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Beyrent E, Wei DT, Beacham GM, Park S, Zheng J, Paszek MJ, Hollopeter G. Dimerization activates the Inversin complex in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594761. [PMID: 38798613 PMCID: PMC11118560 DOI: 10.1101/2024.05.17.594761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Genetic, colocalization, and biochemical studies suggest that the ankyrin repeat-containing proteins Inversin (INVS) and ANKS6 function with the NEK8 kinase to control tissue patterning and maintain organ physiology. It is unknown whether these three proteins assemble into a static "Inversin complex" or one that adopts multiple bioactive forms. Through characterization of hyperactive alleles in C. elegans , we discovered that the Inversin complex is activated by dimerization. Genome engineering of an RFP tag onto the nematode homologs of INVS (MLT-4) and NEK8 (NEKL-2) induced a gain-of-function, cyst-like phenotype that was suppressed by monomerization of the fluorescent tag. Stimulated dimerization of MLT-4 or NEKL-2 using optogenetics was sufficient to recapitulate the phenotype of a constitutively active Inversin complex. Further, dimerization of NEKL-2 bypassed a lethal MLT-4 mutant, demonstrating that the dimeric form is required for function. We propose that dynamic switching between at least two functionally distinct states-an active dimer and an inactive monomer-gates the output of the Inversin complex.
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2
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Valiente-Gabioud AA, Garteizgogeascoa Suñer I, Idziak A, Fabritius A, Basquin J, Angibaud J, Nägerl UV, Singh SP, Griesbeck O. Fluorescent sensors for imaging of interstitial calcium. Nat Commun 2023; 14:6220. [PMID: 37798285 PMCID: PMC10556026 DOI: 10.1038/s41467-023-41928-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 09/22/2023] [Indexed: 10/07/2023] Open
Abstract
Calcium in interstitial fluids is central to systemic physiology and a crucial ion pool for entry into cells through numerous plasma membrane channels. Its study has been limited by the scarcity of methods that allow monitoring in tight inter-cell spaces of living tissues. Here we present high performance ultra-low affinity genetically encoded calcium biosensors named GreenT-ECs. GreenT-ECs combine large fluorescence changes upon calcium binding and binding affinities (Kds) ranging from 0.8 mM to 2.9 mM, making them tuned to calcium concentrations in extracellular organismal fluids. We validated GreenT-ECs in rodent hippocampal neurons and transgenic zebrafish in vivo, where the sensors enabled monitoring homeostatic regulation of tissue interstitial calcium. GreenT-ECs may become useful for recording very large calcium transients and for imaging calcium homeostasis in inter-cell structures in live tissues and organisms.
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Affiliation(s)
- Ariel A Valiente-Gabioud
- Max Planck Institute for Biological Intelligence, Tools for Bio-Imaging, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Inés Garteizgogeascoa Suñer
- Institute de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), 808 Route de Lennik, Université Libre de Bruxelles (ULB), 1070, Brussels, Belgium
| | - Agata Idziak
- Institut Interdisciplinaire de Neurosciences, Synaptic Plasticity and Super-Resolution Microscopy, CNRS - Université de Bordeaux - 146 rue Léo-Saignat, Bordeaux, France
| | - Arne Fabritius
- Max Planck Institute for Biological Intelligence, Tools for Bio-Imaging, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Jérome Basquin
- Structural Cell Biology, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Julie Angibaud
- Institut Interdisciplinaire de Neurosciences, Synaptic Plasticity and Super-Resolution Microscopy, CNRS - Université de Bordeaux - 146 rue Léo-Saignat, Bordeaux, France
| | - U Valentin Nägerl
- Institut Interdisciplinaire de Neurosciences, Synaptic Plasticity and Super-Resolution Microscopy, CNRS - Université de Bordeaux - 146 rue Léo-Saignat, Bordeaux, France
| | - Sumeet Pal Singh
- Institute de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), 808 Route de Lennik, Université Libre de Bruxelles (ULB), 1070, Brussels, Belgium
| | - Oliver Griesbeck
- Max Planck Institute for Biological Intelligence, Tools for Bio-Imaging, Am Klopferspitz 18, 82152, Martinsried, Germany.
