1
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Schindler D, Walker RSK, Cai Y. Methodological advances enabled by the construction of a synthetic yeast genome. Cell Rep Methods 2024; 4:100761. [PMID: 38653205 DOI: 10.1016/j.crmeth.2024.100761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/25/2024]
Abstract
The international Synthetic Yeast Project (Sc2.0) aims to construct the first synthetic designer eukaryote genome. Over the past few years, the Sc2.0 consortium has achieved several significant milestones by synthesizing and characterizing all 16 nuclear chromosomes of the yeast Saccharomyces cerevisiae, as well as a 17thde novo neochromosome containing all nuclear tRNA genes. In this commentary, we discuss the recent technological advances achieved in this project and provide a perspective on how they will impact the emerging field of synthetic genomics in the future.
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Affiliation(s)
- Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, 35032 Marburg, Germany.
| | - Roy S K Walker
- School of Natural Sciences and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
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2
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Lindeboom T, Sanchez Olmos MDC, Schulz K, Brinkmann CK, Ramírez Rojas AA, Hochrein L, Schindler D. An Optimized Genotyping Workflow for Identifying Highly SCRaMbLEd Synthetic Yeasts. ACS Synth Biol 2024; 13:1116-1127. [PMID: 38597458 PMCID: PMC11036488 DOI: 10.1021/acssynbio.3c00476] [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: 08/03/2023] [Revised: 03/01/2024] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Synthetic Sc2.0 yeast strains contain hundreds to thousands of loxPsym recombination sites that allow restructuring of the Saccharomyces cerevisiae genome by SCRaMbLE. Thus, a highly diverse yeast population can arise from a single genotype. The selection of genetically diverse candidates with rearranged synthetic chromosomes for downstream analysis requires an efficient and straightforward workflow. Here we present loxTags, a set of qPCR primers for genotyping across loxPsym sites to detect not only deletions but also inversions and translocations after SCRaMbLE. To cope with the large number of amplicons, we generated qTagGer, a qPCR genotyping primer prediction tool. Using loxTag-based genotyping and long-read sequencing, we show that light-inducible Cre recombinase L-SCRaMbLE can efficiently generate diverse recombination events when applied to Sc2.0 strains containing a linear or a circular version of synthetic chromosome III.
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Affiliation(s)
- Timon
A. Lindeboom
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | | | - Karina Schulz
- Department
of Molecular Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany
| | - Cedric K. Brinkmann
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Adán A. Ramírez Rojas
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Lena Hochrein
- Department
of Molecular Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany
| | - Daniel Schindler
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- Center
for Synthetic Microbiology, Philipps-University
Marburg, Karl-von-Frisch-Str.
14, 35032Marburg, Germany
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3
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Sendker FL, Lo YK, Heimerl T, Bohn S, Persson LJ, Mais CN, Sadowska W, Paczia N, Nußbaum E, Del Carmen Sánchez Olmos M, Forchhammer K, Schindler D, Erb TJ, Benesch JLP, Marklund EG, Bange G, Schuller JM, Hochberg GKA. Emergence of fractal geometries in the evolution of a metabolic enzyme. Nature 2024; 628:894-900. [PMID: 38600380 PMCID: PMC11041685 DOI: 10.1038/s41586-024-07287-2] [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: 04/20/2023] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
Fractals are patterns that are self-similar across multiple length-scales1. Macroscopic fractals are common in nature2-4; however, so far, molecular assembly into fractals is restricted to synthetic systems5-12. Here we report the discovery of a natural protein, citrate synthase from the cyanobacterium Synechococcus elongatus, which self-assembles into Sierpiński triangles. Using cryo-electron microscopy, we reveal how the fractal assembles from a hexameric building block. Although different stimuli modulate the formation of fractal complexes and these complexes can regulate the enzymatic activity of citrate synthase in vitro, the fractal may not serve a physiological function in vivo. We use ancestral sequence reconstruction to retrace how the citrate synthase fractal evolved from non-fractal precursors, and the results suggest it may have emerged as a harmless evolutionary accident. Our findings expand the space of possible protein complexes and demonstrate that intricate and regulatable assemblies can evolve in a single substitution.
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Affiliation(s)
- Franziska L Sendker
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Yat Kei Lo
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Stefan Bohn
- Cryo-EM Platform and Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany
| | - Louise J Persson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | - Wiktoria Sadowska
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Nicole Paczia
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Eva Nußbaum
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Tübingen, Germany
| | | | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Tübingen, Germany
| | - Daniel Schindler
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- MaxGENESYS Biofoundry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J Erb
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Max Planck Fellow Group Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan M Schuller
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany.
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany.
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4
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Ramírez Rojas A, Brinkmann CK, Köbel TS, Schindler D. DuBA.flow─A Low-Cost, Long-Read Amplicon Sequencing Workflow for the Validation of Synthetic DNA Constructs. ACS Synth Biol 2024; 13:457-465. [PMID: 38295293 PMCID: PMC10877597 DOI: 10.1021/acssynbio.3c00522] [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: 08/25/2023] [Revised: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 02/02/2024]
Abstract
Modern biological science, especially synthetic biology, relies heavily on the construction of DNA elements, often in the form of plasmids. Plasmids are used for a variety of applications, including the expression of proteins for subsequent purification, the expression of heterologous pathways for the production of valuable compounds, and the study of biological functions and mechanisms. For all applications, a critical step after the construction of a plasmid is its sequence validation. The traditional method for sequence determination is Sanger sequencing, which is limited to approximately 1000 bp per reaction. Here, we present a highly scalable in-house method for rapid validation of amplified DNA sequences using long-read Nanopore sequencing. We developed two-step amplicon and transposase strategies to provide maximum flexibility for dual barcode sequencing. We also provide an automated analysis pipeline to quickly and reliably analyze sequencing results and provide easy-to-interpret results for each sample. The user-friendly DuBA.flow start-to-finish pipeline is widely applicable. Furthermore, we show that construct validation using DuBA.flow can be performed by barcoded colony PCR amplicon sequencing, thus accelerating research.
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Affiliation(s)
- Adán
A. Ramírez Rojas
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Cedric K. Brinkmann
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Tania S. Köbel
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Daniel Schindler
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- Center
for Synthetic Microbiology, Philipps-University
Marburg, Karl-von-Frisch-Str.
14, 35032 Marburg, Germany
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5
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Cheng L, Zhao S, Li T, Hou S, Luo Z, Xu J, Yu W, Jiang S, Monti M, Schindler D, Zhang W, Hou C, Ma Y, Cai Y, Boeke JD, Dai J. Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae. Nat Commun 2024; 15:770. [PMID: 38278805 PMCID: PMC10817965 DOI: 10.1038/s41467-023-44511-5] [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: 06/30/2023] [Accepted: 12/13/2023] [Indexed: 01/28/2024] Open
Abstract
Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is a promising tool to study genomic rearrangements. However, the potential of SCRaMbLE to study genomic rearrangements is currently hindered, because a strain containing all 16 synthetic chromosomes is not yet available. Here, we construct SparLox83R, a yeast strain containing 83 loxPsym sites distributed across all 16 chromosomes. SCRaMbLE of SparLox83R produces versatile genome-wide genomic rearrangements, including inter-chromosomal events. Moreover, when combined with synthetic chromosomes, SCRaMbLE of hetero-diploids with SparLox83R leads to increased diversity of genomic rearrangements and relatively faster evolution of traits compared to hetero-diploids only with wild-type chromosomes. Analysis of the SCRaMbLEd strain with increased tolerance to nocodazole demonstrates that genomic rearrangements can perturb the transcriptome and 3D genome structure and consequently impact phenotypes. In summary, a genome with sparsely distributed loxPsym sites can serve as a powerful tool for studying the consequence of genomic rearrangements and accelerating strain engineering in Saccharomyces cerevisiae.
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Grants
- 32030004, 32150025 National Natural Science Foundation of China (National Science Foundation of China)
- 32001042 National Natural Science Foundation of China (National Science Foundation of China)
- 32101184 National Natural Science Foundation of China (National Science Foundation of China)
- 32122050 National Natural Science Foundation of China (National Science Foundation of China)
- 2021359 Youth Innovation Promotion Association of the Chinese Academy of Sciences (Youth Innovation Promotion Association CAS)
- National Key R&D Program of China (2022YFF1201800,2018YFA0900100), Guangdong Natural Science Funds for Distinguished Young Scholar (2021B1515020060), Guangdong Provincial Key Laboratory of Synthetic Genomics (2023B1212060054), Bureau of International Cooperation, Chinese Academy of Sciences (172644KYSB20180022), Shenzhen Science and Technology Program (KQTD20180413181837372, KQTD20200925153547003), Innovation Program of Chinese Academy of Agricultural Science and Shenzhen Outstanding Talents Training Fund.
- Guandong Basic and Applied Basic Research Foundation (2023A1515030285)
- UK Biotechnology and Biological Sciences Research Council (BBSRC) grants BB/M005690/1, BB/P02114X/1 and BB/W014483/1, Royal Society Newton Advanced Fellowship (NAF\R2\180590) and a Volkswagen Foundation “Life? Initiative” Grant (Ref. 94 771)
- US NSF grants MCB-1026068, MCB-1443299, MCB-1616111 and MCB-1921641
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Affiliation(s)
- Li Cheng
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shijun Zhao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianyi Li
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Shenzhen Lianghe Biotechnology Co., Ltd., Shenzhen, China
| | - Sha Hou
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhouqing Luo
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Jinsheng Xu
- Department of Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenfei Yu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuangying Jiang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Marco Monti
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Daniel Schindler
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Chunhui Hou
- China State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yingxin Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yizhi Cai
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, 11201, USA
| | - Junbiao Dai
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- College of Life Sciences and Oceanography, Shenzhen University, 1066 Xueyuan Rd, Shenzhen, 518055, Guangdong, China.
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6
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Schindler D, Moldenhawer T, Beta C, Huisinga W, Holschneider M. Three-component contour dynamics model to simulate and analyze amoeboid cell motility in two dimensions. PLoS One 2024; 19:e0297511. [PMID: 38277351 PMCID: PMC10817190 DOI: 10.1371/journal.pone.0297511] [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: 08/27/2023] [Accepted: 01/07/2024] [Indexed: 01/28/2024] Open
Abstract
Amoeboid cell motility is relevant in a wide variety of biomedical processes such as wound healing, cancer metastasis, and embryonic morphogenesis. It is characterized by pronounced changes of the cell shape associated with expansions and retractions of the cell membrane, which result in a crawling kind of locomotion. Despite existing computational models of amoeboid motion, the inference of expansion and retraction components of individual cells, the corresponding classification of cells, and the a priori specification of the parameter regime to achieve a specific motility behavior remain challenging open problems. We propose a novel model of the spatio-temporal evolution of two-dimensional cell contours comprising three biophysiologically motivated components: a stochastic term accounting for membrane protrusions and two deterministic terms accounting for membrane retractions by regularizing the shape and area of the contour. Mathematically, these correspond to the intensity of a self-exciting Poisson point process, the area-preserving curve-shortening flow, and an area adjustment flow. The model is used to generate contour data for a variety of qualitatively different, e.g., polarized and non-polarized, cell tracks that visually resemble experimental data very closely. In application to experimental cell tracks, we inferred the protrusion component and examined its correlation to common biomarkers: the F-actin density close to the membrane and its local motion. Due to the low model complexity, parameter estimation is fast, straightforward, and offers a simple way to classify contour dynamics based on two locomotion types: the amoeboid and a so-called fan-shaped type. For both types, we use cell tracks segmented from fluorescence imaging data of the model organism Dictyostelium discoideum. An implementation of the model is provided within the open-source software package AmoePy, a Python-based toolbox for analyzing and simulating amoeboid cell motility.
