs. Lipid A-pEtN modification improved the OM stability, impeding the penetration of colistin into the OM; this differed from the current literature that lipid A-pEtN modification confers resistance by diminishing the initial interaction with polymyxins. In contrast, the LPS deficiency significantly reduced the negative charges on the OM surface, diminishing the binding of colistin. Moreover, both lipid A-pEtN modification and LPS loss also constituted colistin resistance through disturbing the conformational transitions of the colistin molecule. Collectively, atomic-scale interactions between polymyxins and different bacterial OMs are very different and the findings may facilitate the discovery of new-generation polymyxins against Gram-negative 'superbugs'.
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Affiliation(s)
- Xukai Jiang
- Biomedicine Discovery Institute, Infection & Immunity Program, Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Mei-Ling Han
- Biomedicine Discovery Institute, Infection & Immunity Program, Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia
| | - Bing Yuan
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Jingliang Li
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3217, Australia
| | - Bin Gong
- School of Software, Shandong University, Jinan 250101, China
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz 78467, Germany
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jian Li
- Biomedicine Discovery Institute, Infection & Immunity Program, Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia
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31
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Jiang X, Yang K, Yuan B, Gong B, Wan L, Patil NA, Swarbrick JD, Roberts KD, Schreiber F, Wang L, Velkov T, Li J. Simulations of octapeptin-outer membrane interactions reveal conformational flexibility is linked to antimicrobial potency. J Biol Chem 2020; 295:15902-15912. [PMID: 32913118 DOI: 10.1074/jbc.ra120.014856] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/09/2020] [Indexed: 12/22/2022] Open
Abstract
The octapeptins are lipopeptide antibiotics that are structurally similar to polymyxins yet retain activity against polymyxin-resistant Gram-negative pathogens, suggesting they might be used to treat recalcitrant infections. However, the basis of their unique activity is unclear because of the difficulty in generating high-resolution experimental data of the interaction of antimicrobial peptides with lipid membranes. To elucidate these structure-activity relationships, we employed all-atom molecular dynamics simulations with umbrella sampling to investigate the conformational and energetic landscape of octapeptins interacting with bacterial outer membrane (OM). Specifically, we examined the interaction of octapeptin C4 and FADDI-115, lacking a single hydroxyl group compared with octapeptin C4, with the lipid A-phosphoethanolamine modified OM of Acinetobacter baumannii Octapeptin C4 and FADDI-115 both penetrated into the OM hydrophobic center but experienced different conformational transitions from an unfolded to a folded state that was highly dependent on the structural flexibility of their respective N-terminal fatty acyl groups. The additional hydroxyl group present in the fatty acyl group of octapeptin C4 resulted in the molecule becoming trapped in a semifolded state, leading to a higher free energy barrier for OM penetration. The free energy barrier for the translocation through the OM hydrophobic layer was ∼72 kcal/mol for octapeptin C4 and 62 kcal/mol for FADDI-115. Our results help to explain the lower antimicrobial activity previously observed for octapeptin C4 compared with FADDI-115 and more broadly improve our understanding of the structure-function relationships of octapeptins. These findings may facilitate the discovery of next-generation octapeptins against polymyxin-resistant Gram-negative 'superbugs.'
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Affiliation(s)
- Xukai Jiang
- Biomedicine Discovery Institute, Infection & Immunity Program, Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Bing Yuan
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Bin Gong
- School of Software, Shandong University, Jinan, China
| | - Lin Wan
- School of Software, Shandong University, Jinan, China
| | - Nitin A Patil
- Biomedicine Discovery Institute, Infection & Immunity Program, Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - James D Swarbrick
- Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Victoria, Australia
| | - Kade D Roberts
- Biomedicine Discovery Institute, Infection & Immunity Program, Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Tony Velkov
- Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Victoria, Australia.
| | - Jian Li
- Biomedicine Discovery Institute, Infection & Immunity Program, Department of Microbiology, Monash University, Melbourne, Victoria, Australia.
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32
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Zhu Y, Lu J, Han M, Jiang X, Azad MAK, Patil NA, Lin Y, Zhao J, Hu Y, Yu HH, Chen K, Boyce JD, Dunstan RA, Lithgow T, Barlow CK, Li W, Schneider‐Futschik EK, Wang J, Gong B, Sommer B, Creek DJ, Fu J, Wang L, Schreiber F, Velkov T, Li J. Polymyxins Bind to the Cell Surface of Unculturable Acinetobacter baumannii and Cause Unique Dependent Resistance. Adv Sci (Weinh) 2020; 7:2000704. [PMID: 32775156 PMCID: PMC7403960 DOI: 10.1002/advs.202000704] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/28/2020] [Indexed: 05/13/2023]
Abstract
Multidrug-resistant Acinetobacter baumannii is a top-priority pathogen globally and polymyxins are a last-line therapy. Polymyxin dependence in A. baumannii (i.e., nonculturable on agar without polymyxins) is a unique and highly-resistant phenotype with a significant potential to cause treatment failure in patients. The present study discovers that a polymyxin-dependent A. baumannii strain possesses mutations in both lpxC (lipopolysaccharide biosynthesis) and katG (reactive oxygen species scavenging) genes. Correlative multiomics analyses show a significantly remodeled cell envelope and remarkably abundant phosphatidylglycerol in the outer membrane (OM). Molecular dynamics simulations and quantitative membrane lipidomics reveal that polymyxin-dependent growth emerges only when the lipopolysaccharide-deficient OM distinctively remodels with ≥ 35% phosphatidylglycerol, and with "patch" binding on the OM by the rigid polymyxin molecules containing strong intramolecular hydrogen bonding. Rather than damaging the OM, polymyxins bind to the phosphatidylglycerol-rich OM and strengthen the membrane integrity, thereby protecting bacteria from external reactive oxygen species. Dependent growth is observed exclusively with polymyxin analogues, indicating a critical role of the specific amino acid sequence of polymyxins in forming unique structures for patch-binding to bacterial OM. Polymyxin dependence is a novel antibiotic resistance mechanism and the current findings highlight the risk of 'invisible' polymyxin-dependent isolates in the evolution of resistance.
