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Pakhomov O, Shevchenko N, Chernobai N, Prokopiuk V, Yershov S, Bozhok G. Open-source hardware- and software-based cryomicroscopy system for investigation of phase transitions in cryobiological research. J Microsc 2024; 293:71-85. [PMID: 38093667 DOI: 10.1111/jmi.13253] [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: 09/07/2023] [Revised: 11/08/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
The development of inexpensive equipment adapted for the study of a specific biological object is very important for cryobiology. In the presented work, we have proposed a simple system for microscopy utilising open-source platform Arduino. Testing this system showed that it had sufficient sensitivity to determine the physical processes occurring in a cryopreserved sample such as intra- and extracellular water crystallisation and salt eutectic. Utilising this system, we investigated the mechanisms of cryoprotection and cryodamage of testis interstitial cells (ICs) in cryoprotective media, which included cryoprotective agents such as dimethyl sulphoxide (Me2 SO), as well as foetal bovine serum or polymers (dextran, hydroxyethyl starch and polyethylene glycol). It was shown that a serum-/xeno-free medium that included 0.7 M Me2 SO and 100 mg/mL dextran was able to reduce intracellular water crystallisation in cells, change the structure of extracellular ice, and reduce salt eutectic and recrystallisation. All these effects correlated with better IC survival after cryopreservation in the medium. This medium is potentially less toxic as it has lower concentrations of Me2 SO compared to serum-containing media developed for cryopreservation of testicular cells. This would pave a way for the creation of nontoxic serum-free compositions that does not require removal before use of cryopreserved living cells for laboratory practice or in clinics.
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Affiliation(s)
- Oleksandr Pakhomov
- Department of Cryoendocrinology, Institute for Problems of Cryobiology and Cryomedicine, National Academy of Sciences of Ukraine, Kharkiv, Ukraine
| | - Nadiia Shevchenko
- Department of Cryoendocrinology, Institute for Problems of Cryobiology and Cryomedicine, National Academy of Sciences of Ukraine, Kharkiv, Ukraine
| | - Nadiia Chernobai
- Department of Cryoendocrinology, Institute for Problems of Cryobiology and Cryomedicine, National Academy of Sciences of Ukraine, Kharkiv, Ukraine
| | - Volodymyr Prokopiuk
- Department of Cryoendocrinology, Institute for Problems of Cryobiology and Cryomedicine, National Academy of Sciences of Ukraine, Kharkiv, Ukraine
| | - Serhii Yershov
- Department of Cryoendocrinology, Institute for Problems of Cryobiology and Cryomedicine, National Academy of Sciences of Ukraine, Kharkiv, Ukraine
| | - Galyna Bozhok
- Department of Cryoendocrinology, Institute for Problems of Cryobiology and Cryomedicine, National Academy of Sciences of Ukraine, Kharkiv, Ukraine
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Deschamps J, Kieser C, Hoess P, Deguchi T, Ries J. MicroFPGA: An affordable FPGA platform for microscope control. HARDWAREX 2023; 13:e00407. [PMID: 36875260 PMCID: PMC9982678 DOI: 10.1016/j.ohx.2023.e00407] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Modern microscopy relies increasingly on microscope automation to improve throughput, ensure reproducibility or observe rare events. Automation requires computer control of the important elements of the microscope. Furthermore, optical elements that are usually fixed or manually movable can be placed on electronically-controllable elements. In most cases, a central electronics board is necessary to generate the control signals they require and to communicate with the computer. For such tasks, Arduino microcontrollers are widely used due to their low cost and programming entry barrier. However, they are limiting in their performance for applications that require high-speed or multiple parallel processes. Field programmable gate arrays (FPGA) are the perfect technology for high-speed microscope control, as they are capable of processing signals in parallel and with high temporal precision. While plummeting prices made the technology available to consumers, a major hurdle remaining is the complex languages used to configure them. In this work, we used an affordable FPGA, delivered with an open-source and friendly-to-use programming language, to create a versatile microscope control platform called MicroFPGA. It is capable of synchronously triggering cameras and multiple lasers following complex patterns, as well as generating various signals used to control microscope elements such as filter wheels, servomotor stages, flip-mirrors, laser power or acousto-optic modulators. MicroFPGA is open-source and we provide online Micro-Manager, Java, Python and LabVIEW libraries, together with blueprints and tutorials.