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Affiliation(s)
- Daniel Schindler
- Institute of Mathematics, University of Potsdam, Potsdam, Germany
- CRC 1294 Data Assimilation, University of Potsdam, Potsdam, Germany
| | - Ted Moldenhawer
- Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany
- CRC 1294 Data Assimilation, University of Potsdam, Potsdam, Germany
| | - Carsten Beta
- Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany
- CRC 1294 Data Assimilation, University of Potsdam, Potsdam, Germany
| | - Wilhelm Huisinga
- Institute of Mathematics, University of Potsdam, Potsdam, Germany
- CRC 1294 Data Assimilation, University of Potsdam, Potsdam, Germany
| | - Matthias Holschneider
- Institute of Mathematics, University of Potsdam, Potsdam, Germany
- CRC 1294 Data Assimilation, University of Potsdam, Potsdam, Germany
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7
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Brück M, Berghoff BA, Schindler D. In Silico Design, In Vitro Construction, and In Vivo Application of Synthetic Small Regulatory RNAs in Bacteria. Methods Mol Biol 2024; 2760:479-507. [PMID: 38468105 DOI: 10.1007/978-1-0716-3658-9_27] [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] [Indexed: 03/13/2024]
Abstract
Small regulatory RNAs (sRNAs) are short non-coding RNAs in bacteria capable of post-transcriptional regulation. sRNAs have recently gained attention as tools in basic and applied sciences, for example, to fine-tune genetic circuits or biotechnological processes. Even though sRNAs often have a rather simple and modular structure, the design of functional synthetic sRNAs is not necessarily trivial. This protocol outlines how to use computational predictions and synthetic biology approaches to design, construct, and validate synthetic sRNA functionality for their application in bacteria. The computational tool, SEEDling, matches the optimal seed region with the user-selected sRNA scaffold for repression of target mRNAs. The synthetic sRNAs are assembled using Golden Gate cloning and their functionality is subsequently validated. The protocol uses the acrA mRNA as an exemplary proof-of-concept target in Escherichia coli. Since AcrA is part of a multidrug efflux pump, acrA repression can be revealed by assessing oxacillin susceptibility in a phenotypic screen. However, in case target repression does not result in a screenable phenotype, an alternative validation of synthetic sRNA functionality based on a fluorescence reporter is described.
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Affiliation(s)
- Michel Brück
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Institute for Microbiology and Molecular Biology, Justus-Liebig University Giessen, Giessen, Germany
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus-Liebig University Giessen, Giessen, Germany
| | - Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
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8
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Abramczyk D, Del Carmen Sanchez Olmos M, Rojas AAR, Schindler D, Robertson D, McColm S, Marston AL, Barlow PN. A supernumerary synthetic chromosome in Komagataella phaffii as a repository for extraneous genetic material. Microb Cell Fact 2023; 22:259. [PMID: 38104077 PMCID: PMC10724962 DOI: 10.1186/s12934-023-02262-4] [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: 08/17/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Komagataella phaffii (Pichia pastoris) is a methylotrophic commercially important non-conventional species of yeast that grows in a fermentor to exceptionally high densities on simple media and secretes recombinant proteins efficiently. Genetic engineering strategies are being explored in this organism to facilitate cost-effective biomanufacturing. Small, stable artificial chromosomes in K. phaffii could offer unique advantages by accommodating multiple integrations of extraneous genes and their promoters without accumulating perturbations of native chromosomes or exhausting the availability of selection markers. RESULTS Here, we describe a linear "nano"chromosome (of 15-25 kb) that, according to whole-genome sequencing, persists in K. phaffii over many generations with a copy number per cell of one, provided non-homologous end joining is compromised (by KU70-knockout). The nanochromosome includes a copy of the centromere from K. phaffii chromosome 3, a K. phaffii-derived autonomously replicating sequence on either side of the centromere, and a pair of K. phaffii-like telomeres. It contains, within its q arm, a landing zone in which genes of interest alternate with long (approx. 1-kb) non-coding DNA chosen to facilitate homologous recombination and serve as spacers. The landing zone can be extended along the nanochromosome, in an inch-worming mode of sequential gene integrations, accompanied by recycling of just two antibiotic-resistance markers. The nanochromosome was used to express PDI, a gene encoding protein disulfide isomerase. Co-expression with PDI allowed the production, from a genomically integrated gene, of secreted murine complement factor H, a plasma protein containing 40 disulfide bonds. As further proof-of-principle, we co-expressed, from a nanochromosome, both PDI and a gene for GFP-tagged human complement factor H under the control of PAOX1 and demonstrated that the secreted protein was active as a regulator of the complement system. CONCLUSIONS We have added K. phaffii to the list of organisms that can produce human proteins from genes carried on a stable, linear, artificial chromosome. We envisage using nanochromosomes as repositories for numerous extraneous genes, allowing intensive engineering of K. phaffii without compromising its genome or weakening the resulting strain.
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Affiliation(s)
| | | | | | - Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Daniel Robertson
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Adele L Marston
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Paul N Barlow
- School of Chemistry, University of Edinburgh, Edinburgh, UK.
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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9
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Jiang S, Luo Z, Wu J, Yu K, Zhao S, Cai Z, Yu W, Wang H, Cheng L, Liang Z, Gao H, Monti M, Schindler D, Huang L, Zeng C, Zhang W, Zhou C, Tang Y, Li T, Ma Y, Cai Y, Boeke JD, Zhao Q, Dai J. Building a eukaryotic chromosome arm by de novo design and synthesis. Nat Commun 2023; 14:7886. [PMID: 38036514 PMCID: PMC10689750 DOI: 10.1038/s41467-023-43531-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 07/11/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
The genome of an organism is inherited from its ancestor and continues to evolve over time, however, the extent to which the current version could be altered remains unknown. To probe the genome plasticity of Saccharomyces cerevisiae, here we replace the native left arm of chromosome XII (chrXIIL) with a linear artificial chromosome harboring small sets of reconstructed genes. We find that as few as 12 genes are sufficient for cell viability, whereas 25 genes are required to recover the partial fitness defects observed in the 12-gene strain. Next, we demonstrate that these genes can be reconstructed individually using synthetic regulatory sequences and recoded open-reading frames with a "one-amino-acid-one-codon" strategy to remain functional. Finally, a synthetic neochromsome with the reconstructed genes is assembled which could substitute chrXIIL for viability. Together, our work not only highlights the high plasticity of yeast genome, but also illustrates the possibility of making functional eukaryotic chromosomes from entirely artificial sequences.
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Grants
- National Natural Science Foundation of China (31725002), Shenzhen Science and Technology Program (KQTD20180413181837372), Guangdong Provincial Key Laboratory of Synthetic Genomics (2019B030301006),Bureau of International Cooperation,Chinese Academy of Sciences (172644KYSB20180022) and Shenzhen Outstanding Talents Training Fund.
- National Key Research and Development Program of China (2018YFA0900100),National Natural Science Foundation of China (31800069),Guangdong Basic and Applied Basic Research Foundation (2023A1515030285)
- National Key Research and Development Program of China (2018YFA0900100), National Natural Science Foundation of China (31800082 and 32122050),Guangdong Natural Science Funds for Distinguished Young Scholar (2021B1515020060)
- UK Biotechnology and Biological Sciences Research Council (BBSRC) grants BB/M005690/1, BB/P02114X/1 and BB/W014483/1, and a Volkswagen Foundation “Life? Initiative” Grant (Ref. 94 771)
- US NSF grants MCB-1026068, MCB-1443299, MCB-1616111 and MCB-1921641
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Affiliation(s)
- Shuangying Jiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhouqing Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Jie Wu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Kang Yu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Shijun Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zelin Cai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenfei Yu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Li Cheng
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhenzhen Liang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui Gao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Marco Monti
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Daniel Schindler
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Linsen Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Zeng
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, 10016, USA
| | - Chun Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuanwei Tang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Tianyi Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yizhi Cai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, 11201, USA
| | - Qiao Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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10
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Schindler D, Walker RSK, Jiang S, Brooks AN, Wang Y, Müller CA, Cockram C, Luo Y, García A, Schraivogel D, Mozziconacci J, Pena N, Assari M, Sánchez Olmos MDC, Zhao Y, Ballerini A, Blount BA, Cai J, Ogunlana L, Liu W, Jönsson K, Abramczyk D, Garcia-Ruiz E, Turowski TW, Swidah R, Ellis T, Pan T, Antequera F, Shen Y, Nieduszynski CA, Koszul R, Dai J, Steinmetz LM, Boeke JD, Cai Y. Design, construction, and functional characterization of a tRNA neochromosome in yeast. Cell 2023; 186:5237-5253.e22. [PMID: 37944512 DOI: 10.1016/j.cell.2023.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 10/06/2022] [Revised: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
Here, we report the design, construction, and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo counterpart to the native complement of Saccharomyces cerevisiae. Intending to address one of the central design principles of the Sc2.0 project, the ∼190-kb tRNA neochromosome houses all 275 relocated nuclear tRNA genes. To maximize stability, the design incorporates orthogonal genetic elements from non-S. cerevisiae yeast species. Furthermore, the presence of 283 rox recombination sites enables an orthogonal tRNA SCRaMbLE system. Following construction in yeast, we obtained evidence of a potent selective force, manifesting as a spontaneous doubling in cell ploidy. Furthermore, tRNA sequencing, transcriptomics, proteomics, nucleosome mapping, replication profiling, FISH, and Hi-C were undertaken to investigate questions of tRNA neochromosome behavior and function. Its construction demonstrates the remarkable tractability of the yeast model and opens up opportunities to directly test hypotheses surrounding these essential non-coding RNAs.
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Affiliation(s)
- Daniel Schindler
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, 35032 Marburg, Germany
| | - Roy S K Walker
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3BF, Scotland; School of Natural Sciences and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Shuangying Jiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Aaron N Brooks
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Yun Wang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Carolin A Müller
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, UK
| | - Charlotte Cockram
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Yisha Luo
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Alicia García
- Instituto de Biología Funcional y Genómica (IBFG), CSIC, Universidad de Salamanca, Salamanca, Spain
| | - Daniel Schraivogel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Julien Mozziconacci
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Noah Pena
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Mahdi Assari
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | | | - Yu Zhao
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Alba Ballerini
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Benjamin A Blount
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK
| | - Jitong Cai
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Lois Ogunlana
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland
| | - Wei Liu
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland
| | - Katarina Jönsson
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland
| | - Dariusz Abramczyk
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland
| | - Eva Garcia-Ruiz
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Tomasz W Turowski
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland
| | - Reem Swidah
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Francisco Antequera
- Instituto de Biología Funcional y Genómica (IBFG), CSIC, Universidad de Salamanca, Salamanca, Spain
| | - Yue Shen
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK; BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Conrad A Nieduszynski
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, UK
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Department of Genetics and Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
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11
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Shen Y, Gao F, Wang Y, Wang Y, Zheng J, Gong J, Zhang J, Luo Z, Schindler D, Deng Y, Ding W, Lin T, Swidah R, Zhao H, Jiang S, Zeng C, Chen S, Chen T, Wang Y, Luo Y, Mitchell L, Bader JS, Zhang G, Shen X, Wang J, Fu X, Dai J, Boeke JD, Yang H, Xu X, Cai Y. Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast. Cell Genom 2023; 3:100364. [PMID: 38020968 PMCID: PMC10667312 DOI: 10.1016/j.xgen.2023.100364] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 04/03/2023] [Accepted: 07/06/2023] [Indexed: 12/01/2023]
Abstract
Aneuploidy compromises genomic stability, often leading to embryo inviability, and is frequently associated with tumorigenesis and aging. Different aneuploid chromosome stoichiometries lead to distinct transcriptomic and phenotypic changes, making it helpful to study aneuploidy in tightly controlled genetic backgrounds. By deploying the engineered SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution) system to the newly synthesized megabase Sc2.0 chromosome VII (synVII), we constructed a synthetic disomic yeast and screened hundreds of SCRaMbLEd derivatives with diverse chromosomal rearrangements. Phenotypic characterization and multi-omics analysis revealed that fitness defects associated with aneuploidy could be restored by (1) removing most of the chromosome content or (2) modifying specific regions in the duplicated chromosome. These findings indicate that both chromosome copy number and specific chromosomal regions contribute to the aneuploidy-related phenotypes, and the synthetic chromosome resource opens new paradigms in studying aneuploidy.