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Affiliation(s)
- Yan Zhu
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Jing Lu
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Mei‐Ling Han
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Xukai Jiang
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Mohammad A. K. Azad
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Nitin A. Patil
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Yu‐Wei Lin
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Jinxin Zhao
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Yang Hu
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Heidi H. Yu
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Ke Chen
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - John D. Boyce
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Rhys A. Dunstan
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Trevor Lithgow
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | | | - Weifeng Li
- School of Physics and State Key Laboratory of Crystal MaterialsShandong UniversityJinan250100China
| | | | - Jiping Wang
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Bin Gong
- School of Computer Science and TechnologyShandong UniversityJinan250100China
| | - Bjorn Sommer
- Department of Computer and Information ScienceUniversity of KonstanzKonstanz78457Germany
| | - Darren J. Creek
- Drug Delivery, Disposition and DynamicsMonash Institute of Pharmaceutical SciencesMonash UniversityMelbourne3052Australia
| | - Jing Fu
- Department of Mechanical and Aerospace EngineeringMonash UniversityMelbourne3800Australia
| | - Lushan Wang
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdao CampusQingdao266237China
| | - Falk Schreiber
- Department of Computer and Information ScienceUniversity of KonstanzKonstanz78457Germany
| | - Tony Velkov
- Department of Pharmacology and TherapeuticsUniversity of MelbourneMelbourne3010Australia
| | - Jian Li
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
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Schreiber F, Sommer B, Czauderna T, Golebiewski M, Gorochowski TE, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D. Specifications of standards in systems and synthetic biology: status and developments in 2020. J Integr Bioinform 2020; 17:jib-2020-0022. [PMID: 32598316 PMCID: PMC7756620 DOI: 10.1515/jib-2020-0022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022] Open
Abstract
This special issue of the Journal of Integrative Bioinformatics presents papers related to the 10th COMBINE meeting together with the annual update of COMBINE standards in systems and synthetic biology.
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Affiliation(s)
- Falk Schreiber
- Dept. of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Faculty of Information Technology, Monash University, Melbourne, Australia
| | | | - Tobias Czauderna
- Faculty of Information Technology, Monash University, Melbourne, Australia
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | | | | | | | - Matthias König
- Institute for Theoretical Biology, Humboldt-University Berlin, Berlin, Germany
| | - Chris Myers
- Dept. of Electrical and Computer Engineering, University of Utah, Salt Lake City, USA
| | - David Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
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Waltemath D, Golebiewski M, Blinov ML, Gleeson P, Hermjakob H, Hucka M, Inau ET, Keating SM, König M, Krebs O, Malik-Sheriff RS, Nickerson D, Oberortner E, Sauro HM, Schreiber F, Smith L, Stefan MI, Wittig U, Myers CJ. The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). J Integr Bioinform 2020; 17:jib-2020-0005. [PMID: 32598315 PMCID: PMC7756615 DOI: 10.1515/jib-2020-0005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/14/2020] [Indexed: 01/23/2023] Open
Abstract
This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.
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Affiliation(s)
- Dagmar Waltemath
- Medical Informatics, University Medicine Greifswald, Greifswald, Germany
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | | | - Padraig Gleeson
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | | | - Michael Hucka
- Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Esther Thea Inau
- Medical Informatics, University Medicine Greifswald, Greifswald, Germany
| | | | - Matthias König
- Institute for Theoretical Biology, Humboldt-University Berlin, Berlin, Germany
| | - Olga Krebs
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | | | - David Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Ernst Oberortner
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Labs, Berkeley, CA, USA
| | - Herbert M Sauro
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Falk Schreiber
- Department of Computer and Information Science, University ofKonstanz, Germany.,Faculty of IT, Monash University, Melbourne, VIC, Australia
| | - Lucian Smith
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Melanie I Stefan
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK.,ZJU-UoE Institute, Zhejiang University, Haining, China.,University of Utah, Salt Lake City, UT, USA
| | - Ulrike Wittig
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Chris J Myers
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK
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Pietsch F, O'Neill AJ, Ivask A, Jenssen H, Inkinen J, Kahru A, Ahonen M, Schreiber F. Selection of resistance by antimicrobial coatings in the healthcare setting. J Hosp Infect 2020; 106:115-125. [PMID: 32535196 DOI: 10.1016/j.jhin.2020.06.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022]
Abstract
Antimicrobial touch surfaces have been introduced in healthcare settings with the aim of supporting existing hygiene procedures, and to help combat the increasing threat of antimicrobial resistance. However, concerns have been raised over the potential selection pressure exerted by such surfaces, which may drive the evolution and spread of antimicrobial resistance. This review highlights studies that indicate risks associated with resistance on antimicrobial surfaces by different processes, including evolution by de-novo mutation and horizontal gene transfer, and species sorting of inherently resistant bacteria dispersed on to antimicrobial surfaces. The review focuses on antimicrobial surfaces made of copper, silver and antimicrobial peptides because of the practical application of copper and silver, and the promising characteristics of antimicrobial peptides. The available data point to a potential for resistance selection and a subsequent increase in resistant strains via cross-resistance and co-resistance conferred by metal and antibiotic resistance traits. However, translational studies describing the development of resistance to antimicrobial touch surfaces in healthcare-related environments are rare, and will be needed to assess whether and how antimicrobial surfaces lead to resistance selection in these settings. Such studies will need to consider numerous variables, including the antimicrobial concentrations present in coatings, the occurrence of biofilms on surfaces, and the humidity relevant to dry-surface environments. On-site tests on the efficacy of antimicrobial coatings should routinely evaluate the risk of selection associated with their use.
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Affiliation(s)
- F Pietsch
- Federal Institute for Materials Research and Testing, Department of Materials and Environment, Division of Biodeterioration and Reference Organisms, Berlin, Germany
| | - A J O'Neill
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - A Ivask
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia; Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - H Jenssen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - J Inkinen
- Finnish Institute for Health and Welfare, Department of Health Security, Helsinki, Finland
| | - A Kahru
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - M Ahonen
- Satakunta University of Applied Sciences, Faculty of Technology, WANDER Nordic Water and Materials Institute, Rauma, Finland.
| | - F Schreiber
- Federal Institute for Materials Research and Testing, Department of Materials and Environment, Division of Biodeterioration and Reference Organisms, Berlin, Germany.
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Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, Barillot E, Dopazo J, Orta-Resendiz A, Messina F, Valencia A, Funahashi A, Kitano H, Auffray C, Balling R, Schneider R. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Sci Data 2020; 7:136. [PMID: 32371892 PMCID: PMC7200764 DOI: 10.1038/s41597-020-0477-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 04/24/2020] [Indexed: 11/20/2022] Open
Abstract
Researchers around the world join forces to reconstruct the molecular processes of the virus-host interactions aiming to combat the cause of the ongoing pandemic.