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3
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del Olmo Lianes I, Yubero P, Gómez-Luengo Á, Nogales J, Espeso DR. Technical upgrade of an open-source liquid handler to support bacterial colony screening. Front Bioeng Biotechnol 2023; 11:1202836. [PMID: 37404684 PMCID: PMC10315574 DOI: 10.3389/fbioe.2023.1202836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 06/07/2023] [Indexed: 07/06/2023] Open
Abstract
The optimization of genetically engineered biological constructs is a key step to deliver high-impact biotechnological applications. The use of high-throughput DNA assembly methods allows the construction of enough genotypic variants to successfully cover the target design space. This, however, entails extra workload for researchers during the screening stage of candidate variants. Despite the existence of commercial colony pickers, their high price excludes small research laboratories and budget-adjusted institutions from accessing such extensive screening capability. In this work we present COPICK, a technical solution to automatize colony picking in an open-source liquid handler Opentrons OT-2. COPICK relies on a mounted camera to capture images of regular Petri dishes and detect microbial colonies for automated screening. COPICK's software can then automatically select the best colonies according to different criteria (size, color and fluorescence) and execute a protocol to pick them for further analysis. Benchmark tests performed for E. coli and P. putida colonies delivers a raw picking performance over pickable colonies of 82% with an accuracy of 73.4% at an estimated rate of 240 colonies/h. These results validate the utility of COPICK, and highlight the importance of ongoing technical improvements in open-source laboratory equipment to support smaller research teams.
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Affiliation(s)
- Irene del Olmo Lianes
- Department of Systems Biology, Centro Nacional de Biotecnología—Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Pablo Yubero
- Department of Systems Biology, Centro Nacional de Biotecnología—Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Álvaro Gómez-Luengo
- Department of Systems Biology, Centro Nacional de Biotecnología—Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy—Consejo Superior de Investigaciones Científicas, SusPlast-CSIC, Madrid, Spain
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología—Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy—Consejo Superior de Investigaciones Científicas, SusPlast-CSIC, Madrid, Spain
| | - David R. Espeso
- Department of Systems Biology, Centro Nacional de Biotecnología—Consejo Superior de Investigaciones Científicas, Madrid, Spain
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4
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Liu K, Xu Z, Zhao Z, Chen Y, Chai Y, Ma L, Li S. A Dual Fluorescence Assay Enables High-Throughput Screening for Poly(ethylene terephthalate) Hydrolases. CHEMSUSCHEM 2023; 16:e202202019. [PMID: 36511949 DOI: 10.1002/cssc.202202019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/03/2022] [Indexed: 06/17/2023]
Abstract
The drastically increasing consumption of petroleum-derived plastics hasserious environmental impacts and raises public concerns. Poly(ethylene terephthalate) (PET) is amongst the most extensively produced synthetic polymers. Enzymatic hydrolysis of PET recently emerged as an enticing path for plastic degradation and recycling. In-lab directed evolution has revealed the great potential of PET hydrolases (PETases). However, the time-consuming and laborious PETase assays hinder the identification of effective variants in large mutant libraries. Herein, we devise and validate a dual fluorescence-based high-throughput screening (HTS) assay for a representative IsPETase. The two-round HTS of a pilot library consisting of 2850 IsPETase variants yields six mutant IsPETases with 1.3-4.9 folds improved activities. Compared to the currently used structure- or computational redesign-based PETase engineering, this HTS approach provides a new strategy for discovery of new beneficial mutation patterns of PETases.
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Affiliation(s)
- Kun Liu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Ziping Xu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Zhiyi Zhao
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Yuexing Chen
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Yating Chai
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Li Ma
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, No. 168 Wenhai Middle Rd, Qingdao, Shandong, 266237, P. R. China
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5
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Lee J, Campillo B, Hamidian S, Liu Z, Shorey M, St-Pierre F. Automating the High-Throughput Screening of Protein-Based Optical Indicators and Actuators. Biochemistry 2023; 62:169-177. [PMID: 36315460 PMCID: PMC9852035 DOI: 10.1021/acs.biochem.2c00357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Over the last 25 years, protein engineers have developed an impressive collection of optical tools to interface with biological systems: indicators to eavesdrop on cellular activity and actuators to poke and prod native processes. To reach the performance level required for their downstream applications, protein-based tools are usually sculpted by iterative rounds of mutagenesis. In each round, libraries of variants are made and evaluated, and the most promising hits are then retrieved, sequenced, and further characterized. Early efforts to engineer protein-based optical tools were largely manual, suffering from low throughput, human error, and tedium. Here, we describe approaches to automating the screening of libraries generated as colonies on agar, multiwell plates, and pooled populations of single-cell variants. We also briefly discuss emerging approaches for screening, including cell-free systems and machine learning.