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Affiliation(s)
- Yue Shen
- BGI Research, Shenzhen 518083, China
- BGI Research, Changzhou 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Gao
- BGI Research, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Yun Wang
- BGI Research, Shenzhen 518083, China
- BGI Research, Changzhou 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Yuerong Wang
- BGI Research, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ju Zheng
- BGI Research, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | | | | | - Zhouqing Luo
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Daniel Schindler
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Yang Deng
- BGI Research, Shenzhen 518083, China
| | - Weichao Ding
- BGI Research, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Lin
- BGI Research, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Reem Swidah
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Hongcui Zhao
- BGI Research, Shenzhen 518083, China
- BGI Research, Changzhou 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Shuangying Jiang
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
| | - Cheng Zeng
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
| | | | - Tai Chen
- BGI Research, Shenzhen 518083, China
- BGI Research, Changzhou 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Yong Wang
- BGI Research, Shenzhen 518083, China
| | - Yisha Luo
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Leslie Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Joel S. Bader
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Guojie Zhang
- University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Xia Shen
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Center for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Jian Wang
- BGI Research, Shenzhen 518083, China
| | - Xian Fu
- BGI Research, Shenzhen 518083, China
- BGI Research, Changzhou 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Junbiao Dai
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
| | - Jef D. Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | | | - Xun Xu
- BGI Research, Shenzhen 518083, China
- BGI Research, Changzhou 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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12
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Philipp N, Brinkmann CK, Georg J, Schindler D, Berghoff BA. DIGGER-Bac: prediction of seed regions for high-fidelity construction of synthetic small RNAs in bacteria. Bioinformatics 2023; 39:7136644. [PMID: 37086442 PMCID: PMC10172035 DOI: 10.1093/bioinformatics/btad285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/10/2023] [Accepted: 04/12/2023] [Indexed: 04/23/2023]
Abstract
SUMMARY Synthetic small RNAs are gaining increasing attention in the field of synthetic biology and bioengineering for efficient post-transcriptional regulation of gene expression. However, the optimal design of synthetic small RNAs is challenging because alterations may impair functions or off-target effects can arise. Here, we introduce DIGGER-Bac, a toolbox for Design and Identification of seed regions for Golden Gate assembly and Expression of synthetic small RNAs in Bacteria. The SEEDling tool predicts optimal small RNA seed regions in combination with user-defined small RNA scaffolds for efficient regulation of specified mRNA targets. Results are passed on to the G-GArden tool, which assists with primer design for high-fidelity Golden Gate assembly of the desired synthetic small RNA constructs. AVAILABILITY AND IMPLEMENTATION Both SEEDling and G-GArden are freely available at https://github.com/DIGGER-Bac under the CC BY-NC-SA 4.0 license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Niklas Philipp
- Institute for Microbiology and Molecular Biology, Justus-Liebig University Giessen, Giessen, 35392, Germany
| | - Cedric K Brinkmann
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Jens Georg
- Albert-Ludwigs-Universität Freiburg, Institut für Biologie III, Freiburg, 79104, Germany
| | - Daniel Schindler
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, 35043, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, 35043, Germany
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus-Liebig University Giessen, Giessen, 35392, Germany
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13
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Steube N, Moldenhauer M, Weiland P, Saman D, Kilb A, Ramírez Rojas AA, Garg SG, Schindler D, Graumann PL, Benesch JLP, Bange G, Friedrich T, Hochberg GKA. Fortuitously compatible protein surfaces primed allosteric control in cyanobacterial photoprotection. Nat Ecol Evol 2023; 7:756-767. [PMID: 37012377 PMCID: PMC10172135 DOI: 10.1038/s41559-023-02018-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/21/2023] [Indexed: 04/05/2023]
Abstract
Highly specific interactions between proteins are a fundamental prerequisite for life, but how they evolve remains an unsolved problem. In particular, interactions between initially unrelated proteins require that they evolve matching surfaces. It is unclear whether such surface compatibilities can only be built by selection in small incremental steps, or whether they can also emerge fortuitously. Here, we used molecular phylogenetics, ancestral sequence reconstruction and biophysical characterization of resurrected proteins to retrace the evolution of an allosteric interaction between two proteins that act in the cyanobacterial photoprotection system. We show that this interaction between the orange carotenoid protein (OCP) and its unrelated regulator, the fluorescence recovery protein (FRP), evolved when a precursor of FRP was horizontally acquired by cyanobacteria. FRP's precursors could already interact with and regulate OCP even before these proteins first encountered each other in an ancestral cyanobacterium. The OCP-FRP interaction exploits an ancient dimer interface in OCP, which also predates the recruitment of FRP into the photoprotection system. Together, our work shows how evolution can fashion complex regulatory systems easily out of pre-existing components.
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Affiliation(s)
- Niklas Steube
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Marcus Moldenhauer
- Institute of Chemistry PC14, Technische Universität Berlin, Berlin, Germany
| | - Paul Weiland
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Dominik Saman
- Department of Chemistry, Oxford University, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford University, Oxford, UK
| | - Alexandra Kilb
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | | | - Sriram G Garg
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Peter L Graumann
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Justin L P Benesch
- Department of Chemistry, Oxford University, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford University, Oxford, UK
| | - Gert Bange
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Thomas Friedrich
- Institute of Chemistry PC14, Technische Universität Berlin, Berlin, Germany.
| | - Georg K A Hochberg
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Department of Chemistry, University of Marburg, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
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14
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Haberstroh S, Werner C, Grün M, Kreuzwieser J, Seifert T, Schindler D, Christen A. Central European 2018 hot drought shifts scots pine forest to its tipping point. Plant Biol (Stuttg) 2022; 24:1186-1197. [PMID: 35869655 DOI: 10.1111/plb.13455] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
The occurrence of hot drought, i.e. low water availability and simultaneous high air temperature, represents a severe threat to ecosystems. Here, we investigated how the 2018 hot drought in Central Europe caused a tipping point in tree and ecosystem functioning in a Scots pine (Pinus sylvestris L.) forest in southwest Germany. Measurements of stress indicators, such as needle water potential, carbon assimilation and volatile organic compound (VOC) emissions, of dominant P. sylvestris trees were deployed to evaluate tree functioning during hot drought. Ecosystem impact and recovery were assessed as ecosystem carbon exchange, normalized difference vegetation index (NDVI) from satellite data and tree mortality data. During summer 2018, needle water potentials of trees dropped to minimum values of -7.5 ± 0.2 MPa, which implied severe hydraulic impairment of P. sylvestris. Likewise, carbon assimilation and VOC emissions strongly declined after mid-July. Decreasing NDVI values from August 2018 onwards were detected, along with severe defoliation in P. sylvestris, impairing ecosystem carbon flux recovery in 2019, shifting the forest into a year-round carbon source. A total of 47% of all monitored trees (n = 368) died by September 2020. NDVI recovered to pre-2018 levels in 2019, likely caused by emerging broadleaved understorey species. The 2018 hot drought had severe negative impacts on P. sylvestris. The co-occurrence of unfavourable site-specific conditions with recurrent severe droughts resulted in accelerated mortality. Thus, the 2018 hot drought pushed the P. sylvestris stand towards its tipping point, with a subsequent vegetation shift to a broadleaf-dominated forest.
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Affiliation(s)
- S Haberstroh
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University Freiburg, Freiburg, Germany
| | - C Werner
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University Freiburg, Freiburg, Germany
| | - M Grün
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University Freiburg, Freiburg, Germany
| | - J Kreuzwieser
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University Freiburg, Freiburg, Germany
| | - T Seifert
- Forest Growth and Dendroecology, Faculty of Environment and Natural Resources, University Freiburg, Freiburg, Germany
- Department of Forest and Wood Science, Stellenbosch University, Matieland, South Africa
| | - D Schindler
- Environmental Meteorology, Faculty of Environment and Natural Resources, University Freiburg, Freiburg, Germany
| | - A Christen
- Environmental Meteorology, Faculty of Environment and Natural Resources, University Freiburg, Freiburg, Germany
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15
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Moldenhawer T, Moreno E, Schindler D, Flemming S, Holschneider M, Huisinga W, Alonso S, Beta C. Spontaneous transitions between amoeboid and keratocyte-like modes of migration. Front Cell Dev Biol 2022; 10:898351. [PMID: 36247011 PMCID: PMC9563996 DOI: 10.3389/fcell.2022.898351] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/18/2022] [Indexed: 01/17/2023] Open
Abstract
The motility of adherent eukaryotic cells is driven by the dynamics of the actin cytoskeleton. Despite the common force-generating actin machinery, different cell types often show diverse modes of locomotion that differ in their shape dynamics, speed, and persistence of motion. Recently, experiments in Dictyostelium discoideum have revealed that different motility modes can be induced in this model organism, depending on genetic modifications, developmental conditions, and synthetic changes of intracellular signaling. Here, we report experimental evidence that in a mutated D. discoideum cell line with increased Ras activity, switches between two distinct migratory modes, the amoeboid and fan-shaped type of locomotion, can even spontaneously occur within the same cell. We observed and characterized repeated and reversible switchings between the two modes of locomotion, suggesting that they are distinct behavioral traits that coexist within the same cell. We adapted an established phenomenological motility model that combines a reaction-diffusion system for the intracellular dynamics with a dynamic phase field to account for our experimental findings.
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Affiliation(s)
- Ted Moldenhawer
- Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany
| | - Eduardo Moreno
- Department of Physics, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Daniel Schindler
- Institute of Mathematics, University of Potsdam, Potsdam, Germany
| | - Sven Flemming
- Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany
| | | | - Wilhelm Huisinga
- Institute of Mathematics, University of Potsdam, Potsdam, Germany
| | - Sergio Alonso
- Department of Physics, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Carsten Beta
- Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany
- *Correspondence: Carsten Beta,
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Ramírez Rojas AA, Swidah R, Schindler D. Microbes of traditional fermentation processes as synthetic biology chassis to tackle future food challenges. Front Bioeng Biotechnol 2022; 10:982975. [PMID: 36185425 PMCID: PMC9523148 DOI: 10.3389/fbioe.2022.982975] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022] Open
Abstract
Microbial diversity is magnificent and essential to almost all life on Earth. Microbes are an essential part of every human, allowing us to utilize otherwise inaccessible resources. It is no surprise that humans started, initially unconsciously, domesticating microbes for food production: one may call this microbial domestication 1.0. Sourdough bread is just one of the miracles performed by microbial fermentation, allowing extraction of more nutrients from flour and at the same time creating a fluffy and delicious loaf. There are a broad range of products the production of which requires fermentation such as chocolate, cheese, coffee and vinegar. Eventually, with the rise of microscopy, humans became aware of microbial life. Today our knowledge and technological advances allow us to genetically engineer microbes - one may call this microbial domestication 2.0. Synthetic biology and microbial chassis adaptation allow us to tackle current and future food challenges. One of the most apparent challenges is the limited space on Earth available for agriculture and its major tolls on the environment through use of pesticides and the replacement of ecosystems with monocultures. Further challenges include transport and packaging, exacerbated by the 24/7 on-demand mentality of many customers. Synthetic biology already tackles multiple food challenges and will be able to tackle many future food challenges. In this perspective article, we highlight recent microbial synthetic biology research to address future food challenges. We further give a perspective on how synthetic biology tools may teach old microbes new tricks, and what standardized microbial domestication could look like.