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Affiliation(s)
- Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Alexander Mazein
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- European Institute for Systems Biology and Medicine (EISBM), Vourles, France
| | - Marc E Gillespie
- Ontario Institute for Cancer Research, Toronto, Canada
- College of Pharmacy and Health Sciences, St. John's University, Queens, NY, USA
| | - Inna Kuperstein
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, Paris, France
| | - Anna Niarakis
- Department of Biology, Univ. Évry, University of Paris-Saclay, Genopole, 91025, Évry, France
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States
| | - Egon L Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Chris T Evelo
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands
| | - Jan Hasenauer
- Helmholtz Zentrum München, Institute of Computational Biology, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, Garching, Germany
- Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
| | - Falk Schreiber
- University of Konstanz, Department of Computer and Information Science, Konstanz, Germany
- Monash University, Faculty of Information Technology, Melbourne, Australia
| | - Andreas Dräger
- Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076, Tübingen, Germany
- Department of Computer Science, University of Tübingen, 72076, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site, Tübingen, Germany
| | - Emek Demir
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, USA
| | - Olaf Wolkenhauer
- Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany
- Stellenbosch Institute of Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, 7602, Stellenbosch, South Africa
| | - Laura I Furlong
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain
| | - Emmanuel Barillot
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, Paris, France
| | - Joaquin Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud. Hosp. Virgen del Rocío, Sevilla, Spain
- Bioinformatics in Rare Diseases. Centro de Investigación Biomédica en Red de Enfermedades Raras, Fundación Progreso y Salud, Hosp. Virgen del Rocío, Sevilla, Spain
- INB-ELIXIR-es, FPS, Hospital Virgen del Rocío, Sevilla, 42013, Spain
- Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain
| | - Aurelio Orta-Resendiz
- HIV, Inflammation and Persistence Unit, Virology Department, Institut Pasteur, Paris, France
- Bio Sorbonne Paris Cité, Université de Paris, Paris, France
| | - Francesco Messina
- Dipartimento di Epidemiologia Ricerca Pre-Clinica e Diagnostica Avanzata, National Institute for Infectious Diseases "Lazzaro Spallanzani" I.R.C.C.S., Rome, Italy
- COVID 19 INMI Network Medicine for IDs Study Group, National Institute for Infectious Diseases "Lazzaro Spallanzani" I.R.C.C.S., Rome, Italy
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Institucio Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Hiroaki Kitano
- The Systems Biology Institute, Shinagawa, Tokyo, Japan
- Okinawa Institute of Science and Technology Graduate University, Kunigami, Okinawa, Japan
- Sony Computer Science Laboratories, Inc., Tokyo, Japan
| | - Charles Auffray
- European Institute for Systems Biology and Medicine (EISBM), Vourles, France
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
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37
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Altaner S, Jaeger S, Fotler R, Zemskov I, Wittmann V, Schreiber F, Dietrich DR. Erratum to Machine learning prediction of cyanobacterial toxin (microcystin) toxicodynamics in humans. ALTEX 2020; 37:337-338. [PMID: 32242643 DOI: 10.14573/altex.1904031e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 03/11/2020] [Indexed: 11/23/2022]
Abstract
In this manuscript, which appeared in ALTEX (2020), 37(1), 24-36, doi:10.14573/altex.1904031 , there were errors in Tables 1 and 3.
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Affiliation(s)
- Stefan Altaner
- Human and Environmental Toxicology, University of Konstanz, Konstanz, Germany
| | - Sabrina Jaeger
- Life Science Informatics, University of Konstanz, Konstanz, Germany
| | - Regina Fotler
- Human and Environmental Toxicology, University of Konstanz, Konstanz, Germany
| | - Ivan Zemskov
- Organic and Bioorganic Chemistry, University of Konstanz, Konstanz, Germany
| | - Valentin Wittmann
- Organic and Bioorganic Chemistry, University of Konstanz, Konstanz, Germany
| | - Falk Schreiber
- Life Science Informatics, University of Konstanz, Konstanz, Germany.,Faculty of IT, Monash University, Melbourne, Australia
| | - Daniel R Dietrich
- Human and Environmental Toxicology, University of Konstanz, Konstanz, Germany
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38
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Friedrichs M, Shoshi A, Chmura PJ, Ison J, Schwämmle V, Schreiber F, Hofestädt R, Sommer B. JIB.tools 2.0 - A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools. J Integr Bioinform 2020; 16:/j/jib.2019.16.issue-4/jib-2019-0059/jib-2019-0059.xml. [PMID: 31913853 PMCID: PMC7074141 DOI: 10.1515/jib-2019-0059] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/30/2019] [Accepted: 12/09/2019] [Indexed: 11/15/2022] Open
Abstract
JIB.tools 2.0 is a new approach to more closely embed the curation process in the publication process. This website hosts the tools, software applications, databases and workflow systems published in the Journal of Integrative Bioinformatics (JIB). As soon as a new tool-related publication is published in JIB, the tool is posted to JIB.tools and can afterwards be easily transferred to bio.tools, a large information repository of software tools, databases and services for bioinformatics and the life sciences. In this way, an easily-accessible list of tools is provided which were published in JIB a well as status information regarding the underlying service. With newer registries like bio.tools providing these information on a bigger scale, JIB.tools 2.0 closes the gap between journal publications and registry publication. (Reference: https://jib.tools).