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Affiliation(s)
- Jihwan Lee
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Beatriz Campillo
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shaminta Hamidian
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhuohe Liu
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Matthew Shorey
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - François St-Pierre
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
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6
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Wang X, Delle C, Asiminas A, Akther S, Vittani M, Brøgger P, Kusk P, Vo CT, Radovanovic T, Konno A, Hirai H, Fukuda M, Weikop P, Goldman SA, Nedergaard M, Hirase H. Liver-secreted fluorescent blood plasma markers enable chronic imaging of the microcirculation. CELL REPORTS METHODS 2022; 2:100302. [PMID: 36313804 PMCID: PMC9606131 DOI: 10.1016/j.crmeth.2022.100302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/11/2022] [Accepted: 09/01/2022] [Indexed: 12/25/2022]
Abstract
Studying blood microcirculation is vital for gaining insights into vascular diseases. Blood flow imaging in deep tissue is currently achieved by acute administration of fluorescent dyes in the blood plasma. This is an invasive process, and the plasma fluorescence decreases within an hour of administration. Here, we report an approach for the longitudinal study of vasculature. Using a single intraperitoneal or intravenous administration of viral vectors, we express fluorescent secretory albumin-fusion proteins in the liver to chronically label the blood circulation in mice. This approach allows for longitudinal observation of circulation from 2 weeks to over 4 months after vector administration. We demonstrate the chronic assessment of vascular functions including functional hyperemia and vascular plasticity in micro- and mesoscopic scales. This genetic plasma labeling approach represents a versatile and cost-effective method for the chronic investigation of vasculature functions across the body in health and disease animal models.
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Affiliation(s)
- Xiaowen Wang
- Center for Translational Neuromedicine, Faculty of Health and Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christine Delle
- Center for Translational Neuromedicine, Faculty of Health and Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Antonis Asiminas
- Center for Translational Neuromedicine, Faculty of Health and Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sonam Akther
- Center for Translational Neuromedicine, Faculty of Health and Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marta Vittani
- Center for Translational Neuromedicine, Faculty of Health and Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Brøgger
- Center for Translational Neuromedicine, Faculty of Health and Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Kusk
- Center for Translational Neuromedicine, Faculty of Health and Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Trang Vo
- Center for Translational Neuromedicine, Faculty of Health and Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tessa Radovanovic
- Center for Translational Neuromedicine, Faculty of Health and Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ayumu Konno
- Viral Vector Core, Gunma University Initiative for Advanced Research, Maebashi, Gunma 371-8511, Japan
- Department of Neurophysiology & Neural Repair, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Hirokazu Hirai
- Viral Vector Core, Gunma University Initiative for Advanced Research, Maebashi, Gunma 371-8511, Japan
- Department of Neurophysiology & Neural Repair, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Masahiro Fukuda
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore 169857, Singapore
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Pia Weikop
- Center for Translational Neuromedicine, Faculty of Health and Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Steven A. Goldman
- Center for Translational Neuromedicine, Faculty of Health and Life Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, Faculty of Health and Life Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Hajime Hirase
- Center for Translational Neuromedicine, Faculty of Health and Life Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, USA
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7
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Karsten L, Goett-Zink L, Schmitz J, Hoffrogge R, Grünberger A, Kottke T, Müller KM. Genetically Encoded Ratiometric pH Sensors for the Measurement of Intra- and Extracellular pH and Internalization Rates. BIOSENSORS 2022; 12:bios12050271. [PMID: 35624572 PMCID: PMC9138566 DOI: 10.3390/bios12050271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022]
Abstract