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Key Words
- (s) CMOS, (scientific) complementary metal–oxide–semiconductor
- ACB, analog conversion board
- AOM, acousto-optic modulator
- AOTF, acousto-optic tunable filter
- AOTF-CB, AOTF conversion board
- Automation
- BOM, bill of materials
- EMCCD, electron multiplying charge-coupled device
- Electronics
- FPGA
- FPGA, field-programmable gate array
- GND, ground
- HDL, hardware description language
- I/O, input/output
- Microscopy
- PWM, pulse-width modulation
- SCB, signal conversion board
- SDB, servo distribution board
- Synchronization
- TTL, transistor-transistor logic
- Triggering
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Affiliation(s)
- Joran Deschamps
- Computational Biology Center, Fondazione Human Technopole, Milan, Italy
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christian Kieser
- Electronics Workshop, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Philipp Hoess
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Takahiro Deguchi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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Ambrosini AE, Gelperin A. Reproducible Quantitative Stimulation Allows New Analysis of Crayfish Muscle Receptor Organ Responses. JOURNAL OF UNDERGRADUATE NEUROSCIENCE EDUCATION : JUNE : A PUBLICATION OF FUN, FACULTY FOR UNDERGRADUATE NEUROSCIENCE 2020; 19:A1-A20. [PMID: 33880088 PMCID: PMC8040843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/02/2019] [Accepted: 07/25/2020] [Indexed: 06/12/2023]
Abstract
The crustacean muscle receptor organ (MRO) has provided a particularly accessible preparation for the study of sensory coding, which has been widely used in introductory laboratory courses incorporating extracellular recording from sensory nerves in living preparations. We describe three innovations to the standard laboratory exercise using the MRO: (1) a new form of suction electrode to facilitate extracellular recording; (2) a new, Arduino-driven actuator to allow reproducible and quantifiable mechanical stimulation of the MRO; and (3) a new approach to the crayfish abdomen preparation that allows linear extension of the MRO muscles. These novel approaches allow the collection of data sets comprised of sensory cell spike trains under software control as important mechanical stimulus parameters are varied systematically through software. This additional level of user control facilitates a more robust quantitative approach to the analysis of MRO sensory neuron spike trains, which is facilitated by training in data analysis using python.
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Affiliation(s)
| | - Alan Gelperin
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544
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Trovato F, Parra R, Pracucci E, Landi S, Cozzolino O, Nardi G, Cruciani F, Pillai V, Mosti L, Cwetsch AW, Cancedda L, Gritti L, Sala C, Verpelli C, Maset A, Lodovichi C, Ratto GM. Modelling genetic mosaicism of neurodevelopmental disorders in vivo by a Cre-amplifying fluorescent reporter. Nat Commun 2020; 11:6194. [PMID: 33273479 PMCID: PMC7713426 DOI: 10.1038/s41467-020-19864-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 10/27/2020] [Indexed: 12/20/2022] Open
Abstract
Genetic mosaicism, a condition in which an organ includes cells with different genotypes, is frequently present in monogenic diseases of the central nervous system caused by the random inactivation of the X-chromosome, in the case of X-linked pathologies, or by somatic mutations affecting a subset of neurons. The comprehension of the mechanisms of these diseases and of the cell-autonomous effects of specific mutations requires the generation of sparse mosaic models, in which the genotype of each neuron is univocally identified by the expression of a fluorescent protein in vivo. Here, we show a dual-color reporter system that, when expressed in a floxed mouse line for a target gene, leads to the creation of mosaics with tunable degree. We demonstrate the generation of a knockout mosaic of the autism/epilepsy related gene PTEN in which the genotype of each neuron is reliably identified, and the neuronal phenotype is accurately characterized by two-photon microscopy.
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Affiliation(s)
- Francesco Trovato
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy.
| | - Riccardo Parra
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Enrico Pracucci
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Silvia Landi
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
- Institute of Neuroscience CNR, Pisa, Italy
| | - Olga Cozzolino
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Gabriele Nardi
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Federica Cruciani
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Vinoshene Pillai
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Laura Mosti
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Andrzej W Cwetsch
- Istituto Italiano di Tecnologia, Genoa, Italy
- Università degli studi di Genova, Genoa, Italy
| | - Laura Cancedda
- Istituto Italiano di Tecnologia, Genoa, Italy
- Istituto Telethon Dulbecco, Rome, Italy
| | | | - Carlo Sala
- Institute of Neuroscience CNR, Milan, Italy
| | | | - Andrea Maset
- Veneto Institute of Molecular Medicine, Padua, Italy
- Padova Neuroscience Center, Padova Università di Padova, Padua, Italy
| | - Claudia Lodovichi
- Veneto Institute of Molecular Medicine, Padua, Italy
- Padova Neuroscience Center, Padova Università di Padova, Padua, Italy
- Institute of Neuroscience CNR, Padua, Italy
| | - Gian Michele Ratto
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy.