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Affiliation(s)
- Marcel Friedrichs
- Bielefeld University, Faculty of Technology, Bioinformatics/Medical Informatics Department, Bielefeld, Germany
| | - Alban Shoshi
- Bielefeld University, Faculty of Technology, Bioinformatics/Medical Informatics Department, Bielefeld, Germany
| | | | - Jon Ison
- Technical University of Denmark, Department of Bio and Health Informatics, Lyngby, Denmark
| | - Veit Schwämmle
- University of Southern Denmark, Department of Biochemistry and Molecular Biology, Protein Research Group, Odense, Denmark
| | - Falk Schreiber
- Konstanz University, Life Science Informatics, Konstanz, Germany
| | - Ralf Hofestädt
- Bielefeld University, Faculty of Technology, Bioinformatics/Medical Informatics Department, Bielefeld, Germany
| | - Bjorn Sommer
- Royal College of Art, School of Design, London, UK
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39
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Dietz A, Wichmann G, Kuhnt T, Pfreundner L, Hagen R, Scheich M, Kölbl O, Hautmann MG, Strutz J, Schreiber F, Bockmühl U, Schilling V, Feyer P, de Wit M, Maschmeyer G, Jungehülsing M, Schroeder U, Wollenberg B, Sittel C, Münter M, Lenarz T, Klussmann JP, Guntinas-Lichius O, Rudack C, Eich HT, Foerg T, Preyer S, Westhofen M, Welkoborsky HJ, Esser D, Thurnher D, Remmert S, Sudhoff H, Görner M, Bünzel J, Budach V, Held S, Knödler M, Lordick F, Wiegand S, Vogel K, Boehm A, Flentje M, Keilholz U. Induction chemotherapy (IC) followed by radiotherapy (RT) versus cetuximab plus IC and RT in advanced laryngeal/hypopharyngeal cancer resectable only by total laryngectomy-final results of the larynx organ preservation trial DeLOS-II. Ann Oncol 2019; 29:2105-2114. [PMID: 30412221 DOI: 10.1093/annonc/mdy332] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background The German multicenter randomized phase II larynx organ preservation (LOP) trial DeLOS-II was carried out to prove the hypothesis that cetuximab (E) added to induction chemotherapy (IC) and radiotherapy improves laryngectomy-free survival (LFS; survival with preserved larynx) in locally advanced laryngeal/hypopharyngeal cancer (LHSCC). Patients and methods Treatment-naïve patients with stage III/IV LHSCC amenable to total laryngectomy (TL) were randomized to three cycles IC with TPF [docetaxel (T) and cisplatin (P) 75 mg/m2/day 1, 5-FU (F) 750 mg/m2/day days 1-5] followed by radiotherapy (69.6 Gy) without (A) or with (B) standard dose cetuximab for 16 weeks throughout IC and radiotherapy (TPFE). Response to first IC-cycle (IC-1) with ≥30% endoscopically estimated tumor surface shrinkage (ETSS) was used to define early responders; early salvage TL was recommended to non-responders. The primary objective was 24 months LFS above 35% in arm B. Results Of 180 patients randomized (July 2007 to September 2012), 173 fulfilled eligibility criteria (A/B: larynx 44/42, hypopharynx 41/46). Because of 4 therapy-related deaths among the first 64 randomized patients, 5-FU was omitted from IC in the subsequent 112 patients reducing further fatal toxicities. Thus, IC was TPF in 61 patients and TP in 112 patients, respectively. The primary objective (24 months LFS above 35%) was equally met by arms A (40/85, 47.1%) as well as B (41/88, 46.6%). One hundred and twenty-three early responders completed IC+RT; their overall response rates (TPF/TP) were 94.7%/87.2% in A versus 80%/86.0% in B. The 24 months overall survival (OS) rates were 68.2% and 69.3%. Conclusions Despite being accompanied by an elevated frequency in adverse events, the IC with TPF/TP plus cetuximab was feasible but showed no superiority to IC with TPF/TP regarding LFS and OS at 24 months. Both early response and 24 months LFS compare very well to previous LOP trials and recommend effective treatment selection and stratification by ETSS. Clinical trial information NCT00508664.
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Affiliation(s)
- A Dietz
- Department of Otolaryngology, Head and Neck Surgery, University Leipzig, Leipzig, Germany.
| | - G Wichmann
- Department of Otolaryngology, Head and Neck Surgery, University Leipzig, Leipzig, Germany
| | - T Kuhnt
- Department of Radiation Oncology, University Leipzig, Leipzig, Germany
| | - L Pfreundner
- Department of Radiation Oncology, University Würzburg, Würzburg, Germany
| | - R Hagen
- Department of Otolaryngology, Head and Neck Surgery, University Würzburg, Würzburg, Germany
| | - M Scheich
- Department of Otolaryngology, Head and Neck Surgery, University Würzburg, Würzburg, Germany
| | - O Kölbl
- Department of Radiation Oncology, University Regensburg, Regensburg, Germany
| | - M G Hautmann
- Department of Radiation Oncology, University Regensburg, Regensburg, Germany
| | - J Strutz
- Department of Otolaryngology, Head and Neck Surgery, University Regensburg, Regensburg, Germany
| | - F Schreiber
- Department of Otolaryngology, Head and Neck Surgery, Klinikum Kassel, Kassel, Germany
| | - U Bockmühl
- Department of Otolaryngology, Head and Neck Surgery, Klinikum Kassel, Kassel, Germany
| | - V Schilling
- Department of Otolaryngology, Head and Neck Surgery, Vivantes, Berlin, Neukölln, Germany
| | - P Feyer
- Department of Radiation Oncology, Vivantes, Berlin, Neukölln, Germany
| | - M de Wit
- Department of Hemato-Oncology, Vivantes, Berlin, Neukölln, Germany
| | - G Maschmeyer
- Department of Hematology, Oncology and Palliative Care, Klinikum Ernst von Bergmann, Potsdam, Germany
| | - M Jungehülsing
- Department of Otolaryngology, Head and Neck Surgery, Potsdam Klinikum, Potsdam, Germany
| | - U Schroeder
- Department of Otolaryngology, Head and Neck Surgery, University Lübeck, Lübeck, Germany
| | - B Wollenberg
- Department of Otolaryngology, Head and Neck Surgery, University Lübeck, Lübeck, Germany
| | - C Sittel
- Department of Otolaryngology, Head and Neck Surgery, Katharinen Hospital, Stuttgart, Germany
| | - M Münter
- Department of Radiation Oncology, Katharinen Hospital, Stuttgart, Germany
| | - T Lenarz
- Department of Otolaryngology, Head and Neck Surgery, MHH Hannover, Hannover, Germany
| | - J P Klussmann
- Department of Otolaryngology, Head and Neck Surgery, University Gießen, Gießen, Germany
| | - O Guntinas-Lichius
- Department of Otolaryngology, Head and Neck Surgery, Jena University Hospital, Jena, Germany
| | - C Rudack
- Department of Otolaryngology, Head and Neck Surgery, University Münster, Münster, Germany
| | - H T Eich
- Department of Radiation Oncology, University Münster, Münster, Germany
| | - T Foerg
- Department of Radiation Oncology, Head and Neck Surgery, St. Vincentius, ViDia Christliche Kliniken Karlsruhe, Karlsruhe, Germany
| | - S Preyer
- Department of Otolaryngology, Head and Neck Surgery, St. Vincentius, ViDia Christliche Kliniken Karlsruhe, Karlsruhe, Germany
| | - M Westhofen
- Department of Otolaryngology, Head and Neck Surgery, University Aachen, Aachen, Germany
| | - H J Welkoborsky
- Department of Otolaryngology, Head and Neck Surgery, Klinikum Nordstadt, Hannover, Germany
| | - D Esser
- Department of Otolaryngology, Head and Neck Surgery, Helios Klinikum, Erfurt, Germany
| | - D Thurnher
- Department of Otolaryngology, Head and Neck Surgery, University Graz, Graz, Austria
| | - S Remmert
- Department of Otolaryngology, Head and Neck Surgery, Malteser Hospital Duisburg, Duisburg, Germany
| | - H Sudhoff
- Department of Otolaryngology, Head and Neck Surgery, Klinikum Bielefeld, Bielefeld, Germany
| | - M Görner
- Department of Hemato-Oncology, Klinikum Bielefeld, Bielefeld, Germany
| | - J Bünzel
- Department of Otolaryngology, Head and Neck Surgery, Klinikum Nordhausen, Nordhausen, Germany
| | - V Budach
- Department of Radiation Oncology, CCC, Charité-University Medicine, Berlin, Germany
| | - S Held
- ClinAssess GmbH, Leverkusen, Germany
| | - M Knödler
- Department of Oncology, University Cancer Center Leipzig (UCCL), Leipzig, Germany
| | - F Lordick
- Department of Oncology, University Cancer Center Leipzig (UCCL), Leipzig, Germany
| | - S Wiegand
- Department of Otolaryngology, Head and Neck Surgery, University Leipzig, Leipzig, Germany
| | - K Vogel
- Department of Otolaryngology, Head and Neck Surgery, University Leipzig, Leipzig, Germany
| | - A Boehm
- Department of Otolaryngology, Head and Neck Surgery, St. Georg Hospital Leipzig, Leipzig, Germany
| | - M Flentje
- Department of Radiation Oncology, University Würzburg, Würzburg, Germany
| | - U Keilholz
- Charité Comprehensive Cancer Center, Berlin, Germany
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Schreiber S, Wilisch-Neumann A, Schreiber F, Assmann A, Scheumann V, Perosa V, Jandke S, Mawrin C, Carare RO, Werring DJ. Invited Review: The spectrum of age-related small vessel diseases: potential overlap and interactions of amyloid and nonamyloid vasculopathies. Neuropathol Appl Neurobiol 2019; 46:219-239. [PMID: 31386773 DOI: 10.1111/nan.12576] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022]
Abstract
Deep perforator arteriopathy (DPA) and cerebral amyloid angiopathy (CAA) are the commonest known cerebral small vessel diseases (CSVD), which cause ischaemic stroke, intracebral haemorrhage (ICH) and vascular cognitive impairment (VCI). While thus far mainly considered as separate entities, we here propose that DPA and CAA share similarities, overlap and interact, so that 'pure' DPA or CAA are extremes along a continuum of age-related small vessel pathologies. We suggest blood-brain barrier (BBB) breakdown, endothelial damage and impaired perivascular β-amyloid (Aβ) drainage are hallmark common mechanisms connecting DPA and CAA. We also suggest a need for new biomarkers (e.g. high-resolution imaging) to deepen understanding of the complex relationships between DPA and CAA.