pH-sensitive fluorescent proteins as genetically encoded pH sensors are promising tools for monitoring intra- and extracellular pH. However, there is a lack of ratiometric pH sensors, which offer a good dynamic range and can be purified and applied extracellularly to investigate uptake. In our study, the bright fluorescent protein CoGFP_V0 was C-terminally fused to the ligand epidermal growth factor (EGF) and retained its dual-excitation and dual-emission properties as a purified protein. The tandem fluorescent variants EGF-CoGFP-mTagBFP2 (pK′ = 6.6) and EGF-CoGFP-mCRISPRed (pK′ = 6.1) revealed high dynamic ranges between pH 4.0 and 7.5. Using live-cell fluorescence microscopy, both pH sensor molecules permitted the conversion of fluorescence intensity ratios to detailed intracellular pH maps, which revealed pH gradients within endocytic vesicles. Additionally, extracellular binding of the pH sensors to cells expressing the EGF receptor (EGFR) enabled the tracking of pH shifts inside cultivation chambers of a microfluidic device. Furthermore, the dual-emission properties of EGF-CoGFP-mCRISPRed upon 488 nm excitation make this pH sensor a valuable tool for ratiometric flow cytometry. This high-throughput method allowed for the determination of internalization rates, which represents a promising kinetic parameter for the in vitro characterization of protein–drug conjugates in cancer therapy.
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Affiliation(s)
- Lennard Karsten
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| | - Lukas Goett-Zink
- Biophysical Chemistry and Diagnostics, Medical School OWL, Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany; (L.G.-Z.); (T.K.)
| | - Julian Schmitz
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (J.S.); (A.G.)
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Raimund Hoffrogge
- Cell Culture Technology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (J.S.); (A.G.)
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Tilman Kottke
- Biophysical Chemistry and Diagnostics, Medical School OWL, Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany; (L.G.-Z.); (T.K.)
| | - Kristian M. Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
- Correspondence:
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8
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Baumkircher A, Seme K, Munih M, Mihelj M. Collaborative Robot Precision Task in Medical Microbiology Laboratory. SENSORS 2022; 22:s22082862. [PMID: 35458847 PMCID: PMC9025832 DOI: 10.3390/s22082862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 11/16/2022]
Abstract
This study focuses on the feasibility of collaborative robot implementation in a medical microbiology laboratory by demonstrating fine tasks using kinesthetic teaching. Fine tasks require sub-millimetre positioning accuracy. Bacterial colony picking and identification was used as a case study. Colonies were picked from Petri dishes and identified using matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry. We picked and identified 56 colonies (36 colonies of Gram-negative Acinetobacter baumannii and 20 colonies of Gram-positive Staphylococcus epidermidis). The overall identification error rate was around 11%, although it was significantly lower for Gram-positive bacteria (5%) than Gram-negative bacteria (13.9%). Based on the identification scores, it was concluded that the system works similarly well as a manual operator. It was determined that tasks were successfully demonstrated using kinesthetic teaching and generalized using dynamic movement primitives (DMP). Further improvement of the identification error rate is possible by choosing a different deposited sample treatment method (e.g., semi-extraction, wet deposition).
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Affiliation(s)
- Aljaz Baumkircher
- Laboratory of Robotics, Faculty of Electrical Engineering, University of Ljubljana, Tržaška Cesta 25, 1000 Ljubljana, Slovenia
| | - Katja Seme
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
| | - Marko Munih
- Laboratory of Robotics, Faculty of Electrical Engineering, University of Ljubljana, Tržaška Cesta 25, 1000 Ljubljana, Slovenia
| | - Matjaž Mihelj
- Laboratory of Robotics, Faculty of Electrical Engineering, University of Ljubljana, Tržaška Cesta 25, 1000 Ljubljana, Slovenia
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9
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Wu T, Pang Y, Ai HW. Circularly Permuted Far-Red Fluorescent Proteins. BIOSENSORS 2021; 11:438. [PMID: 34821654 PMCID: PMC8615523 DOI: 10.3390/bios11110438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022]
Abstract
The color palette of genetically encoded fluorescent protein indicators (GEFPIs) has expanded rapidly in recent years. GEFPIs with excitation and emission within the "optical window" above 600 nm are expected to be superior in many aspects, such as enhanced tissue penetration, reduced autofluorescence and scattering, and lower phototoxicity. Circular permutation of fluorescent proteins (FPs) is often the first step in the process of developing single-FP-based GEFPIs. This study explored the tolerance of two far-red FPs, mMaroon1 and mCarmine, towards circular permutation. Several initial constructs were built according to previously reported circularly permuted topologies for other FP analogs. Mutagenesis was then performed on these constructs and screened for fluorescent variants. As a result, five circularly permuted far-red FPs (cpFrFPs) with excitation and emission maxima longer than 600 nm were identified. Some displayed appreciable brightness and efficient chromophore maturation. These cpFrFPs variants could be intriguing starting points to further engineer far-red GEFPIs for in vivo tissue imaging.