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Quiñones DR, Fernández-Mollá LM, Pacheco-Torres J, Caramés JM, Canals S, Moratal D. TherMouseDuino: An affordable Open-Source temperature control system for functional magnetic resonance imaging experimentation with mice. Magn Reson Imaging 2019; 58:67-75. [PMID: 30660705 DOI: 10.1016/j.mri.2019.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/12/2018] [Accepted: 01/11/2019] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Functional magnetic resonance imaging (fMRI) is one of the most highly regarded techniques in the neuroimaging field. This technique is based on vascular responses to neuronal activation and is extensively used in clinical and animal research studies. In preclinical settings, fMRI is usually applied to anesthetized animals. However, anesthetics cause alterations, e.g. hypothermia, in the physiology of the animals and this has the potential to disrupt fMRI signals. The current temperature control method involves a technician, as well as monitoring the acquisition MRI sequences, also controlling the temperature of the animal; this is inefficient. METHODS In order to avoid hypothermia in anesthetized rodents an Open-Source automatic temperature control device is presented. It takes signals from an intrarectal temperature sensor, as well as signals from a thermal bath, which warms up the body of the animal under study, in order to determine the mathematical model of the thermal response of the animal. RESULTS A Proportional-Integral-Derivative (PID) algorithm, which was discretized in an Arduino microcontroller, was developed to automatically keep stable the body temperature of the animal under study. The PID algorithm has been shown to be accurate in preserving the body temperature of the animal. CONCLUSION This work presents the TherMouseDuino. It is an Open-Source automatic temperature control system and reduces temperature fluctuations, thus providing robust conditions in which to perform fMRI experiments. Furthermore, our device frees up the technician to focus solely on monitoring the MRI sequences.
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Affiliation(s)
- Darío R Quiñones
- Centre for Biomaterials and Tissue Engineering, Universitat Politècnica de València, Camí de Vera s/n, 46022 Valencia, Spain
| | - Luis Miguel Fernández-Mollá
- Centre for Biomaterials and Tissue Engineering, Universitat Politècnica de València, Camí de Vera s/n, 46022 Valencia, Spain
| | - Jesús Pacheco-Torres
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Santiago Ramón y Cajal s/n, 03550 Sant Joan d'Alacant, Alicante, Spain
| | - José M Caramés
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Santiago Ramón y Cajal s/n, 03550 Sant Joan d'Alacant, Alicante, Spain
| | - Santiago Canals
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Santiago Ramón y Cajal s/n, 03550 Sant Joan d'Alacant, Alicante, Spain
| | - David Moratal
- Centre for Biomaterials and Tissue Engineering, Universitat Politècnica de València, Camí de Vera s/n, 46022 Valencia, Spain.
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Simultaneous two-photon imaging of intracellular chloride concentration and pH in mouse pyramidal neurons in vivo. Proc Natl Acad Sci U S A 2017; 114:E8770-E8779. [PMID: 28973889 DOI: 10.1073/pnas.1702861114] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Intracellular chloride ([Cl-]i) and pH (pHi) are fundamental regulators of neuronal excitability. They exert wide-ranging effects on synaptic signaling and plasticity and on development and disorders of the brain. The ideal technique to elucidate the underlying ionic mechanisms is quantitative and combined two-photon imaging of [Cl-]i and pHi, but this has never been performed at the cellular level in vivo. Here, by using a genetically encoded fluorescent sensor that includes a spectroscopic reference (an element insensitive to Cl- and pH), we show that ratiometric imaging is strongly affected by the optical properties of the brain. We have designed a method that fully corrects for this source of error. Parallel measurements of [Cl-]i and pHi at the single-cell level in the mouse cortex showed the in vivo presence of the widely discussed developmental fall in [Cl-]i and the role of the K-Cl cotransporter KCC2 in this process. Then, we introduce a dynamic two-photon excitation protocol to simultaneously determine the changes of pHi and [Cl-]i in response to hypercapnia and seizure activity.
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