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Affiliation(s)
- S Schreiber
- Department of Neurology, Otto-von-Guericke University, Magdeburg, Germany.,German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association, Magdeburg, Germany.,Center for behavioral brain sciences (CBBS), Magdeburg, Germany
| | - A Wilisch-Neumann
- Department of Neurology, Otto-von-Guericke University, Magdeburg, Germany.,German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association, Magdeburg, Germany
| | - F Schreiber
- Department of Neurology, Otto-von-Guericke University, Magdeburg, Germany.,German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association, Magdeburg, Germany
| | - A Assmann
- Department of Neurology, Otto-von-Guericke University, Magdeburg, Germany.,German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association, Magdeburg, Germany
| | - V Scheumann
- Department of Neurology, Otto-von-Guericke University, Magdeburg, Germany
| | - V Perosa
- Department of Neurology, Otto-von-Guericke University, Magdeburg, Germany.,German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association, Magdeburg, Germany
| | - S Jandke
- Department of Neurology, Otto-von-Guericke University, Magdeburg, Germany.,German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association, Magdeburg, Germany
| | - C Mawrin
- Department of Neuropathology, Otto-von-Guericke University, Magdeburg, Germany
| | - R O Carare
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - D J Werring
- Stroke Research Centre, Department of Brain Repair & Rehabilitation, UCL Institute of Neurology, The National Hospital for Neurology and Neurosurgery, London, UK
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Delp J, Gutbier S, Klima S, Hoelting L, Pinto-Gil K, Hsieh JH, Aichem M, Klein K, Schreiber F, Tice RR, Pastor M, Behl M, Leist M. Corrigendum to A high-throughput approach to identify specific neurotoxicants / developmental toxicants in human neuronal cell function assays. ALTEX 2019; 36:505. [PMID: 31329253 DOI: 10.14573/altex.1904111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this manuscript, which appeared in ALTEX 35 , 235-253 ( doi:10.14573/altex.1712182 ), the Acknowledgements should read: This work was supported by the Land BW, the Doerenkamp-Zbinden Foundation, the DFG (RTG1331, KoRS-CB), the BMBF (NeuriTox), and it has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 681002 (EU-ToxRisk).
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Affiliation(s)
- Johannes Delp
- In vitro Toxicology and Biomedicine, Dept inaugurated by the Doerenkamp-Zbinden foundation, University of Konstanz, Konstanz, Germany.,Research Training Group RTG1331, University of Konstanz, Konstanz, Germany.,Cooperative doctorate college InViTe, University of Konstanz, Konstanz, Germany
| | - Simon Gutbier
- In vitro Toxicology and Biomedicine, Dept inaugurated by the Doerenkamp-Zbinden foundation, University of Konstanz, Konstanz, Germany.,Research Training Group RTG1331, University of Konstanz, Konstanz, Germany
| | - Stefanie Klima
- In vitro Toxicology and Biomedicine, Dept inaugurated by the Doerenkamp-Zbinden foundation, University of Konstanz, Konstanz, Germany.,Research Training Group RTG1331, University of Konstanz, Konstanz, Germany.,Cooperative doctorate college InViTe, University of Konstanz, Konstanz, Germany
| | - Lisa Hoelting
- In vitro Toxicology and Biomedicine, Dept inaugurated by the Doerenkamp-Zbinden foundation, University of Konstanz, Konstanz, Germany
| | - Kevin Pinto-Gil
- Research Programme on Biomedical Informatics (GRIB), Dept. of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Michael Aichem
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Karsten Klein
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.,Faculty of Information Technology, Monash University, Melbourne, Australia
| | - Raymond R Tice
- Division of National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Manuel Pastor
- Research Programme on Biomedical Informatics (GRIB), Dept. of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mamta Behl
- Division of National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Marcel Leist
- In vitro Toxicology and Biomedicine, Dept inaugurated by the Doerenkamp-Zbinden foundation, University of Konstanz, Konstanz, Germany
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42
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Schreiber F, Sommer B, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. J Integr Bioinform 2019; 16:/j/jib.2019.16.issue-2/jib-2019-0035/jib-2019-0035.xml. [PMID: 31301675 PMCID: PMC6798822 DOI: 10.1515/jib-2019-0035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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] [Indexed: 01/04/2023] Open
Abstract
This special issue of the Journal of Integrative Bioinformatics presents an overview of COMBINE standards and their latest specifications. The standards cover representation formats for computational modeling in synthetic and systems biology and include BioPAX, CellML, NeuroML, SBML, SBGN, SBOL and SED-ML. The articles in this issue contain updated specifications of SBGN Process Description Level 1 Version 2, SBML Level 3 Core Version 2 Release 2, SBOL Version 2.3.0, and SBOL Visual Version 2.1.