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Affiliation(s)
- Tianchen Wu
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA; (T.W.); (Y.P.)
| | - Yu Pang
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA; (T.W.); (Y.P.)
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui-wang Ai
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA; (T.W.); (Y.P.)
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
- The UVA Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
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10
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Vitelli M, Budman H, Pritzker M, Tamer M. Applications of flow cytometry sorting in the pharmaceutical industry: A review. Biotechnol Prog 2021; 37:e3146. [PMID: 33749147 DOI: 10.1002/btpr.3146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022]
Abstract
The article reviews applications of flow cytometry sorting in manufacturing of pharmaceuticals. Flow cytometry sorting is an extremely powerful tool for monitoring, screening and separating single cells based on any property that can be measured by flow cytometry. Different applications of flow cytometry sorting are classified into groups and discussed in separate sections as follows: (a) isolation of cell types, (b) high throughput screening, (c) cell surface display, (d) droplet fluorescent-activated cell sorting (FACS). Future opportunities are identified including: (a) sorting of particular fractions of the cell population based on a property of interest for generating inoculum that will result in improved outcomes of cell cultures and (b) the use of population balance models in combination with FACS to design and optimize cell cultures.
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Affiliation(s)
- Michael Vitelli
- Department of Chemical Engineering, University of Waterloo, Waterloo, Canada
| | - Hector Budman
- Department of Chemical Engineering, University of Waterloo, Waterloo, Canada
| | - Mark Pritzker
- Department of Chemical Engineering, University of Waterloo, Waterloo, Canada
| | - Melih Tamer
- Department of Manufacturing Technology, Sanofi Pasteur, Toronto, Canada
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11
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Pakhomov AA, Pastukhova AA, Tishkin GV, Martynov VI. Transformations of the Chromophore in the Course of Maturation of a Chromoprotein from Actinia equina. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021010167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Frolova AY, Pakhomov AA, Martynov VI. Physicochemical Properties of Photoconvertible Fluorescent Protein from Montastraea cavernosa. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Betolngar DB, Mota É, Fabritius A, Nielsen J, Hougaard C, Christoffersen CT, Yang J, Kehler J, Griesbeck O, Castro LRV, Vincent P. Phosphodiesterase 1 Bridges Glutamate Inputs with NO- and Dopamine-Induced Cyclic Nucleotide Signals in the Striatum. Cereb Cortex 2020; 29:5022-5036. [PMID: 30877787 DOI: 10.1093/cercor/bhz041] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 02/14/2019] [Indexed: 12/15/2022] Open
Abstract
The calcium-regulated phosphodiesterase 1 (PDE1) family is highly expressed in the brain, but its functional role in neurones is poorly understood. Using the selective PDE1 inhibitor Lu AF64196 and biosensors for cyclic nucleotides including a novel biosensor for cGMP, we analyzed the effect of PDE1 on cAMP and cGMP in individual neurones in brain slices from male newborn mice. Release of caged NMDA triggered a transient increase of intracellular calcium, which was associated with a decrease in cAMP and cGMP in medium spiny neurones in the striatum. Lu AF64196 alone did not increase neuronal cyclic nucleotide levels, but blocked the NMDA-induced reduction in cyclic nucleotides indicating that this was mediated by calcium-activated PDE1. Similar effects were observed in the prefrontal cortex and the hippocampus. Upon corelease of dopamine and NMDA, PDE1 was shown to down-regulate the D1-receptor mediated increase in cAMP. PDE1 inhibition increased long-term potentiation in rat ventral striatum, showing that PDE1 is implicated in the regulation of synaptic plasticity. Overall, our results show that PDE1 reduces cyclic nucleotide signaling in the context of glutamate and dopamine coincidence. This effect could have a therapeutic value for treating brain disorders related to dysfunctions in dopamine neuromodulation.