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Köbel T, Melo Palhares R, Fromm C, Szymanski W, Angelidou G, Glatter T, Georg J, Berghoff BA, Schindler D. An Easy-to-Use Plasmid Toolset for Efficient Generation and Benchmarking of Synthetic Small RNAs in Bacteria. ACS Synth Biol 2022; 11:2989-3003. [PMID: 36044590 PMCID: PMC9486967 DOI: 10.1021/acssynbio.2c00164] [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] [Indexed: 01/24/2023]
Abstract
Synthetic biology approaches life from the perspective of an engineer. Standardized and de novo design of genetic parts to subsequently build reproducible and controllable modules, for example, for circuit design, is a key element. To achieve this, natural systems and elements often serve as a blueprint for researchers. Regulation of protein abundance is controlled at DNA, mRNA, and protein levels. Many tools for the activation or repression of transcription or the destabilization of proteins are available, but easy-to-handle minimal regulatory elements on the mRNA level are preferable when translation needs to be modulated. Regulatory RNAs contribute considerably to regulatory networks in all domains of life. In particular, bacteria use small regulatory RNAs (sRNAs) to regulate mRNA translation. Slowly, sRNAs are attracting the interest of using them for broad applications in synthetic biology. Here, we promote a "plug and play" plasmid toolset to quickly and efficiently create synthetic sRNAs to study sRNA biology or their application in bacteria. We propose a simple benchmarking assay by targeting the acrA gene of Escherichia coli and rendering cells sensitive toward the β-lactam antibiotic oxacillin. We further highlight that it may be necessary to test multiple seed regions and sRNA scaffolds to achieve the desired regulatory effect. The described plasmid toolset allows quick construction and testing of various synthetic sRNAs based on the user's needs.
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Affiliation(s)
- Tania
S. Köbel
- RG
Schindler, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,MaxGENESYS
Biofoundry, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany
| | - Rafael Melo Palhares
- RG
Schindler, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,Institute
for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Christin Fromm
- Institute
for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Witold Szymanski
- Mass
Spectrometry and Proteomics Core Facility, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, 35043 Marburg, Germany
| | - Georgia Angelidou
- Mass
Spectrometry and Proteomics Core Facility, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, 35043 Marburg, Germany
| | - Timo Glatter
- Mass
Spectrometry and Proteomics Core Facility, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, 35043 Marburg, Germany
| | - Jens Georg
- Institut
für Biologie III, Albert-Ludwigs-Universität
Freiburg, Schänzlestraße
1, 79104 Freiburg, Germany
| | - Bork A. Berghoff
- Institute
for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany,
| | - Daniel Schindler
- RG
Schindler, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,MaxGENESYS
Biofoundry, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,
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18
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Schindler D, Moldenhawer T, Stange M, Lepro V, Beta C, Holschneider M, Huisinga W. Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows. PLoS Comput Biol 2021; 17:e1009268. [PMID: 34424898 PMCID: PMC8412247 DOI: 10.1371/journal.pcbi.1009268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Received: 10/29/2020] [Revised: 09/02/2021] [Accepted: 07/12/2021] [Indexed: 11/18/2022] Open
Abstract
Amoeboid cell motility is essential for a wide range of biological processes including wound healing, embryonic morphogenesis, and cancer metastasis. It relies on complex dynamical patterns of cell shape changes that pose long-standing challenges to mathematical modeling and raise a need for automated and reproducible approaches to extract quantitative morphological features from image sequences. Here, we introduce a theoretical framework and a computational method for obtaining smooth representations of the spatiotemporal contour dynamics from stacks of segmented microscopy images. Based on a Gaussian process regression we propose a one-parameter family of regularized contour flows that allows us to continuously track reference points (virtual markers) between successive cell contours. We use this approach to define a coordinate system on the moving cell boundary and to represent different local geometric quantities in this frame of reference. In particular, we introduce the local marker dispersion as a measure to identify localized membrane expansions and provide a fully automated way to extract the properties of such expansions, including their area and growth time. The methods are available as an open-source software package called AmoePy, a Python-based toolbox for analyzing amoeboid cell motility (based on time-lapse microscopy data), including a graphical user interface and detailed documentation. Due to the mathematical rigor of our framework, we envision it to be of use for the development of novel cell motility models. We mainly use experimental data of the social amoeba Dictyostelium discoideum to illustrate and validate our approach. Amoeboid motion is a crawling-like cell migration that plays an important key role in multiple biological processes such as wound healing and cancer metastasis. This type of cell motility results from expanding and simultaneously contracting parts of the cell membrane. From fluorescence images, we obtain a sequence of points, representing the cell membrane, for each time step. By using regression analysis on these sequences, we derive smooth representations, so-called contours, of the membrane. Since the number of measurements is discrete and often limited, the question is raised of how to link consecutive contours with each other. In this work, we present a novel mathematical framework in which these links are described by regularized flows allowing a certain degree of concentration or stretching of neighboring reference points on the same contour. This stretching rate, the so-called local dispersion, is used to identify expansions and contractions of the cell membrane providing a fully automated way of extracting properties of these cell shape changes. We applied our methods to time-lapse microscopy data of the social amoeba Dictyostelium discoideum.
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Affiliation(s)
- Daniel Schindler
- Institute of Mathematics, University of Potsdam, Potsdam, Germany
| | - Ted Moldenhawer
- Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany
| | - Maike Stange
- Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany
| | - Valentino Lepro
- Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Carsten Beta
- Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany
| | | | - Wilhelm Huisinga
- Institute of Mathematics, University of Potsdam, Potsdam, Germany
- * E-mail:
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19
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Luo Z, Yu K, Xie S, Monti M, Schindler D, Fang Y, Zhao S, Liang Z, Jiang S, Luan M, Xiao C, Cai Y, Dai J. Compacting a synthetic yeast chromosome arm. Genome Biol 2021; 22:5. [PMID: 33397424 PMCID: PMC7780613 DOI: 10.1186/s13059-020-02232-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/10/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Redundancy is a common feature of genomes, presumably to ensure robust growth under different and changing conditions. Genome compaction, removing sequences nonessential for given conditions, provides a novel way to understand the core principles of life. The synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) system is a unique feature implanted in the synthetic yeast genome (Sc2.0), which is proposed as an effective tool for genome minimization. As the Sc2.0 project is nearing its completion, we have begun to explore the application of the SCRaMbLE system in genome compaction. RESULTS We develop a method termed SCRaMbLE-based genome compaction (SGC) and demonstrate that a synthetic chromosome arm (synXIIL) can be efficiently reduced. The pre-introduced episomal essential gene array significantly enhances the compacting ability of SGC, not only by enabling the deletion of nonessential genes located in essential gene containing loxPsym units but also by allowing more chromosomal sequences to be removed in a single SGC process. Further compaction is achieved through iterative SGC, revealing that at least 39 out of 65 nonessential genes in synXIIL can be removed collectively without affecting cell viability at 30 °C in rich medium. Approximately 40% of the synthetic sequence, encoding 28 genes, is found to be dispensable for cell growth at 30 °C in rich medium and several genes whose functions are needed under specified conditions are identified. CONCLUSIONS We develop iterative SGC with the aid of eArray as a generic yet effective tool to compact the synthetic yeast genome.
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Affiliation(s)
- Zhouqing Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Kang Yu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shangqian Xie
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, 570228, China
| | - Marco Monti
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Daniel Schindler
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Present Address: Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Yuan Fang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shijun Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhenzhen Liang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shuangying Jiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Meiwei Luan
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, 570228, China
| | - Chuanle Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Yizhi Cai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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20
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Zhao Y, Yao Z, Ploessl D, Ghosh S, Monti M, Schindler D, Gao M, Cai Y, Qiao M, Yang C, Cao M, Shao Z. Leveraging the Hermes Transposon to Accelerate the Development of Nonconventional Yeast-based Microbial Cell Factories. ACS Synth Biol 2020; 9:1736-1752. [PMID: 32396718 DOI: 10.1021/acssynbio.0c00123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 02/06/2023]
Abstract
We broadened the usage of DNA transposon technology by demonstrating its capacity for the rapid creation of expression libraries for long biochemical pathways, which is beyond the classical application of building genome-scale knockout libraries in yeasts. This strategy efficiently leverages the readily available fine-tuning impact provided by the diverse transcriptional environment surrounding each random integration locus. We benchmark the transposon-mediated integration against the nonhomologous end joining-mediated strategy. The latter strategy was demonstrated for achieving pathway random integration in other yeasts but is associated with a high false-positive rate in the absence of a high-throughput screening method. Our key innovation of a nonreplicable circular DNA platform increased the possibility of identifying top-producing variants to 97%. Compared to the classical DNA transposition protocol, the design of a nonreplicable circular DNA skipped the step of counter-selection for plasmid removal and thus not only reduced the time required for the step of library creation from 10 to 5 d but also efficiently removed the "transposition escapers", which undesirably represented almost 80% of the entire population as false positives. Using one endogenous product (i.e., shikimate) and one heterologous product (i.e., (S)-norcoclaurine) as examples, we presented a streamlined procedure to rapidly identify high-producing variants with titers significantly higher than the reported data in the literature. We selected Scheffersomyces stipitis, a representative nonconventional yeast, as a demo, but the strategy can be generalized to other nonconventional yeasts. This new exploration of transposon technology, therefore, adds a highly versatile tool to accelerate the development of novel species as microbial cell factories for producing value-added chemicals.
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Affiliation(s)
- Yuxin Zhao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Zhanyi Yao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Deon Ploessl
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Saptarshi Ghosh
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Marco Monti
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, U.K
| | - Daniel Schindler
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, U.K
| | - Meirong Gao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Yizhi Cai
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, U.K
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Chao Yang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Mingfeng Cao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa, United States
- Bioeconomy Institute, Iowa State University, Ames, Iowa, United States
- Interdepartmental Microbiology Program, Iowa State University, Ames, Iowa, United States
- The Ames Laboratory, Ames, Iowa, United States
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Rustler P, Schindler D, Voll R, Kollert F. FRI0502 SEASONAL CLUSTERING OF ACUTE SARCOIDOSIS IN GERMANY AND ASSOCIATIONS WITH AIR POLLUTION. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.4609] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Background:Sarcoidosis is a multisystemic granulomatous disorder of unknown origin. The central role of macrophages and granuloma formation, the predominant involvement of lung and skin, and certain risk populations (e.g. firefighters1, 2) might be explained by causative airborne antigen(s)3. Whether air pollution is involved in pathogenesis and seasonal clustering of sarcoidosis is uncertain.Objectives:This study has been set to analyze seasonal clustering of acute sarcoidosis and associations to air pollution.Methods:Patients with acute sarcoidosis, defined by bihilar lymphadenopathy, ankle swelling, and/or erythema nodosum plus physician’s diagnosis,were included in this retrospective study. Disease onset (seasonal clustering) and associations to air pollution (particulate matter (PM10) and nitrogen dixoide (NO2)) were analyzed. Google Trends queries were conducted to address seasonal clustering on a global scale.Results:A total of 185 patients with acute sarcoidosis were included; 48.7 % of the enrolled patients were female and Löfgren triad was complete in 73.5 % of patients. Acute sarcoidosis clustered from December to June in West Germany (p<0.005, Kendall τ=-0.68), peaking in January (17.8 % of cases) and in the first third of the year (54.5 %). Mean PM10values clustered from December to April with values between 15 and 40 µg/m3. NO2levels were measured highest from November to March (45 µg/m3) and lowest between April and August (25 µg/m3). Elevated air pollution markers (PM10and NO2) were associated with higher monthly incidence rates of acute sarcoidosis (Cross correlation coefficient ranging between 0.7 -0.8). Google Trends analysis yielded seasonal clustering (p<0.005, Kendall τ = -0.64) in winter and spring months on the northern hemisphere.Conclusion:In Central Europe acute sarcoidosis peaks in winter and spring months (December until March) shortly after PM10and NO2maxima are reached. Whether components of particulate matter might be involved in the pathogenesis of sarcoidosis has to be elucidated by further studies.References:[1] Prezant DJ, Dhala A, Goldstein A, Janus D, Ortiz F, Aldrich TK, et al. The incidence, prevalence, and severity of sarcoidosis in New York City firefighters. Chest. 1999;[2] Webber MP, Yip J, Zeig-Owens R, Moir W, Ungprasert P, Crowson CS, et al. Post-9/11 sarcoidosis in WTC-exposed firefighters and emergency medical service workers. Respir Med [Internet]. 2017;132:232–7.[3] Newman LS, Rose CS, Bresnitz EA, Rossman MD, Barnard J, Frederick M, et al. A case control etiologic study of sarcoidosis: Environmental and occupational risk factors. Am J Respir Crit Care Med. 2004;170(12):1324–30.Disclosure of Interests:Philipp Rustler: None declared, Dirk Schindler: None declared, Reinhard Voll: None declared, Florian Kollert Employee of: Novartis
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22
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Rao SM, Galioto R, Sokolowski M, McGinley M, Freiburger J, Weber M, Dey T, Mourany L, Schindler D, Reece C, Miller DM, Bethoux F, Bermel RA, Williams JR, Levitt N, Phillips GA, Rhodes JK, Alberts J, Rudick RA. Multiple Sclerosis Performance Test: validation of self-administered neuroperformance modules. Eur J Neurol 2020; 27:878-886. [PMID: 32009276 DOI: 10.1111/ene.14162] [Citation(s) in RCA: 23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 10/07/2019] [Accepted: 12/03/2019] [Indexed: 11/28/2022]
Abstract
BACKGROUND AND PURPOSE The purpose was to determine the test-retest reliability, practice effects, convergent validity and sensitivity to multiple sclerosis (MS) disability of neuroperformance subtests from the patient self-administered Multiple Sclerosis Performance Test (MSPT) designed to assess low contrast vision (Contrast Sensitivity Test, CST), upper extremity motor function (Manual Dexterity Test, MDT) and lower extremity motor function (Walking Speed Test, WST) and to introduce the concept of regression-based norms to aid clinical interpretation of performance scores using the MSPT cognition test (Processing Speed Test, PST) as an example. METHODS Substudy 1 assessed test-retest reliability, practice effects and convergent validity of the CST, MDT and WST in 30 MS patients and 30 healthy controls. Substudy 2 examined sensitivity to MS disability in over 600 MS patients as part of their routine clinic assessment. Substudy 3 compared performance on the PST in research volunteers and clinical samples. RESULTS The CST, MDT and WST were shown to be reliable, valid and sensitive to MS outcomes. Performance was comparable to technician-administered testing. PST performance was poorer in the clinical sample compared with the research volunteer sample. CONCLUSIONS The self-administered MSPT neuroperformance modules produce reliable, objective metrics that can be used in clinical practice and support outcomes research. Published studies which require patient voluntary consent may underestimate the rate of cognitive dysfunction observed in a clinical setting.