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Affiliation(s)
- Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Faculty of IT, Monash University, Clayton, Australia
| | - Björn Sommer
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Gary D. Bader
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Padraig Gleeson
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Michael Hucka
- California Institute of Technology, Pasadena, CA, USA
| | | | | | | | - David Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
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43
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Altaner S, Jaeger S, Fotler R, Zemskov I, Wittmann V, Schreiber F, Dietrich DR. Machine learning prediction of cyanobacterial toxin (microcystin) toxicodynamics in humans. ALTEX 2019; 37:24-36. [PMID: 31280325 DOI: 10.14573/altex.1904031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/27/2019] [Indexed: 11/23/2022]
Abstract
Microcystins (MC) represent a family of cyclic peptides with approx. 250 congeners presumed harmful to human health due to their ability to inhibit ser/thr-proteinphosphatases (PPP), albeit all hazard and risk assessments (RA) are based on data of one MC-congener (MC-LR) only. MC congener structural diversity is a challenge for the risk assessment of these toxins, especially as several different PPPs have to be included in the RA. Consequently, the inhibition of PPP1, PPP2A and PPP5 was determined with 18 structurally different MC and demonstrated MC congener dependent inhibition activity and a lower susceptibility of PPP5 to inhibition than PPP1 and PPP2A. The latter data were employed to train a machine learning algorithm that should allow prediction of PPP inhibition (toxicity) based on MCs 2D chemical structure. IC50 values were classified in toxicity classes and three machine learning models were used to predict the toxicity class, resulting in 80-90% correct predictions.
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Affiliation(s)
- Stefan Altaner
- Human and Environmental Toxicology, University of Konstanz, Konstanz, Germany
| | - Sabrina Jaeger
- Life Science Informatics, University of Konstanz, Germany
| | - Regina Fotler
- Human and Environmental Toxicology, University of Konstanz, Konstanz, Germany
| | - Ivan Zemskov
- Organic and Bioorganic Chemistry, University of Konstanz, Germany
| | | | - Falk Schreiber
- Life Science Informatics, University of Konstanz, Germany.,Faculty of IT, Monash University, Melbourne, Australia
| | - Daniel R Dietrich
- Human and Environmental Toxicology, University of Konstanz, Konstanz, Germany
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44
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Garkov D, Klein K, Klukas C, Schreiber F. Mental-Map Preserving Visualisation of Partitioned Networks in Vanted. J Integr Bioinform 2019; 16:/j/jib.ahead-of-print/jib-2019-0026/jib-2019-0026.xml. [PMID: 31199771 PMCID: PMC6798853 DOI: 10.1515/jib-2019-0026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 04/05/2019] [Accepted: 04/29/2019] [Indexed: 11/23/2022] Open
Abstract
Biological networks can be large and complex, often consisting of different sub-networks or parts. Separation of networks into parts, network partitioning and layouts of overview and sub-graphs are of importance for understandable visualisations of those networks. This article presents NetPartVis to visualise non-overlapping clusters or partitions of graphs in the Vanted framework based on a method for laying out overview graph and several sub-graphs (partitions) in a coordinated, mental-map preserving way.
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Affiliation(s)
- Dimitar Garkov
- Department of Computer and Information Science, University of Konstanz, 78464 Konstanz, Germany
| | - Karsten Klein
- Department of Computer and Information Science, University of Konstanz, 78464 Konstanz, Germany
| | - Christian Klukas
- Digitalization of Research and Development, BASF SE, 67056 Ludwigshafen am Rhein, Germany
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, 78464 Konstanz, Germany.,Faculty of Information Technology, Monash University, Clayton, Victoria 3800, Australia
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45
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Rougny A, Touré V, Moodie S, Balaur I, Czauderna T, Borlinghaus H, Dogrusoz U, Mazein A, Dräger A, Blinov ML, Villéger A, Haw R, Demir E, Mi H, Sorokin A, Schreiber F, Luna A. Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. J Integr Bioinform 2019; 16:/j/jib.ahead-of-print/jib-2019-0022/jib-2019-0022.xml. [PMID: 31199769 PMCID: PMC6798820 DOI: 10.1515/jib-2019-0022] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/21/2019] [Indexed: 12/01/2022] Open
Abstract
The Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for readers with diverse scientific backgrounds as well as to support an efficient and accurate exchange of biological knowledge between disparate research communities, industry, and other players in systems biology. SBGN comprises the three languages Entity Relationship, Activity Flow, and Process Description (PD) to cover biological and biochemical systems at distinct levels of detail. PD is closest to metabolic and regulatory pathways found in biological literature and textbooks. Its well-defined semantics offer a superior precision in expressing biological knowledge. PD represents mechanistic and temporal dependencies of biological interactions and transformations as a graph. Its different types of nodes include entity pools (e.g. metabolites, proteins, genes and complexes) and processes (e.g. reactions, associations and influences). The edges describe relationships between the nodes (e.g. consumption, production, stimulation and inhibition). This document details Level 1 Version 2.0 of the PD specification, including several improvements, in particular: 1) the addition of the equivalence operator, subunit, and annotation glyphs, 2) modification to the usage of submaps, and 3) updates to clarify the use of various glyphs (i.e. multimer, empty set, and state variable).