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Affiliation(s)
| | - Élia Mota
- Sorbonne Université, CNRS, Biological Adaptation and Ageing, Paris, France
| | - Arne Fabritius
- Max Planck Institute for Neurobiology, Tools for Bio-Imaging, Am Klopferspitz 18, Martinsried, Germany
| | | | | | | | - Jun Yang
- Shanghai Chempartner Co. Ltd., Shanghai, China
| | - Jan Kehler
- H. Lundbeck A/S, Ottiliavej 9, Valby, Denmark
| | - Oliver Griesbeck
- Max Planck Institute for Neurobiology, Tools for Bio-Imaging, Am Klopferspitz 18, Martinsried, Germany
| | - Liliana R V Castro
- Sorbonne Université, CNRS, Biological Adaptation and Ageing, Paris, France
| | - Pierre Vincent
- Sorbonne Université, CNRS, Biological Adaptation and Ageing, Paris, France
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14
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Hofmann UAT, Fabritius A, Rebling J, Estrada H, Deán-Ben XL, Griesbeck O, Razansky D. High-Throughput Platform for Optoacoustic Probing of Genetically Encoded Calcium Ion Indicators. iScience 2019; 22:400-408. [PMID: 31812810 PMCID: PMC6911978 DOI: 10.1016/j.isci.2019.11.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 11/15/2019] [Accepted: 11/19/2019] [Indexed: 12/15/2022] Open
Abstract
Functional optoacoustic (OA) imaging assisted with genetically encoded calcium ion indicators (GECIs) holds promise for imaging large-scale neuronal activity at depths and spatiotemporal resolutions not attainable with existing optical microscopic techniques. However, currently available GECIs optimized for fluorescence (FL) imaging lack sufficient contrast for OA imaging and respond at wavelengths having limited penetration into the mammalian brain. Here we present an imaging platform capable of rapid assessment and cross-validation between OA and FL responses of sensor proteins expressed in Escherichia coli colonies. The screening system features optimized pulsed light excitation combined with ultrasensitive ultrasound detection to mitigate photobleaching while further allowing the dynamic characterization of calcium ion responses with millisecond precision. Targeted probing of up to six individual colonies per second in both calcium-loaded and calcium-unloaded states was possible with the system. The new platform greatly facilitates optimization of absorption-based labels, thus setting the stage for directed evolution of OA GECIs.
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Affiliation(s)
- Urs A T Hofmann
- Institute of Pharmacology and Toxicology and Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Biomedical Engineering and Department of Information Technology and Electrical Engineering, ETH Zurich, Gloriastrasse 35, 8092 Zurich, Switzerland
| | - Arne Fabritius
- Tools for Bio-Imaging, Max Planck Institute, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Johannes Rebling
- Institute of Pharmacology and Toxicology and Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Biomedical Engineering and Department of Information Technology and Electrical Engineering, ETH Zurich, Gloriastrasse 35, 8092 Zurich, Switzerland
| | - Héctor Estrada
- Institute of Pharmacology and Toxicology and Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Biomedical Engineering and Department of Information Technology and Electrical Engineering, ETH Zurich, Gloriastrasse 35, 8092 Zurich, Switzerland
| | - X Luís Deán-Ben
- Institute of Pharmacology and Toxicology and Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Biomedical Engineering and Department of Information Technology and Electrical Engineering, ETH Zurich, Gloriastrasse 35, 8092 Zurich, Switzerland
| | - Oliver Griesbeck
- Tools for Bio-Imaging, Max Planck Institute, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Daniel Razansky
- Institute of Pharmacology and Toxicology and Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Biomedical Engineering and Department of Information Technology and Electrical Engineering, ETH Zurich, Gloriastrasse 35, 8092 Zurich, Switzerland.