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Affiliation(s)
- S M Rao
- Mellen Center for Multiple Sclerosis, Neurological Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.,Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - R Galioto
- Mellen Center for Multiple Sclerosis, Neurological Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - M Sokolowski
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - M McGinley
- Mellen Center for Multiple Sclerosis, Neurological Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - J Freiburger
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - M Weber
- Mellen Center for Multiple Sclerosis, Neurological Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - T Dey
- Department of Quantitative Health Sciences, Learner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - L Mourany
- Mellen Center for Multiple Sclerosis, Neurological Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - D Schindler
- Department of Biomedical Engineering, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.,Qr8Health, Boston, MA, USA
| | - C Reece
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - D M Miller
- Mellen Center for Multiple Sclerosis, Neurological Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - F Bethoux
- Mellen Center for Multiple Sclerosis, Neurological Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - R A Bermel
- Mellen Center for Multiple Sclerosis, Neurological Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | | | | | | | | | - J Alberts
- Department of Biomedical Engineering, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
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Bruhn M, Schindler D, Kemter FS, Wiley MR, Chase K, Koroleva GI, Palacios G, Sozhamannan S, Waldminghaus T. Functionality of Two Origins of Replication in Vibrio cholerae Strains With a Single Chromosome. Front Microbiol 2018; 9:2932. [PMID: 30559732 PMCID: PMC6284228 DOI: 10.3389/fmicb.2018.02932] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/14/2018] [Indexed: 12/16/2022] Open
Abstract
Chromosomal inheritance in bacteria usually entails bidirectional replication of a single chromosome from a single origin into two copies and subsequent partitioning of one copy each into daughter cells upon cell division. However, the human pathogen Vibrio cholerae and other Vibrionaceae harbor two chromosomes, a large Chr1 and a small Chr2. Chr1 and Chr2 have different origins, an oriC-type origin and a P1 plasmid-type origin, respectively, driving the replication of respective chromosomes. Recently, we described naturally occurring exceptions to the two-chromosome rule of Vibrionaceae: i.e., Chr1 and Chr2 fused single chromosome V. cholerae strains, NSCV1 and NSCV2, in which both origins of replication are present. Using NSCV1 and NSCV2, here we tested whether two types of origins of replication can function simultaneously on the same chromosome or one or the other origin is silenced. We found that in NSCV1, both origins are active whereas in NSCV2 ori2 is silenced despite the fact that it is functional in an isolated context. The ori2 activity appears to be primarily determined by the copy number of the triggering site, crtS, which in turn is determined by its location with respect to ori1 and ori2 on the fused chromosome.
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Affiliation(s)
- Matthias Bruhn
- LOEWE Centre for Synthetic Microbiology-SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Daniel Schindler
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Franziska S Kemter
- LOEWE Centre for Synthetic Microbiology-SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Michael R Wiley
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Kitty Chase
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Galina I Koroleva
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Shanmuga Sozhamannan
- Defense Biological Product Assurance Office, Frederick, MD, United States.,The Tauri Group, LLC, Alexandria, VA, United States
| | - Torsten Waldminghaus
- LOEWE Centre for Synthetic Microbiology-SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
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24
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Schindler D, Dai J, Cai Y. Synthetic genomics: a new venture to dissect genome fundamentals and engineer new functions. Curr Opin Chem Biol 2018; 46:56-62. [PMID: 29751161 PMCID: PMC6351456 DOI: 10.1016/j.cbpa.2018.04.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/05/2018] [Accepted: 04/09/2018] [Indexed: 12/17/2022]
Abstract
Since the first synthetic gene was synthesized in 1970s, the efficiency and the capacity of made-to-order DNA sequence synthesis has increased by several orders of magnitude. Advances in DNA synthesis and assembly over the past years has resulted in a steep drop in price for custom made DNA. Similar effects were observed in DNA sequencing technologies which underpin DNA-reading projects. Today, synthetic DNA sequences with more than 10000bps and turn-around times of a few weeks are commercially available. This enables researchers to perform large-scale projects to write synthetic chromosomes and characterize their functionalities in vivo. Synthetic genomics opens up new paradigms to study the genome fundamentals and engineer novel biological functions.
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Affiliation(s)
- Daniel Schindler
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN Manchester, UK
| | - Junbiao Dai
- Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN Manchester, UK; Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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25
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Harris PR, Zègre-Hemsey JK, Schindler D, Bai Y, Pelter MM, Hu X. Patient characteristics associated with false arrhythmia alarms in intensive care. Ther Clin Risk Manag 2017; 13:499-513. [PMID: 28458554 PMCID: PMC5403122 DOI: 10.2147/tcrm.s126191] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION A high rate of false arrhythmia alarms in the intensive care unit (ICU) leads to alarm fatigue, the condition of desensitization and potentially inappropriate silencing of alarms due to frequent invalid and nonactionable alarms, often referred to as false alarms. OBJECTIVE The aim of this study was to identify patient characteristics, such as gender, age, body mass index, and diagnosis associated with frequent false arrhythmia alarms in the ICU. METHODS This descriptive, observational study prospectively enrolled patients who were consecutively admitted to one of five adult ICUs (77 beds) at an urban medical center over a period of 31 days in 2013. All monitor alarms and continuous waveforms were stored on a secure server. Nurse scientists with expertise in cardiac monitoring used a standardized protocol to annotate six clinically important types of arrhythmia alarms (asystole, pause, ventricular fibrillation, ventricular tachycardia, accelerated ventricular rhythm, and ventricular bradycardia) as true or false. Total monitoring time for each patient was measured, and the number of false alarms per hour was calculated for these six alarm types. Medical records were examined to acquire data on patient characteristics. RESULTS A total of 461 unique patients (mean age =60±17 years) were enrolled, generating a total of 2,558,760 alarms, including all levels of arrhythmia, parameter, and technical alarms. There were 48,404 hours of patient monitoring time, and an average overall alarm rate of 52 alarms/hour. Investigators annotated 12,671 arrhythmia alarms; 11,345 (89.5%) were determined to be false. Two hundred and fifty patients (54%) generated at least one of the six annotated alarm types. Two patients generated 6,940 arrhythmia alarms (55%). The number of false alarms per monitored hour for patients' annotated arrhythmia alarms ranged from 0.0 to 7.7, and the duration of these false alarms per hour ranged from 0.0 to 158.8 seconds. Patient characteristics were compared in relation to 1) the number and 2) the duration of false arrhythmia alarms per 24-hour period, using nonparametric statistics to minimize the influence of outliers. Among the significant associations were the following: age ≥60 years (P=0.013; P=0.034), confused mental status (P<0.001 for both comparisons), cardiovascular diagnoses (P<0.001 for both comparisons), electrocardiographic (ECG) features, such as wide ECG waveforms that correspond to ventricular depolarization known as QRS complex due to bundle branch block (BBB) (P=0.003; P=0.004) or ventricular paced rhythm (P=0.002 for both comparisons), respiratory diagnoses (P=0.004 for both comparisons), and support with mechanical ventilation, including those with primary diagnoses other than respiratory ones (P<0.001 for both comparisons). CONCLUSION Patients likely to trigger a higher number of false arrhythmia alarms may be those with older age, confusion, cardiovascular diagnoses, and ECG features that indicate BBB or ventricular pacing, respiratory diagnoses, and mechanical ventilatory support. Algorithm improvements could focus on better noise reduction (eg, motion artifact with confused state) and distinguishing BBB and paced rhythms from ventricular arrhythmias. Increasing awareness of patient conditions that apparently trigger a higher rate of false arrhythmia alarms may be useful for reducing unnecessary noise and improving alarm management.
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Affiliation(s)
- Patricia R Harris
- Department of Nursing, School of Health and Natural Sciences, Dominican University of California, San Rafael.,Department of Physiological Nursing, School of Nursing, University of California, San Francisco, CA
| | - Jessica K Zègre-Hemsey
- School of Nursing.,Department of Emergency Medicine, School of Medicine, University of North Carolina at Chapel Hill, NC
| | - Daniel Schindler
- Intensive Care Unit, The Neuroscience Center, Sutter Eden Medical Center, Castro Valley
| | - Yong Bai
- Hu Research Laboratory, Department of Physiological Nursing, School of Nursing, University of California, San Francisco
| | - Michele M Pelter
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, CA.,ECG Monitoring Research Lab, Department of Physiological Nursing, School of Nursing
| | - Xiao Hu
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, CA.,Physiological Nursing and Neurological Surgery, Affiliate Faculty of Institute for Computational Health Sciences Core Faculty UCB/UCSF Joint Bio-Engineering Graduate Program, University of California, San Francisco, CA, USA
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26
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Messerschmidt SJ, Schindler D, Zumkeller CM, Kemter FS, Schallopp N, Waldminghaus T. Optimization and Characterization of the Synthetic Secondary Chromosome synVicII in Escherichia coli. Front Bioeng Biotechnol 2016; 4:96. [PMID: 28066763 PMCID: PMC5179572 DOI: 10.3389/fbioe.2016.00096] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/09/2016] [Indexed: 11/15/2022] Open
Abstract
Learning by building is one of the core ideas of synthetic biology research. Consequently, building synthetic chromosomes is the way to fully understand chromosome characteristics. The last years have seen exciting synthetic chromosome studies. We had previously introduced the synthetic secondary chromosome synVicII in Escherichia coli. It is based on the replication mechanism of the secondary chromosome in Vibrio cholerae. Here, we present a detailed analysis of its genetic characteristics and a selection approach to optimize replicon stability. We probe the origin diversity of secondary chromosomes from Vibrionaceae by construction of several new respective replicons. Finally, we present a synVicII version 2.0 with several innovations including its full compatibility with the popular modular cloning (MoClo) assembly system.