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Affiliation(s)
- Adrien Rougny
- Biotechnology Research Institute for Drug Discovery, AIST, Tokyo135-0064, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo 169-8555, Japan
| | - Vasundra Touré
- Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Stuart Moodie
- Eight Pillars Ltd, 19 Redford Walk, EdinburghEH13 0AG,UK
| | - Irina Balaur
- European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, 69007 Lyon, France
| | - Tobias Czauderna
- Faculty of Information Technology, Monash University, Melbourne, Australia
| | - Hanna Borlinghaus
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Ugur Dogrusoz
- Computer Engineering Department, Bilkent University, Ankara 06800, Turkey.,i-Vis Research Lab, Bilkent University, Ankara 06800, Turkey
| | - Alexander Mazein
- European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, 69007 Lyon, France.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg.,Institute of Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, Pushchino, Moscow Region, 142290, Russia
| | - Andreas Dräger
- Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Center for Bioinformatics Tübingen (ZBIT), 72076 Tübingen, Germany.,Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Michael L Blinov
- Center for Cell Analysis and Modeling, UConn Health, Farmington CT 06030, USA
| | | | - Robin Haw
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada
| | - Emek Demir
- Computational Biology Program, Oregon Health and Science University, Portland, Oregon, USA.,Oregon Health and Science University, Department of Molecular and Medical Genetics, Portland, Oregon, USA
| | - Huaiyu Mi
- Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90033, USA
| | - Anatoly Sorokin
- Institute of Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, Pushchino, Moscow Region, 142290, Russia
| | - Falk Schreiber
- Faculty of Information Technology, Monash University, Melbourne, Australia.,Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Augustin Luna
- cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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46
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Klein K, Sommer B, Nim HT, Flack A, Safi K, Nagy M, Feyer SP, Zhang Y, Rehberg K, Gluschkow A, Quetting M, Fiedler W, Wikelski M, Schreiber F. Fly with the flock: immersive solutions for animal movement visualization and analytics. J R Soc Interface 2019; 16:20180794. [PMID: 30940026 PMCID: PMC6505562 DOI: 10.1098/rsif.2018.0794] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 11/12/2022] Open
Abstract
Understanding the movement of animals is important for a wide range of scientific interests including migration, disease spread, collective movement behaviour and analysing motion in relation to dynamic changes of the environment such as wind and thermal lifts. Particularly, the three-dimensional (3D) spatial-temporal nature of bird movement data, which is widely available with high temporal and spatial resolution at large volumes, presents a natural option to explore the potential of immersive analytics (IA). We investigate the requirements and benefits of a wide range of immersive environments for explorative visualization and analytics of 3D movement data, in particular regarding design considerations for such 3D immersive environments, and present prototypes for IA solutions. Tailored to biologists studying bird movement data, the immersive solutions enable geo-locational time-series data to be investigated interactively, thus enabling experts to visually explore interesting angles of a flock and its behaviour in the context of the environment. The 3D virtual world presents the audience with engaging and interactive content, allowing users to 'fly with the flock', with the potential to ascertain an intuitive overview of often complex datasets, and to provide the opportunity thereby to formulate and at least qualitatively assess hypotheses. This work also contributes to ongoing research efforts to promote better understanding of bird migration and the associated environmental factors at the global scale, thereby providing a visual vehicle for driving public awareness of environmental issues and bird migration patterns.
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Affiliation(s)
- Karsten Klein
- Department of Computer and
Information Science, University of Konstanz, Fach
76, 78457 Konstanz, Germany,Faculty of Information
Technology, Monash University,
Melbourne, Australia
| | - Björn Sommer
- Department of Computer and
Information Science, University of Konstanz, Fach
76, 78457 Konstanz, Germany,School of Design, Royal
College of Arts, London,
UK
| | - Hieu T. Nim
- Faculty of Information
Technology, Monash University,
Melbourne, Australia
| | - Andrea Flack
- Max-Planck-Institute for
Ornithology, Radolfzell,
Germany,Centre for the Advanced Study
of Collective Behaviour, University of Konstanz,
Konstanz, Germany
| | - Kamran Safi
- Max-Planck-Institute for
Ornithology, Radolfzell,
Germany,Department of Biology,
University of Konstanz, Konstanz,
Germany
| | - Máté Nagy
- Max-Planck-Institute for
Ornithology, Radolfzell,
Germany,Department of Biology,
University of Konstanz, Konstanz,
Germany,Centre for the Advanced Study
of Collective Behaviour, University of Konstanz,
Konstanz, Germany,MTA-ELTE Statistical and
Biological Physics Research Group, Hungarian Academy of
Sciences, Budapest,
Hungary
| | - Stefan P. Feyer
- Department of Computer and
Information Science, University of Konstanz, Fach
76, 78457 Konstanz, Germany
| | - Ying Zhang
- Department of Computer and
Information Science, University of Konstanz, Fach
76, 78457 Konstanz, Germany
| | - Kim Rehberg
- Department of Computer and
Information Science, University of Konstanz, Fach
76, 78457 Konstanz, Germany
| | - Alexej Gluschkow
- Department of Computer and
Information Science, University of Konstanz, Fach
76, 78457 Konstanz, Germany
| | | | | | - Martin Wikelski
- Max-Planck-Institute for
Ornithology, Radolfzell,
Germany,Department of Biology,
University of Konstanz, Konstanz,
Germany,Centre for the Advanced Study
of Collective Behaviour, University of Konstanz,
Konstanz, Germany
| | - Falk Schreiber
- Department of Computer and
Information Science, University of Konstanz, Fach
76, 78457 Konstanz, Germany,Faculty of Information
Technology, Monash University,
Melbourne, Australia,Centre for the Advanced Study
of Collective Behaviour, University of Konstanz,
Konstanz, Germany
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47
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Zhu Y, Zhao J, Maifiah MHM, Velkov T, Schreiber F, Li J. Metabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic Modeling. mSystems 2019; 4:e00157-18. [PMID: 30746493 PMCID: PMC6365644 DOI: 10.1128/msystems.00157-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/08/2019] [Indexed: 02/04/2023] Open
Abstract
Multidrug-resistant (MDR) Acinetobacter baumannii has emerged as a very problematic pathogen over the past decades, with a high incidence in nosocomial infections. Discovered in the late 1940s but abandoned in the 1970s, polymyxins (i.e., polymyxin B and colistin) have been revived as the last-line therapy against Gram-negative "superbugs," including MDR A. baumannii. Worryingly, resistance to polymyxins in A. baumannii has been increasingly reported, urging the development of novel antimicrobial therapies to rescue this last-line class of antibiotics. In the present study, we integrated genome-scale metabolic modeling with multiomics data to elucidate the mechanisms of cellular responses to colistin treatment in A. baumannii. A genome-scale metabolic model, iATCC19606, was constructed for strain ATCC 19606 based on the literature and genome annotation, containing 897 genes, 1,270 reactions, and 1,180 metabolites. After extensive curation, prediction of growth on 190 carbon sources using iATCC19606 achieved an overall accuracy of 84.3% compared to Biolog experimental results. Prediction of gene essentiality reached a high accuracy of 86.1% and 82.7% compared to two transposon mutant libraries of AB5075 and ATCC 17978, respectively. Further integrative modeling with our correlative transcriptomics and metabolomics data deciphered the complex regulation on metabolic responses to colistin treatment, including (i) upregulated fluxes through gluconeogenesis, the pentose phosphate pathway, and amino acid and nucleotide biosynthesis; (ii) downregulated TCA cycle and peptidoglycan and lipopolysaccharide biogenesis; and (iii) altered fluxes over respiratory chain. Our results elucidated the interplay of multiple metabolic pathways under colistin treatment in A. baumannii and provide key mechanistic insights into optimizing polymyxin combination therapy. IMPORTANCE Combating antimicrobial resistance has been highlighted as a critical global health priority. Due to the drying drug discovery pipeline, polymyxins have been employed as the last-line therapy against Gram-negative "superbugs"; however, the detailed mechanisms of antibacterial killing remain largely unclear, hampering the improvement of polymyxin therapy. Our integrative modeling using the constructed genome-scale metabolic model iATCC19606 and the correlative multiomics data provide the fundamental understanding of the complex metabolic responses to polymyxin treatment in A. baumannii at the systems level. The model iATCC19606 may have a significant potential in antimicrobial systems pharmacology research in A. baumannii.
