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Reabel S, Queiroz-Williams P, Nevarez J, Da Cunha A, Cremer J, Hampton C, Liu C. Assessment of four different doses of intramuscular alfaxalone combined with hydromorphone and dexmedetomidine to allow endoscopy-guided orotracheal intubation in domestic rabbits. Vet Anaesth Analg 2019. [DOI: 10.1016/j.vaa.2019.08.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Cremer J, Melbinger A, Wienand K, Henriquez T, Jung H, Frey E. Cooperation in Microbial Populations: Theory and Experimental Model Systems. J Mol Biol 2019; 431:4599-4644. [PMID: 31634468 DOI: 10.1016/j.jmb.2019.09.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 01/07/2023]
Abstract
Cooperative behavior, the costly provision of benefits to others, is common across all domains of life. This review article discusses cooperative behavior in the microbial world, mediated by the exchange of extracellular products called public goods. We focus on model species for which the production of a public good and the related growth disadvantage for the producing cells are well described. To unveil the biological and ecological factors promoting the emergence and stability of cooperative traits we take an interdisciplinary perspective and review insights gained from both mathematical models and well-controlled experimental model systems. Ecologically, we include crucial aspects of the microbial life cycle into our analysis and particularly consider population structures where ensembles of local communities (subpopulations) continuously emerge, grow, and disappear again. Biologically, we explicitly consider the synthesis and regulation of public good production. The discussion of the theoretical approaches includes general evolutionary concepts, population dynamics, and evolutionary game theory. As a specific but generic biological example, we consider populations of Pseudomonas putida and its regulation and use of pyoverdines, iron scavenging molecules, as public goods. The review closes with an overview on cooperation in spatially extended systems and also provides a critical assessment of the insights gained from the experimental and theoretical studies discussed. Current challenges and important new research opportunities are discussed, including the biochemical regulation of public goods, more realistic ecological scenarios resembling native environments, cell-to-cell signaling, and multispecies communities.
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Schmitz D, Nooij S, Janssens T, Cremer J, Vennema H, Kroneman A, Koopmans M. A43 Translational research: NGS metagenomics into clinical diagnostics. Virus Evol 2019. [PMCID: PMC6735915 DOI: 10.1093/ve/vez002.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
As research next-generation sequencing (NGS) metagenomic pipelines transition to clinical diagnostics, the user-base changes from bioinformaticians to biologists, medical doctors, and lab-technicians. Besides the obvious need for benchmarking and assessment of diagnostic outcomes of the pipelines and tools, other focus points remain: reproducibility, data immutability, user-friendliness, portability/scalability, privacy, and a clear audit trail. We have a research metagenomics pipeline that takes raw fastq files and produces annotated contigs, but it is too complicated for non-bioinformaticians. Here, we present preliminary findings in adapting this pipeline for clinical diagnostics. We used information available on relevant fora (www.bioinfo-core.org) and experiences and publications from colleague bioinformaticians in other institutes (COMPARE, UBC, and LUMC). From this information, a robust and user-friendly storage and analysis workflow was designed for non-bioinformaticians in a clinical setting. Via Conda [https://conda.io] and Docker containers [http://www.docker.com], we made our disparate pipeline processes self-contained and reproducible. Furthermore, we moved all pipeline settings into a separate JSON file. After every analysis, the pipeline settings and virtual-environment recipes will be archived (immutably) under a persistent unique identifier. This allows long-term precise reproducibility. Likewise, after every run the raw data and final products will be automatically archived, complying with data retention laws/guidelines. All the disparate processes in the pipeline are parallelized and automated via Snakemake1 (i.e. end-users need no coding skills). In addition, interactive web-reports such as MultiQC [http://multiqc.info] and Krona2 are generated automatically. By combining Snakemake, Conda, and containers, our pipeline is highly portable and easily scaled up for outbreak situations, or scaled down to reduce costs. Since patient privacy is a concern, our pipeline automatically removes human genetic data. Moreover, all source code will be stored on an internal Gitlab server, and, combined with the archived data, ensures a clear audit trail. Nevertheless, challenges remain: (1) reproducible reference databases, e.g. being able to revert to an older version to reproduce old analyses. (2) A user-friendly GUI. (3) Connecting the pipeline and NGS data to in-house LIMS. (4) Efficient long-term storage, e.g. lossless compression algorithms. Nevertheless, this work represents a step forward in making user-friendly clinical diagnostic workflows.