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Affiliation(s)
- Sonja J Messerschmidt
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Daniel Schindler
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Celine M Zumkeller
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Franziska S Kemter
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Nadine Schallopp
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Torsten Waldminghaus
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
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27
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Schindler D, Milbredt S, Sperlea T, Waldminghaus T. Design and Assembly of DNA Sequence Libraries for Chromosomal Insertion in Bacteria Based on a Set of Modified MoClo Vectors. ACS Synth Biol 2016; 5:1362-1368. [PMID: 27306697 DOI: 10.1021/acssynbio.6b00089] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 11/28/2022]
Abstract
Efficient assembly of large DNA constructs is a key technology in synthetic biology. One of the most popular assembly systems is the MoClo standard in which restriction and ligation of multiple fragments occurs in a one-pot reaction. The system is based on a smart vector design and type IIs restriction enzymes, which cut outside their recognition site. While the initial MoClo vectors had been developed for the assembly of multiple transcription units of plants, some derivatives of the vectors have been developed over the last years. Here we present a new set of MoClo vectors for the assembly of fragment libraries and insertion of constructs into bacterial chromosomes. The vectors are accompanied by a computer program that generates a degenerate synthetic DNA sequence that excludes "forbidden" DNA motifs. We demonstrate the usability of the new approach by construction of a stable fluorescence repressor operator system (FROS).
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Affiliation(s)
- Daniel Schindler
- Chromosome Biology Group,
LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043 Marburg, Germany
| | - Sarah Milbredt
- Chromosome Biology Group,
LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043 Marburg, Germany
| | - Theodor Sperlea
- Chromosome Biology Group,
LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043 Marburg, Germany
| | - Torsten Waldminghaus
- Chromosome Biology Group,
LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043 Marburg, Germany
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28
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Pfeifer K, Schürmann P, Bogdanova N, Neuhäuser K, Kostovska IM, Plaseska-Karanfilska D, Park-Simon TW, Schindler D, Dörk T. Frameshift variant FANCL*c.1096_1099dupATTA is not associated with high breast cancer risk. Clin Genet 2016; 90:385-6. [PMID: 27506598 DOI: 10.1111/cge.12837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/12/2016] [Accepted: 07/15/2016] [Indexed: 11/29/2022]
Affiliation(s)
- K Pfeifer
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - P Schürmann
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - N Bogdanova
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany.,Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - K Neuhäuser
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany.,Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - I Maleva Kostovska
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany.,Macedonian Academy of Sciences and Arts, Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Skopje, Republic of Macedonia
| | - D Plaseska-Karanfilska
- Macedonian Academy of Sciences and Arts, Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Skopje, Republic of Macedonia
| | - T-W Park-Simon
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - D Schindler
- Institute of Human Genetics, Biocenter, University of Würzburg, Würzburg, Germany
| | - T Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany.
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29
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Ramogida CF, Schindler D, Schneider C, Tan YK, Huh S, Ferreira CL, Adam MJ, Orvig C. Synthesis and characterization of lipophilic cationic Ga(iii) complexes based on the H2CHXdedpa and H2dedpa ligands and their 67/68Ga radiolabeling studies. RSC Adv 2016. [DOI: 10.1039/c6ra24070d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Novel lipophilic H2dedpa or H2CHXdedpa analogues have been synthesized, characterized, and radiolabeled with 67/68Ga3+ in 10 minutes at ambient temperature.
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Affiliation(s)
- C. F. Ramogida
- Medicinal Inorganic Chemistry Group
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada V6T 1Z1
| | - D. Schindler
- Medicinal Inorganic Chemistry Group
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada V6T 1Z1
| | - C. Schneider
- Medicinal Inorganic Chemistry Group
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada V6T 1Z1
| | - Y. L. K. Tan
- Medicinal Inorganic Chemistry Group
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada V6T 1Z1
| | - S. Huh
- Medicinal Inorganic Chemistry Group
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada V6T 1Z1
| | | | - M. J. Adam
- Life Sciences Division
- TRIUMF
- Vancouver
- Canada V6T 2A3
| | - C. Orvig
- Medicinal Inorganic Chemistry Group
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada V6T 1Z1
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31
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Chao MM, Kuehl JS, Strauss G, Hanenberg H, Schindler D, Neitzel H, Niemeyer C, Baumann I, von Bernuth H, Rascon J, Nagy M, Zimmermann M, Kratz CP, Ebell W. Outcomes of mismatched and unrelated donor hematopoietic stem cell transplantation in Fanconi anemia conditioned with chemotherapy only. Ann Hematol 2015; 94:1311-8. [PMID: 25862235 DOI: 10.1007/s00277-015-2370-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 03/27/2015] [Indexed: 01/13/2023]
Abstract
Fanconi anemia (FA) is a genomic instability syndrome associated with bone marrow failure, myelodysplastic syndrome (MDS), and/or acute myeloid leukemia (AML) requiring hematopoietic stem cell transplantation (HSCT) to restore normal hematopoiesis. Although low-intensity fludarabine-based preparative regimens without radiation confer excellent outcomes in FA HSCTs with HLA-matched sibling donors, outcomes for FA patients with alternative donors are less encouraging, albeit improving. We present our experience with 17 FA patients who completed mismatched related or unrelated donor HSCT using a non-radiation fludarabine-based preparative regimen at Charité University Medicine Berlin. All patients engrafted; however, one patient had unstable chimerism in the setting of multi-viral infections that necessitated a stem cell boost to revert to full donor chimerism. Forty-seven percent of patients developed grade I acute graft-verus-host disease (aGVHD). No grade II-IV aGVHD or chronic graft-versus-host disease of any severity occurred. At a median follow-up of 30 months, 88 % of patients are alive with normal hematopoiesis. Two patients died of infections 4 months post-transplantation. These results demonstrate that short-term outcomes for FA patients with mismatched and unrelated donor HSCTs can be excellent using chemotherapy only conditioning. Viral reactivation, however, was a major treatment-related complication.
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Affiliation(s)
- M M Chao
- Department of Pediatric Hematology Oncology, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany,
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32
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Falschlehner S, Petrovic M, Czuchajda E, Ott B, Forster A, Berger A, Subhieh M, Schindler D, Derka I, Zwick RH. The effect of outpatient pulmonary rehabilitation on CAT Score and the new GOLD guidelines Auswirkungen der ambulanten pneumologischen Rehabilitation auf den CAT Score und die neuen GOLD Guidelines. Pneumologie 2015. [DOI: 10.1055/s-0035-1544673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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33
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Messerschmidt SJ, Kemter FS, Schindler D, Waldminghaus T. Synthetic secondary chromosomes in Escherichia coli based on the replication origin of chromosome II in Vibrio cholerae. Biotechnol J 2014; 10:302-14. [PMID: 25359671 DOI: 10.1002/biot.201400031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 10/02/2014] [Accepted: 10/30/2014] [Indexed: 01/25/2023]
Abstract
Recent developments in DNA-assembly methods make the synthesis of synthetic chromosomes a reachable goal. However, the redesign of primary chromosomes bears high risks and still requires enormous resources. An alternative approach is the addition of synthetic chromosomes to the cell. The natural secondary chromosome of Vibrio cholerae could potentially serve as template for a synthetic secondary chromosome in Escherichia coli. To test this assumption we constructed a replicon named synVicII based on the replication module of V. cholerae chromosome II (oriII). A new assay for the assessment of replicon stability was developed based on flow-cytometric analysis of unstable GFP variants. Application of this assay to cells carrying synVicII revealed an improved stability compared to a secondary replicon based on E. coli oriC. Cell cycle analysis and determination of cellular copy numbers of synVicII indicate that replication timing of the synthetic replicon in E. coli is comparable to the natural chromosome II (ChrII) in V. cholerae. The presented synthetic biology work provides the basis to use secondary chromosomes in E. coli to answer basic research questions as well as for several biotechnological applications.
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Affiliation(s)
- Sonja J Messerschmidt
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Germany
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34
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Drew BJ, Harris P, Zègre-Hemsey JK, Mammone T, Schindler D, Salas-Boni R, Bai Y, Tinoco A, Ding Q, Hu X. Insights into the problem of alarm fatigue with physiologic monitor devices: a comprehensive observational study of consecutive intensive care unit patients. PLoS One 2014; 9:e110274. [PMID: 25338067 PMCID: PMC4206416 DOI: 10.1371/journal.pone.0110274] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 09/12/2014] [Indexed: 11/23/2022] Open
Abstract
Purpose Physiologic monitors are plagued with alarms that create a cacophony of sounds and visual alerts causing “alarm fatigue” which creates an unsafe patient environment because a life-threatening event may be missed in this milieu of sensory overload. Using a state-of-the-art technology acquisition infrastructure, all monitor data including 7 ECG leads, all pressure, SpO2, and respiration waveforms as well as user settings and alarms were stored on 461 adults treated in intensive care units. Using a well-defined alarm annotation protocol, nurse scientists with 95% inter-rater reliability annotated 12,671 arrhythmia alarms. Results A total of 2,558,760 unique alarms occurred in the 31-day study period: arrhythmia, 1,154,201; parameter, 612,927; technical, 791,632. There were 381,560 audible alarms for an audible alarm burden of 187/bed/day. 88.8% of the 12,671 annotated arrhythmia alarms were false positives. Conditions causing excessive alarms included inappropriate alarm settings, persistent atrial fibrillation, and non-actionable events such as PVC's and brief spikes in ST segments. Low amplitude QRS complexes in some, but not all available ECG leads caused undercounting and false arrhythmia alarms. Wide QRS complexes due to bundle branch block or ventricular pacemaker rhythm caused false alarms. 93% of the 168 true ventricular tachycardia alarms were not sustained long enough to warrant treatment. Discussion The excessive number of physiologic monitor alarms is a complex interplay of inappropriate user settings, patient conditions, and algorithm deficiencies. Device solutions should focus on use of all available ECG leads to identify non-artifact leads and leads with adequate QRS amplitude. Devices should provide prompts to aide in more appropriate tailoring of alarm settings to individual patients. Atrial fibrillation alarms should be limited to new onset and termination of the arrhythmia and delays for ST-segment and other parameter alarms should be configurable. Because computer devices are more reliable than humans, an opportunity exists to improve physiologic monitoring and reduce alarm fatigue.