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Affiliation(s)
- Yan Zhu
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
| | - Jinxin Zhao
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
| | - Mohd Hafidz Mahamad Maifiah
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Tony Velkov
- Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Australia
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Jian Li
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
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48
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Zhu Y, Czauderna T, Zhao J, Klapperstueck M, Maifiah MHM, Han ML, Lu J, Sommer B, Velkov T, Lithgow T, Song J, Schreiber F, Li J. Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa. Gigascience 2018; 7:4931736. [PMID: 29688451 PMCID: PMC6333913 DOI: 10.1093/gigascience/giy021] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 10/17/2017] [Accepted: 02/22/2018] [Indexed: 01/06/2023] Open
Abstract
Background Pseudomonas aeruginosa often causes multidrug-resistant infections in immunocompromised patients, and polymyxins are often used as the last-line therapy. Alarmingly, resistance to polymyxins has been increasingly reported worldwide recently. To rescue this last-resort class of antibiotics, it is necessary to systematically understand how P. aeruginosa alters its metabolism in response to polymyxin treatment, thereby facilitating the development of effective therapies. To this end, a genome-scale metabolic model (GSMM) was used to analyze bacterial metabolic changes at the systems level. Findings A high-quality GSMM iPAO1 was constructed for P. aeruginosa PAO1 for antimicrobial pharmacological research. Model iPAO1 encompasses an additional periplasmic compartment and contains 3022 metabolites, 4265 reactions, and 1458 genes in total. Growth prediction on 190 carbon and 95 nitrogen sources achieved an accuracy of 89.1%, outperforming all reported P. aeruginosa models. Notably, prediction of the essential genes for growth achieved a high accuracy of 87.9%. Metabolic simulation showed that lipid A modifications associated with polymyxin resistance exert a limited impact on bacterial growth and metabolism but remarkably change the physiochemical properties of the outer membrane. Modeling with transcriptomics constraints revealed a broad range of metabolic responses to polymyxin treatment, including reduced biomass synthesis, upregulated amino acid catabolism, induced flux through the tricarboxylic acid cycle, and increased redox turnover. Conclusions Overall, iPAO1 represents the most comprehensive GSMM constructed to date for Pseudomonas. It provides a powerful systems pharmacology platform for the elucidation of complex killing mechanisms of antibiotics.
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Affiliation(s)
- Yan Zhu
- Monash Biomedicine Discovery Institute, Department of Microbiology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne 3800, Australia
| | - Tobias Czauderna
- Faculty of Information Technology, Monash University, Melbourne 3800, Australia
| | - Jinxin Zhao
- Monash Biomedicine Discovery Institute, Department of Microbiology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne 3800, Australia
| | | | | | - Mei-Ling Han
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Melbourne 3052, Australia
| | - Jing Lu
- Monash Institute of Cognitive and Clinical Neurosciences, Department of Anatomy and development biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne 3800, Australia
| | - Björn Sommer
- Department of Computer and Information Science, University of Konstanz, Konstanz 78457, Germany
| | - Tony Velkov
- Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne 3010, Australia
| | - Trevor Lithgow
- Monash Biomedicine Discovery Institute, Department of Microbiology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne 3800, Australia
| | - Jiangning Song
- Monash Biomedicine Discovery Institute, Department of Microbiology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne 3800, Australia
| | - Falk Schreiber
- Faculty of Information Technology, Monash University, Melbourne 3800, Australia.,Department of Computer and Information Science, University of Konstanz, Konstanz 78457, Germany
| | - Jian Li
- Monash Biomedicine Discovery Institute, Department of Microbiology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne 3800, Australia
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49
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Bleibel J, Habiger M, Lütje M, Hirschmann F, Roosen-Runge F, Seydel T, Zhang F, Schreiber F, Oettel M. Two time scales for self and collective diffusion near the critical point in a simple patchy model for proteins with floating bonds. Soft Matter 2018; 14:8006-8016. [PMID: 30187060 DOI: 10.1039/c8sm00599k] [Citation(s) in RCA: 2] [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] [Indexed: 06/08/2023]
Abstract
Using dynamic Monte Carlo and Brownian dynamics, we investigate a floating bond model in which particles can bind through mobile bonds. The maximum number of bonds (here fixed to 4) can be tuned by appropriately choosing the repulsive, nonadditive interactions among bonds and particles. We compute the static and dynamic structure factor (intermediate scattering function) in the vicinity of the gas-liquid critical point. The static structure exhibits a weak tetrahedral network character. The intermediate scattering function shows a temporal decay deviating from a single exponential, which can be described by a double exponential decay where the two time scales differ approximately by one order of magnitude. This time scale separation is robust over a range of wave numbers. The analysis of clusters in real space indicates the formation of noncompact clusters and shows a considerable stretch in the instantaneous size distribution when approaching the critical point. The average time evolution of the largest subcluster of given initial clusters with 10 or more particles also shows a double exponential decay. The observation of two time scales in the intermediate scattering function at low packing fractions is consistent with similar findings in globular protein solutions with trivalent metal ions that act as bonds between proteins.
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Affiliation(s)
- J Bleibel
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany.
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50
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Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, Olivier BG, Rodriguez N, Schreiber F, Smith L, Zhang F, Bonnet E. Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Stand Genomic Sci 2018; 13:17. [PMID: 30117501 PMCID: PMC6083578 DOI: 10.1186/s40793-018-0320-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
[This corrects the article DOI: 10.4056/sigs.5279417.].
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Affiliation(s)
- Dagmar Waltemath
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Frank T. Bergmann
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA USA
| | - Claudine Chaouiya
- Instituto Gulbenkian de Ciência - IGC, Rua da Quinta Grande, Oeiras, Portugal
| | | | - Padraig Gleeson
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Carole Goble
- School of Computer Science, The University of Manchester, Manchester, UK
| | | | - Michael Hucka
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA USA
| | - Nick Juty
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Olga Krebs
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Nicolas Le Novère
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Huaiyu Mi
- Department of preventive medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Ion I. Moraru
- Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT USA
| | - Chris J. Myers
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, USA
| | - David Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Brett G. Olivier
- Systems Bioinformatics, VU University Amsterdam, Amsterdam, The Netherlands
| | | | - Falk Schreiber
- IPK Gatersleben, Gatersleben, Germany
- Martin Luther University Halle-Wittenberg, Halle, Germany
- Monash University, Melbourne, Australia
| | - Lucian Smith
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA USA
| | - Fengkai Zhang
- Computational Biology Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD USA
| | - Eric Bonnet
- Institut Curie, Paris, France
- INSERM U900, 75248 Paris, France
- Mines ParisTech, 77300 Fontainebleau, Paris, France
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