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Lapatschek M, Uhlrich N, Weingarten B, Astashkina Y, Cremer R, Hertlein S, Reichhuber S, Melchior W, Donner H, Cremer J. Performance evaluation of the new cobas e 801 instrument in medical routine. Clin Chim Acta 2019. [DOI: 10.1016/j.cca.2019.03.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Puehler T, Huenges K, Friedrich C, Salem M, Cremer J, Assad H. IS TOTAL ARCH REPLACEMENT ASSOCIATED WITH AN INCREASED RISK FOR 30-DAY MORTALITY AFTER SURGERY FOR ACUTE TYPE A DISSECTION. Chest 2019. [DOI: 10.1016/j.chest.2019.02.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Warren MR, Sun H, Yan Y, Cremer J, Li B, Hwa T. Spatiotemporal establishment of dense bacterial colonies growing on hard agar. eLife 2019; 8:e41093. [PMID: 30855227 PMCID: PMC6411370 DOI: 10.7554/elife.41093] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 02/20/2019] [Indexed: 01/21/2023] Open
Abstract
The physical interactions of growing bacterial cells with each other and with their surroundings significantly affect the structure and dynamics of biofilms. Here a 3D agent-based model is formulated to describe the establishment of simple bacterial colonies expanding by the physical force of their growth. With a single set of parameters, the model captures key dynamical features of colony growth by non-motile, non EPS-producing E. coli cells on hard agar. The model, supported by experiment on colony growth in different types and concentrations of nutrients, suggests that radial colony expansion is not limited by nutrients as commonly believed, but by mechanical forces. Nutrient penetration instead governs vertical colony growth, through thin layers of vertically oriented cells lifting up their ancestors from the bottom. Overall, the model provides a versatile platform to investigate the influences of metabolic and environmental factors on the growth and morphology of bacterial colonies.
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Grothusen C, Lankeit M, Olsson K, Panholzer B, Haneya A, Cremer J. Akute Lungenembolie. ZEITSCHRIFT FUR HERZ THORAX UND GEFASSCHIRURGIE 2019. [DOI: 10.1007/s00398-018-0286-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Bax L, Huenges K, Pokorny S, Loger K, Cremer J, Lutter G. Transapical Mitral Valve Implantation—Macroscopic and Histologic Findings after Up to 8 Weeks Follow-up. Thorac Cardiovasc Surg 2019. [DOI: 10.1055/s-0039-1678843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Huenges K, Salem M, Panholzer B, Friedrich C, Schöttler J, Schoeneich F, Pühler T, Cremer J, Haneya A. Influence of Acute Kidney Injury in Patients with Acute Aortic Dissection Type A. Thorac Cardiovasc Surg 2019. [DOI: 10.1055/s-0039-1678855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Panholzer B, Pilarczyk K, Huenges K, Morun G, Eide A, Rusch R, Balke L, Bewig B, Haake N, Cremer J, Haneya A. Acute Kidney Injury in Patients with Severe Acute Respiratory Distress Syndrome Requiring Extracorporeal Membrane Oxygenation: Incidence, Prognostic Impact, and Risk Factors. Thorac Cardiovasc Surg 2019. [DOI: 10.1055/s-0039-1678929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Panholzer B, Wegner M, Oldenburg P, Pilarczyk K, Huenges K, Salem M, Cremer J, Haneya A. Preoperative Serum Cystatin C as a Predictor of Acute Kidney Injury after Thoracic Aortic Surgery with Deep Hypothermic Circulatory Arrest. Thorac Cardiovasc Surg 2019. [DOI: 10.1055/s-0039-1678850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Saeed D, Potapov E, Loforte A, Morshuis M, Schibilsky D, Zimpfer D, Riebandt J, Pappalardo F, Attisani M, Haneya A, Ramjankhan F, Donker D, Tsyganenko D, Jorde U, Wieloch R, Cremer J, Beyersdorf F, Lichtenberg A, Gummert J. Transition from Short Term to Durable Mechanical Circulatory Support Systems. Outcome and Patient Selection. On Behalf of ECMO-VAD Study Group. Thorac Cardiovasc Surg 2019. [DOI: 10.1055/s-0039-1678886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Demertzis S, Wahlers T, Schüfers HJ, Wippermann J, Jurmann M, Cremer J, Haverich A. Myocardial preservation with the UW solution. First European results in clinical heart transplantation. Transpl Int 2018. [DOI: 10.1111/tri.1992.5.s1.343] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Baumgartner H, Cremer J, Eggebrecht H, Diegeler A, Hamm C, Welz A, Haude M, Beyersdorf F, Ince H, Walther T, Kuck KH, Falk V. Kommentar zu den Leitlinien (2017) der ESC/EACTS zum Management von Herzklappenerkrankungen. ZEITSCHRIFT FUR HERZ THORAX UND GEFASSCHIRURGIE 2018. [DOI: 10.1007/s00398-018-0244-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Abstract
The human gut microbiota is highly dynamic, and host physiology and diet exert major influences on its composition. In our recent study, we integrated new quantitative measurements on bacterial growth physiology with a reanalysis of published data on human physiology to build a comprehensive modeling framework. This can generate predictions of how changes in different host factors influence microbiota composition. For instance, hydrodynamic forces in the colon, along with colonic water absorption that manifests as transit time, exert a major impact on microbiota density and composition. This can be mechanistically explained by their effect on colonic pH which directly affects microbiota competition for food. In this addendum, we describe the underlying analysis in more detail. In particular, we discuss the mixing dynamics of luminal content by wall contractions and its implications for bacterial growth and density, as well as the broader implications of our insights for the field of gut microbiota research.