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15
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Optimizing the fluorescent protein toolbox and its use. Curr Opin Biotechnol 2019; 58:183-191. [DOI: 10.1016/j.copbio.2019.04.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/24/2019] [Indexed: 01/07/2023]
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16
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Isozaki A, Mikami H, Hiramatsu K, Sakuma S, Kasai Y, Iino T, Yamano T, Yasumoto A, Oguchi Y, Suzuki N, Shirasaki Y, Endo T, Ito T, Hiraki K, Yamada M, Matsusaka S, Hayakawa T, Fukuzawa H, Yatomi Y, Arai F, Di Carlo D, Nakagawa A, Hoshino Y, Hosokawa Y, Uemura S, Sugimura T, Ozeki Y, Nitta N, Goda K. A practical guide to intelligent image-activated cell sorting. Nat Protoc 2019; 14:2370-2415. [PMID: 31278398 DOI: 10.1038/s41596-019-0183-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/18/2019] [Indexed: 02/08/2023]
Abstract
Intelligent image-activated cell sorting (iIACS) is a machine-intelligence technology that performs real-time intelligent image-based sorting of single cells with high throughput. iIACS extends beyond the capabilities of fluorescence-activated cell sorting (FACS) from fluorescence intensity profiles of cells to multidimensional images, thereby enabling high-content sorting of cells or cell clusters with unique spatial chemical and morphological traits. Therefore, iIACS serves as an integral part of holistic single-cell analysis by enabling direct links between population-level analysis (flow cytometry), cell-level analysis (microscopy), and gene-level analysis (sequencing). Specifically, iIACS is based on a seamless integration of high-throughput cell microscopy (e.g., multicolor fluorescence imaging, bright-field imaging), cell focusing, cell sorting, and deep learning on a hybrid software-hardware data management infrastructure, enabling real-time automated operation for data acquisition, data processing, intelligent decision making, and actuation. Here, we provide a practical guide to iIACS that describes how to design, build, characterize, and use an iIACS machine. The guide includes the consideration of several important design parameters, such as throughput, sensitivity, dynamic range, image quality, sort purity, and sort yield; the development and integration of optical, microfluidic, electrical, computational, and mechanical components; and the characterization and practical usage of the integrated system. Assuming that all components are readily available, a team of several researchers experienced in optics, electronics, digital signal processing, microfluidics, mechatronics, and flow cytometry can complete this protocol in ~3 months.
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Affiliation(s)
- Akihiro Isozaki
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Hideharu Mikami
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | | | - Shinya Sakuma
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Nagoya, Japan
| | - Yusuke Kasai
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Nagoya, Japan
| | - Takanori Iino
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Takashi Yamano
- Laboratory of Applied Molecular Microbiology, Kyoto University, Kyoto, Japan
| | - Atsushi Yasumoto
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yusuke Oguchi
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Nobutake Suzuki
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | | | | | - Takuro Ito
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.,Japan Science and Technology Agency, Saitama, Japan
| | - Kei Hiraki
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Makoto Yamada
- Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University, Kyoto, Japan
| | - Satoshi Matsusaka
- Clinical Research and Regional Innovation, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Takeshi Hayakawa
- Department of Precision Mechanics, Chuo University, Tokyo, Japan
| | - Hideya Fukuzawa
- Laboratory of Applied Molecular Microbiology, Kyoto University, Kyoto, Japan
| | - Yutaka Yatomi
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Fumihito Arai
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Nagoya, Japan
| | - Dino Di Carlo
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.,Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Mechanical Engineering, University of California, Los Angeles, Los Angeles, CA, USA.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Atsuhiro Nakagawa
- Department of Neurosurgery, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yu Hoshino
- Department of Chemical Engineering, Kyushu University, Fukuoka, Japan
| | - Yoichiroh Hosokawa
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeaki Sugimura
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.,Japan Science and Technology Agency, Saitama, Japan
| | - Yasuyuki Ozeki
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Nao Nitta
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.,Japan Science and Technology Agency, Saitama, Japan
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo, Tokyo, Japan. .,Japan Science and Technology Agency, Saitama, Japan. .,Department of Electrical Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
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