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Affiliation(s)
- Barbara J. Drew
- Department of Physiological Nursing, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
| | - Patricia Harris
- Department of Physiological Nursing, University of California San Francisco, San Francisco, California, United States of America
| | - Jessica K. Zègre-Hemsey
- School of Nursing, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Tina Mammone
- Department of Nursing, University of California San Francisco Medical Center, San Francisco, California, United States of America
| | - Daniel Schindler
- Department of Physiological Nursing, University of California San Francisco, San Francisco, California, United States of America
| | - Rebeca Salas-Boni
- Department of Physiological Nursing, University of California San Francisco, San Francisco, California, United States of America
| | - Yong Bai
- Department of Physiological Nursing, University of California San Francisco, San Francisco, California, United States of America
| | - Adelita Tinoco
- Department of Physiological Nursing, University of California San Francisco, San Francisco, California, United States of America
| | - Quan Ding
- Department of Physiological Nursing, University of California San Francisco, San Francisco, California, United States of America
| | - Xiao Hu
- Department of Physiological Nursing, University of California San Francisco, San Francisco, California, United States of America
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35
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Bai Y, Do DH, Harris PRE, Schindler D, Boyle NG, Drew BJ, Hu X. Integrating monitor alarms with laboratory test results to enhance patient deterioration prediction. J Biomed Inform 2014; 53:81-92. [PMID: 25240252 DOI: 10.1016/j.jbi.2014.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [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: 03/10/2014] [Revised: 09/06/2014] [Accepted: 09/09/2014] [Indexed: 11/24/2022]
Abstract
Patient monitors in modern hospitals have become ubiquitous but they generate an excessive number of false alarms causing alarm fatigue. Our previous work showed that combinations of frequently co-occurring monitor alarms, called SuperAlarm patterns, were capable of predicting in-hospital code blue events at a lower alarm frequency. In the present study, we extend the conceptual domain of a SuperAlarm to incorporate laboratory test results along with monitor alarms so as to build an integrated data set to mine SuperAlarm patterns. We propose two approaches to integrate monitor alarms with laboratory test results and use a maximal frequent itemsets mining algorithm to find SuperAlarm patterns. Under an acceptable false positive rate FPRmax, optimal parameters including the minimum support threshold and the length of time window for the algorithm to find the combinations of monitor alarms and laboratory test results are determined based on a 10-fold cross-validation set. SuperAlarm candidates are generated under these optimal parameters. The final SuperAlarm patterns are obtained by further removing the candidates with false positive rate>FPRmax. The performance of SuperAlarm patterns are assessed using an independent test data set. First, we calculate the sensitivity with respect to prediction window and the sensitivity with respect to lead time. Second, we calculate the false SuperAlarm ratio (ratio of the hourly number of SuperAlarm triggers for control patients to that of the monitor alarms, or that of regular monitor alarms plus laboratory test results if the SuperAlarm patterns contain laboratory test results) and the work-up to detection ratio, WDR (ratio of the number of patients triggering any SuperAlarm patterns to that of code blue patients triggering any SuperAlarm patterns). The experiment results demonstrate that when varying FPRmax between 0.02 and 0.15, the SuperAlarm patterns composed of monitor alarms along with the last two laboratory test results are triggered at least once for [56.7-93.3%] of code blue patients within an 1-h prediction window before code blue events and for [43.3-90.0%] of code blue patients at least 1-h ahead of code blue events. However, the hourly number of these SuperAlarm patterns occurring in control patients is only [2.0-14.8%] of that of regular monitor alarms with WDR varying between 2.1 and 6.5 in a 12-h window. For a given FPRmax threshold, the SuperAlarm set generated from the integrated data set has higher sensitivity and lower WDR than the SuperAlarm set generated from the regular monitor alarm data set. In addition, the McNemar's test also shows that the performance of the SuperAlarm set from the integrated data set is significantly different from that of the SuperAlarm set from the regular monitor alarm data set. We therefore conclude that the SuperAlarm patterns generated from the integrated data set are better at predicting code blue events.
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Affiliation(s)
- Yong Bai
- Department of Bioengineering, University of California, Los Angeles, CA, United States
| | - Duc H Do
- UCLA Cardiac Arrhythmia Center, David Geffen School of Medicine, University of California, Los Angeles, CA, United States
| | | | - Daniel Schindler
- Department of Physiological Nursing, University of California, San Francisco, CA, United States
| | - Noel G Boyle
- UCLA Cardiac Arrhythmia Center, David Geffen School of Medicine, University of California, Los Angeles, CA, United States
| | - Barbara J Drew
- Department of Physiological Nursing, University of California, San Francisco, CA, United States
| | - Xiao Hu
- Department of Physiological Nursing, University of California, San Francisco, CA, United States; Department of Neurosurgery, University of California, San Francisco, CA, United States; Institute for Computational Health Sciences, University of California, San Francisco, CA, United States; UCB/UCSF Graduate Group in Bioengineering, University of California, San Francisco, CA, United States.
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Falschlehner S, Petrovic M, Czuchajda E, Ott B, Forster A, Berger A, Subhieh M, Schindler D, Derka I, Harun Zwick R. Auswirkungen der ambulanten pneumologischen Rehabilitation auf den CAT Score und die neuen GOLD Guidelines. Pneumologie 2014. [DOI: 10.1055/s-0034-1375914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Schindler D, Nowrousian M. The polyketide synthase gene pks4 is essential for sexual development and regulates fruiting body morphology in Sordaria macrospora. Fungal Genet Biol 2014; 68:48-59. [PMID: 24792494 DOI: 10.1016/j.fgb.2014.04.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [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: 12/03/2013] [Revised: 04/02/2014] [Accepted: 04/21/2014] [Indexed: 01/02/2023]
Abstract
Filamentous ascomycetes have long been known as producers of a variety of secondary metabolites, many of which have toxic effects on other organisms. However, the role of these metabolites in the biology of the fungi that produce them remains in most cases enigmatic. A major group of fungal secondary metabolites are polyketides. They are chemically diverse, but have in common that their chemical scaffolds are synthesized by polyketide synthases (PKSs). In a previous study, we analyzed development-dependent expression of pks genes in the filamentous ascomycete Sordaria macrospora. Here, we show that a deletion mutant of the pks4 gene is sterile, producing only protoperithecia but no mature perithecia, whereas overexpression of pks4 leads to enlarged, malformed fruiting bodies. Thus, correct expression levels of pks4 are essential for wild type-like perithecia formation. The predicted PKS4 protein has a domain structure that is similar to homologs in other fungi, but conserved residues of a methyl transferase domain present in other fungi are mutated in PKS4. Expression of several developmental genes is misregulated in the pks4 mutant. Surprisingly, the development-associated app gene is not downregulated in the mutant, in contrast to all other previously studied mutants with a block at the protoperithecial stage. Our data show that the polyketide synthase gene pks4 is essential for sexual development and plays a role in regulating fruiting body morphology.
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Affiliation(s)
- Daniel Schindler
- Lehrstuhl für Allgemeine und Molekulare Botanik, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Minou Nowrousian
- Lehrstuhl für Allgemeine und Molekulare Botanik, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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Schindler D, Wagner S, Schönfeld N, Rüssmann H, Bauer TT. Actinomyces graevenitzii: ein zunehmend als pathogen erkannter Erreger von Atemwegsinfektionen. Pneumologie 2014. [DOI: 10.1055/s-0034-1367853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Schindler D, Waldminghaus T. "Non-canonical protein-DNA interactions identified by ChIP are not artifacts": response. BMC Genomics 2013; 14:638. [PMID: 24053571 PMCID: PMC3870955 DOI: 10.1186/1471-2164-14-638] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 09/18/2013] [Indexed: 11/10/2022] Open
Abstract
Background Studies of protein association with DNA on a genome wide scale are possible through methods like ChIP-Chip or ChIP-Seq. Massive problems with false positive signals in our own experiments motivated us to revise the standard ChIP-Chip protocol. Analysis of chromosome wide binding of the alternative sigma factor σ32 in Escherichia coli with this new protocol resulted in detection of only a subset of binding sites found in a previous study by Wade and colleagues. We suggested that the remainder of binding sites detected in the previous study are likely to be false positives. In a recent article the Wade group claimed that our conclusion is wrong and that the disputed sites are genuine σ32 binding sites. They further claimed that the non-detection of these sites in our study was due to low data quality. Results/discussion We respond to the criticism of Wade and colleagues and discuss some general questions of ChIP-based studies. We outline why the quality of our data is sufficient to derive meaningful results. Specific points are: (i) the modifications we introduced into the standard ChIP-Chip protocol do not necessarily result in a low dynamic range, (ii) correlation between ChIP-Chip replicates should not be calculated based on the whole data set as done in transcript analysis, (iii) control experiments are essential for identifying false positives. Suggestions are made how ChIP-based methods could be further optimized and which alternative approaches can be used to strengthen conclusions. Conclusion We appreciate the ongoing discussion about the ChIP-Chip method and hope that it helps other scientist to analyze and interpret their results. The modifications we introduced into the ChIP-Chip protocol are a first step towards reducing false positive signals but there is certainly potential for further optimization. The discussion about the σ32 binding sites in question highlights the need for alternative approaches and further investigation of appropriate methods for verification.
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Affiliation(s)
- Daniel Schindler
- LOEWE-Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Hans-Meerwein-Str, 6, D-35043, Marburg, Germany.
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Gesing S, Schindler D, Nowrousian M. Suppression subtractive hybridization and comparative expression analysis to identify developmentally regulated genes in filamentous fungi. J Basic Microbiol 2012; 53:742-51. [PMID: 22961396 DOI: 10.1002/jobm.201200223] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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: 04/24/2012] [Accepted: 06/06/2012] [Indexed: 11/06/2022]
Abstract
Ascomycetes differentiate four major morphological types of fruiting bodies (apothecia, perithecia, pseudothecia and cleistothecia) that are derived from an ancestral fruiting body. Thus, fruiting body differentiation is most likely controlled by a set of common core genes. One way to identify such genes is to search for genes with evolutionary conserved expression patterns. Using suppression subtractive hybridization (SSH), we selected differentially expressed transcripts in Pyronema confluens (Pezizales) by comparing two cDNA libraries specific for sexual and for vegetative development, respectively. The expression patterns of selected genes from both libraries were verified by quantitative real time PCR. Expression of several corresponding homologous genes was found to be conserved in two members of the Sordariales (Sordaria macrospora and Neurospora crassa), a derived group of ascomycetes that is only distantly related to the Pezizales. Knockout studies with N. crassa orthologues of differentially regulated genes revealed a functional role during fruiting body development for the gene NCU05079, encoding a putative MFS peptide transporter. These data indicate conserved gene expression patterns and a functional role of the corresponding genes during fruiting body development; such genes are candidates of choice for further functional analysis.
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Affiliation(s)
- Stefan Gesing
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
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Serra A, Eirich K, Winkler A, Mrasek K, Göhring G, Barbi G, Cario H, Schlegelberger B, Pokora B, Liehr T, Leriche C, Henne-Bruns D, Barth T, Schindler D. Shared Copy Number Variation in Simultaneous Nephroblastoma and Neuroblastoma due to Fanconi Anemia. Mol Syndromol 2012; 3:120-130. [PMID: 23112754 PMCID: PMC3473353 DOI: 10.1159/000341935] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2012] [Indexed: 11/19/2022] Open
Abstract
Concurrent emergence of nephroblastoma (Wilms Tumor; WT) and neuroblastoma (NB) is rare and mostly observed in patients with severe subtypes of Fanconi anemia (FA) with or without VACTER-L association (VL). We investigated the hypothesis that early consequences of genomic instability result in shared regions with copy number variation in different precursor cells that originate distinct embryonal tumors. We observed a newborn girl with FA and VL (aplasia of the thumbs, cloacal atresia (urogenital sinus), tethered cord at L3/L4, muscular ventricular septum defect, and horseshoe-kidney with a single ureter) who simultaneously acquired an epithelial-type WT in the left portion of the kidney and a poorly differentiated adrenal NB in infancy. A novel homozygous germline frameshift mutation in PALB2 (c.1676_c1677delAAinsG) leading to protein truncation (pGln526ArgfsX1) inherited from consanguineous parents formed the genetic basis of FA-N. Spontaneous and induced chromosomal instability was detected in the majority of cells analyzed from peripheral lymphocytes, bone marrow, and cultured fibroblasts. Bone marrow cells also showed complex chromosome rearrangements consistent with the myelodysplastic syndrome at 11 months of age. Array-comparative genomic hybridization analyses of both WT and NB showed shared gains or amplifications within the chromosomal regions 11p15.5 and 17q21.31-q25.3, including genes that are reportedly implicated in tumor development such as IGF2, H19, WT2, BIRC5, and HRAS.