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Jurmann M, Averich AH, Demertzis S, Schaefers H, Zahner H, Endrigkeit K, Wahlers T, Cremer J, Borst H. Extracorporeal Membrane Oxygenation (Ecmo): Extended Indications for Artificial Support of Both Heart and Lungs. Int J Artif Organs 2018. [DOI: 10.1177/039139889101401205] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Extracorporeal membrane oxygenation (ECMO) was used to achieve temporary artificial support in cardiac and pulmonary function in 22 patients from 1987 to September 1990. Standard indications were postcardiotomy cardiogenic shock (n=4), neonatal (n=1) and adult respiratory distress syndrome (n=4). ECMO was also used for extended indications, such as graft failure following heart (n=11) or lung transplantation (n=2). In six of these cases ECMO was instituted as a bridge device to subsequent retransplantation of either the heart (n=4) or one lung (n=2). One out of nine patients supported by ECMO for standard indications, and two out of 13 patients supported for extended indications are long-term survivors. This series illustrates the results with ECMO in emergency situations, in patients under immunosuppressive protocols, or in patients with advanced lung failure requiring almost complete artificial gas exchange. In such complex situations, ECMO does provide stabilization until additional therapeutic measures are in effect. ECMO cannot be recommended for postoperative cardiogenic shock but short-term ECMO support is an accepted method in most cases with graft failure or pulmonary failure or other origin.
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Stock U, Bohuslavizki KH, Brenner W, Costard-Jaekle A, Cremer J, Clausen M, Tönshoff G. Szintigraphischer Nachweis einer stillen Aspiration nach beidseitiger Lungentransplantation. Nuklearmedizin 2018. [DOI: 10.1055/s-0038-1629828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
ZusammenfassungVorgestellt wird der Fall einer 25jährigen Patientin nach beidseitiger Lungentransplantation und rezidivierenden Pneumonien. Klinisch bestand der Verdacht auf eine stille Aspiration. Szintigraphisch gelang sowohl der Aspirationsnachweis als auch eine Differenzierung hinsichtlich der Genese: direkte oro-pulmonale Aspiration versus Aspiration nach gastro-öspohagealem Reflux.
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Puehler T, Salem M, Huenges K, Panholzer B, Friedrich C, Schoettler J, Schoeneich F, Cremer J, Haneya A. Is Total Arch Replacement Associated with an Increased Risk for 30-day Mortality after Surgery for Acute Type A Dissection. Thorac Cardiovasc Surg 2018. [DOI: 10.1055/s-0038-1627889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Salem M, Salem A, Düver S, Erdal Y, Psykalla N, Friedrich C, Panholzer B, Huenges K, Pühler T, Schoettler J, Schoeneich F, Cremer J, Haneya A. Effect of Deep Hypothermia Circulatory Arrest on Neurological Outcomes in Patients Undergoing Replacement of Ascending Aorta: A Comparison between Young and Elderly Adults. Thorac Cardiovasc Surg 2018. [DOI: 10.1055/s-0038-1628051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Grothusen C, Ohnewald E, Friedrich C, Ashbahs M, Meinert J, Huenges K, Attmann T, Haneya A, Schoettler J, Cremer J. Sex-dependent Differences after Early Operative Myocardial Revascularization in Acute Myocardial Infarction. Thorac Cardiovasc Surg 2018. [DOI: 10.1055/s-0038-1627489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Lagos-Carvajal A, Queiroz-Williams P, Ricco C, Nevarez J, Cremer J, da Cunha A, Liu C. The use of priming alfaxalone as an induction technique in cats. Vet Anaesth Analg 2017. [DOI: 10.1016/j.vaa.2017.09.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Lagos-Carvajal A, Queiroz-Williams P, Nevarez J, Ricco C, da Cunha A, Cremer J, Liu C. Priming alfaxalone and alfaxalone–midazolam co-induction techniques in dogs. Vet Anaesth Analg 2017. [DOI: 10.1016/j.vaa.2017.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Cremer J, Ricco C. The cardiovascular, respiratory and sedative effects of intramuscular administration of alfaxalone with butorphanol, and dexmedetomidine compared to ketamine, butorphanol, and dexmedetomidine in healthy cats. Vet Anaesth Analg 2017. [DOI: 10.1016/j.vaa.2017.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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49
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Cremer J. Der Titan geht von Bord. ZEITSCHRIFT FUR HERZ THORAX UND GEFASSCHIRURGIE 2017. [DOI: 10.1007/s00398-017-0170-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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50
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Pilarczyk K, Panholzer B, Haneya A, Cremer J, Haake N. „Tissue inhibitor of metalloproteinase 2“ und „insulin-like growth factor-binding protein 7“. ZEITSCHRIFT FUR HERZ THORAX UND GEFASSCHIRURGIE 2017. [DOI: 10.1007/s00398-017-0142-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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