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Affiliation(s)
- A. Serra
- Department of Pediatric Surgery, Ulm University, Ulm, Jena, Germany
| | - K. Eirich
- Department of Human Genetics, Julius-Maximilian University, Würzburg, Jena, Germany
| | - A.K. Winkler
- Department of Pediatric Surgery, Ulm University, Ulm, Jena, Germany
| | - K. Mrasek
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - G. Göhring
- Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany
| | - G. Barbi
- Institute of Human Genetics, Ulm University, Ulm, Jena, Germany
| | - H. Cario
- Department of Pediatric Oncology, Ulm University, Ulm, Jena, Germany
| | - B. Schlegelberger
- Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany
| | - B. Pokora
- Institute of Human Genetics and Anthropology, Heinrich Heine University Medical Faculty, Düsseldorf, Germany
| | - T. Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - C. Leriche
- Department of Pediatric Surgery, Ulm University, Ulm, Jena, Germany
| | - D. Henne-Bruns
- Department of General Surgery, Ulm University, Ulm, Jena, Germany
| | - T.F. Barth
- Department of Pathology, Ulm University, Ulm, Jena, Germany
| | - D. Schindler
- Department of Human Genetics, Julius-Maximilian University, Würzburg, Jena, Germany
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Gesing S, Schindler D, Fränzel B, Wolters D, Nowrousian M. The histone chaperone ASF1 is essential for sexual development in the filamentous fungus Sordaria macrospora. Mol Microbiol 2012; 84:748-65. [PMID: 22463819 DOI: 10.1111/j.1365-2958.2012.08058.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ascomycetes develop four major types of fruiting bodies that share a common ancestor, and a set of common core genes most likely controls this process. One way to identify such genes is to search for conserved expression patterns. We analysed microarray data of Fusarium graminearum and Sordaria macrospora, identifying 78 genes with similar expression patterns during fruiting body development. One of these genes was asf1 (anti-silencing function 1), encoding a predicted histone chaperone. asf1 expression is also upregulated during development in the distantly related ascomycete Pyronema confluens. To test whether asf1 plays a role in fungal development, we generated an S. macrospora asf1 deletion mutant. The mutant is sterile and can be complemented to fertility by transformation with the wild-type asf1 and its P. confluens homologue. An ASF1-EGFP fusion protein localizes to the nucleus. By tandem-affinity purification/mass spectrometry as well as yeast two-hybrid analysis, we identified histones H3 and H4 as ASF1 interaction partners. Several developmental genes are dependent on asf1 for correct transcriptional expression. Deletion of the histone chaperone genes rtt106 and cac2 did not cause any developmental phenotypes. These data indicate that asf1 of S. macrospora encodes a conserved histone chaperone that is required for fruiting body development.
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Affiliation(s)
- Stefan Gesing
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Universitätsstraße 150, 44780 Bochum, Germany
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Jang TB, Schindler D, Kaji AH. Bedside ultrasonography for the detection of small bowel obstruction in the emergency department. Emerg Med J 2010; 28:676-8. [DOI: 10.1136/emj.2010.095729] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Kalb R, Neveling K, Nanda I, Schindler D, Hoehn H. Fanconi anemia: causes and consequences of genetic instability. Genome Dyn 2008; 1:218-242. [PMID: 18724063 DOI: 10.1159/000092510] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Fanconi anemia (FA) is a rare recessive disease that reflects the cellular and phenotypic consequences of genetic instability: growth retardation, congenital malformations, bone marrow failure, high risk of neoplasia, and premature aging. At the cellular level, manifestations of genetic instability include chromosomal breakage, cell cycle disturbance, and increased somatic mutation rates. FA cells are exquisitely sensitive towards oxygen and alkylating drugs such as mitomycin C or diepoxybutane, pointing to a function of FA genes in the defense against reactive oxygen species and other DNA damaging agents. FA is caused by biallelic mutations in at least 12 different genes which appear to function in the maintenance of genomic stability. Eight of the FA proteins form a nuclear core complex with a catalytic function involving ubiquitination of the central FANCD2 protein. The posttranslational modification of FANCD2 promotes its accumulation in nuclear foci, together with known DNA maintenance proteins such as BRCA1, BRCA2, and the RAD51 recombinase. Biallelic mutations in BRCA2 cause a severe FA-like phenotype, as do biallelic mutations in FANCD2. In fact, only leaky or hypomorphic mutations in this central group of FA genes appear to be compatible with life birth and survival. The newly discovered FANCJ (= BRIP1) and FANCM (= Hef ) genes correspond to known DNA-maintenance genes (helicase resp. helicase-associated endonuclease for fork-structured DNA). These genes provide the most convincing evidence to date of a direct involvement of FA genes in DNA repair functions associated with the resolution of DNA crosslinks and stalled replication forks. Even though genetic instability caused by mutational inactivation of the FANC genes has detrimental effects for the majority of FA patients, around 20% of patients appear to benefit from genetic instability since genetic instability also increases the chance of somatic reversion of their constitutional mutations. Intragenic crossover, gene conversion, back mutation and compensating mutations in cis have all been observed in revertant, and, consequently, mosaic FA-patients, leading to improved bone marrow function. There probably is no other experiment of nature in our species in which causes and consequences of genetic instability, including the role of reactive oxygen species, can be better documented and explored than in FA.
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Affiliation(s)
- R Kalb
- Department of Human Genetics, University of Würzburg, Biocenter, Würzburg, Germany
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Ouimet LA, Stewart A, Collins B, Schindler D, Bielajew C. Measuring neuropsychological change following breast cancer treatment: An analysis of statistical models. J Clin Exp Neuropsychol 2008; 31:73-89. [DOI: 10.1080/13803390801992725] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- L. A. Ouimet
- a University of Ottawa , Ottawa, Ontario, Canada
| | - A. Stewart
- a University of Ottawa , Ottawa, Ontario, Canada
| | - B. Collins
- b Ottawa Hospital , Ottawa, Ontario, Canada
| | - D. Schindler
- a University of Ottawa , Ottawa, Ontario, Canada
| | - C. Bielajew
- a University of Ottawa , Ottawa, Ontario, Canada
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Rauch A, Thiel CT, Schindler D, Wick U, Crow YJ, Ekici AB, van Essen AJ, Goecke TO, Al-Gazali L, Chrzanowska KH, Zweier C, Brunner HG, Becker K, Curry CJ, Dallapiccola B, Devriendt K, Dorfler A, Kinning E, Megarbane A, Meinecke P, Semple RK, Spranger S, Toutain A, Trembath RC, Voss E, Wilson L, Hennekam R, de Zegher F, Dorr HG, Reis A. Mutations in the Pericentrin (PCNT) Gene Cause Primordial Dwarfism. Science 2008; 319:816-9. [DOI: 10.1126/science.1151174] [Citation(s) in RCA: 316] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Galetzka D, Weis E, Rittner G, Schindler D, Haaf T. Microarray mRNA expression analysis of Fanconi anemia fibroblasts. Cytogenet Genome Res 2008; 121:10-3. [DOI: 10.1159/000124375] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2007] [Indexed: 11/19/2022] Open
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Neveling K, Kalb R, Florl AR, Herterich S, Friedl R, Hoehn H, Hader C, Hartmann FH, Nanda I, Steinlein C, Schmid M, Tonnies H, Hurst CD, Knowles MA, Hanenberg H, Schulz WA, Schindler D. Disruption of the FA/BRCA pathway in bladder cancer. Cytogenet Genome Res 2007; 118:166-76. [PMID: 18000367 DOI: 10.1159/000108297] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Accepted: 02/23/2007] [Indexed: 12/18/2022] Open
Abstract
Bladder carcinomas frequently show extensive deletions of chromosomes 9p and/or 9q, potentially including the loci of the Fanconi anemia (FA) genes FANCC and FANCG. FA is a rare recessive disease due to defects in anyone of 13 FANC genes manifesting with genetic instability and increased risk of neoplasia. FA cells are hypersensitive towards DNA crosslinking agents such as mitomycin C and cisplatin that are commonly employed in the chemotherapy of bladder cancers. These observations suggest the possibility of disruption of the FA/BRCA DNA repair pathway in bladder tumors. However, mutations in FANCC or FANCG could not be detected in any of 23 bladder carcinoma cell lines and ten surgical tumor specimens by LOH analysis or by FANCD2 immunoblotting assessing proficiency of the pathway. Only a single cell line, BFTC909, proved defective for FANCD2 monoubiquitination and was highly sensitive towards mitomycin C. This increased sensitivity was restored specifically by transfer of the FANCF gene. Sequencing of FANCF in BFTC909 failed to identify mutations, but methylation of cytosine residues in the FANCF promoter region was demonstrated by methylation-specific PCR, HpaII restriction and bisulfite DNA sequencing. Methylation-specific PCR uncovered only a single instance of FANCF promoter hypermethylation in surgical specimens of further 41 bladder carcinomas. These low proportions suggest that in contrast to other types of tumors silencing of FANCF is a rare event in bladder cancer and that an intact FA/BRCA pathway might be advantageous for tumor progression.
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Affiliation(s)
- K Neveling
- Department of Human Genetics, University of WürzburgBiozentrum, B107, Am Hubland, DE-97074 Würzburg, Germany
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Schindler D, Jang T. Sonography for the Assessment of Small Bowel Obstruction. Acad Emerg Med 2007. [DOI: 10.1197/j.aem.2007.03.976] [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: 11/10/2022]
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Grunewald TGP, Kammerer U, Winkler C, Schindler D, Sickmann A, Honig A, Butt E. Overexpression of LASP-1 mediates migration and proliferation of human ovarian cancer cells and influences zyxin localisation. Br J Cancer 2007; 96:296-305. [PMID: 17211471 PMCID: PMC2359999 DOI: 10.1038/sj.bjc.6603545] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
LIM and SH3 protein 1 (LASP-1), initially identified from human breast cancer, is a specific focal adhesion protein involved in cell proliferation and migration. In the present work, we analysed the effect of LASP-1 on biology and function of human ovarian cancer cell line SKOV-3 using small interfering RNA technique (siRNA). Transfection with LASP-1-specific siRNA resulted in a reduced protein level of LASP-1 in SKOV-3 cells. The siRNA-treated cells were arrested in G(2)/M phase of the cell cycle and proliferation of the tumour cells was suppressed by 60-90% corresponding to around 70% of the cells being transfected successfully as seen by immunofluorescence. Moreover, transfected tumour cells showed a 40% reduced migration. LASP-1 silencing is accompanied by a reduced binding of the LASP-1-binding partner zyxin to focal contacts without changes in actin stress fibre and microtubule organisation or focal adhesion morphology as observed by immunofluorescence. In contrast, silencing of zyxin is not influencing cell migration and had neither influence on LASP-1 expression nor actin cytoskeleton and focal contact morphology suggesting that LASP-1 is necessary and sufficient for recruiting zyxin to focal contacts. The data provide evidence for an essential role of LASP-1 in tumour cell growth and migration, possibly through influencing zyxin localization.
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Affiliation(s)
- T G P Grunewald
- Institute of Clinical Biochemistry and Pathobiochemistry, University of Wurzburg, Grombuehlstr. 12, D-97080 Wurzburg, Germany
| | - U Kammerer
- Department of Obstetrics and Gynecology, University of Wurzburg, Josef-Schneider-Str. 4, D-97080 Wurzburg, Germany
| | - C Winkler
- Protein Mass Spectrometry and Functional Proteomics Group, Rudolf-Virchow-Center for Experimental Biomedicine, Versbacher Straße 9, 97078 Wurzburg, Germany
| | - D Schindler
- Department of Human Genetics, University of Wurzburg, Biozentrum am Hubland, D-97074 Wurzburg, Germany
| | - A Sickmann
- Protein Mass Spectrometry and Functional Proteomics Group, Rudolf-Virchow-Center for Experimental Biomedicine, Versbacher Straße 9, 97078 Wurzburg, Germany
| | - A Honig
- Department of Obstetrics and Gynecology, University of Wurzburg, Josef-Schneider-Str. 4, D-97080 Wurzburg, Germany
| | - E Butt
- Institute of Clinical Biochemistry and Pathobiochemistry, University of Wurzburg, Grombuehlstr. 12, D-97080 Wurzburg, Germany
- E-mail:
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