Special Issue "Optogenetics: From Light-Activated Proteins to Optical Spatio-Temporal Control"

A special issue of Methods and Protocols (ISSN 2409-9279).

Deadline for manuscript submissions: closed (30 November 2018)

Special Issue Editor

Guest Editor
Dr. Leonardo Sacconi

National Institute of Optics (INO-CNR) c/o LENS - European Laboratory for Non-linear Spectroscopy; Via Nello Carrara 1, 50019 Sesto Fiorentino (FI), Italy
Website | E-Mail
Interests: Optical microscopy; Imaging system; Cardiac electrophysiology; Voltage sensitive dye; Calcium imaging; Optogenetics

Special Issue Information

Dear Colleagues,

Optogenetics provides a tool for controlling cellular function by means of the interaction of photons with light-gated proteins. Since the discovery of activating microbial rhodopsins by Nagel and colleagues, optogenetic applications in mammals have exploded. A true “optical” revolution occurred in neuroscience, and, more recently, in cardiovascular research with the publication of thousands of discoveries and insights. Among the latest achievements, for instance, optogenetics has been used to understand the functional roles of neuronal populations, to identify neuronal circuits controlling action initiation, to resynchronize and defibrillate arrhythmic hearts. The perspective of this optical approach to perturb neuronal network and cardiac electrical activity is unimaginable, especially when the spatio-temporal qualities of light are fully exploited.

In this Special Issue, we welcome researchers to submit original research and review articles on all optical methods for achieving a full spatio-temporal control and their applications.

Dr. Leonardo Sacconi
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Methods and Protocols is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) is waived for well-prepared manuscripts submitted to this issue. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Photo-stimulation
  • Optical manipulation
  • Photo-chemistry
  • Channelrhodopsin
  • Halorhodopsin
  • Neuro-photonics
  • Cardiac imaging
  • Optical microscopy
  • Light spatial modulator
  • Digital micro-mirror device
  • Laser scanning
  • Photo-uncaging

Published Papers (4 papers)

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Research

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Open AccessArticle
Fast Calculation of Computer Generated Holograms for 3D Photostimulation through Compressive-Sensing Gerchberg–Saxton Algorithm
Methods Protoc. 2019, 2(1), 2; https://doi.org/10.3390/mps2010002
Received: 29 October 2018 / Revised: 1 December 2018 / Accepted: 18 December 2018 / Published: 20 December 2018
Cited by 1 | PDF Full-text (1087 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The use of spatial light modulators to project computer generated holograms is a common strategy for optogenetic stimulation of multiple structures of interest within a three-dimensional volume. A common requirement when addressing multiple targets sparsely distributed in three dimensions is the generation of [...] Read more.
The use of spatial light modulators to project computer generated holograms is a common strategy for optogenetic stimulation of multiple structures of interest within a three-dimensional volume. A common requirement when addressing multiple targets sparsely distributed in three dimensions is the generation of a points cloud, focusing excitation light in multiple diffraction-limited locations throughout the sample. Calculation of this type of holograms is most commonly performed with either the high-speed, low-performance random superposition algorithm, or the low-speed, high performance Gerchberg–Saxton algorithm. This paper presents a variation of the Gerchberg–Saxton algorithm that, by only performing iterations on a subset of the data, according to compressive sensing principles, is rendered significantly faster while maintaining high quality outputs. The algorithm is presented in high-efficiency and high-uniformity variants. All source code for the method implementation is available as Supplementary Materials and as open-source software. The method was tested computationally against existing algorithms, and the results were confirmed experimentally on a custom setup for in-vivo multiphoton optogenetics. The results clearly show that the proposed method can achieve computational speed performances close to the random superposition algorithm, while retaining the high performance of the Gerchberg–Saxton algorithm, with a minimal hologram quality loss. Full article
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Review

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Open AccessReview
A Light Wand to Untangle the Myocardial Cell Network
Methods Protoc. 2019, 2(2), 34; https://doi.org/10.3390/mps2020034
Received: 21 March 2019 / Revised: 24 April 2019 / Accepted: 28 April 2019 / Published: 3 May 2019
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Abstract
The discovery of optogenetics has revolutionized research in neuroscience by providing the tools for noninvasive, cell-type selective modulation of membrane potential and cellular function in vitro and in vivo. Rhodopsin-based optogenetics has later been introduced in experimental cardiology studies and used as a [...] Read more.
The discovery of optogenetics has revolutionized research in neuroscience by providing the tools for noninvasive, cell-type selective modulation of membrane potential and cellular function in vitro and in vivo. Rhodopsin-based optogenetics has later been introduced in experimental cardiology studies and used as a tool to photoactivate cardiac contractions or to identify the sites, timing, and location most effective for defibrillating impulses to interrupt cardiac arrhythmias. The exploitation of cell-selectivity of optogenetics, and the generation of model organisms with myocardial cell type targeted expression of opsins has started to yield novel and sometimes unexpected notions on myocardial biology. This review summarizes the main results, the different uses, and the prospective developments of cardiac optogenetics. Full article
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Other

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Open AccessLetter
Large Scale Double-Path Illumination System with Split Field of View for the All-Optical Study of Inter-and Intra-Hemispheric Functional Connectivity on Mice
Methods Protoc. 2019, 2(1), 11; https://doi.org/10.3390/mps2010011
Received: 30 November 2018 / Revised: 14 January 2019 / Accepted: 18 January 2019 / Published: 29 January 2019
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Abstract
Recent improvements in optical tools that can perturb brain activity and simultaneously reveal the elicited alterations in the associated regions offer an exceptional means to understand and map the connectivity of the brain. In this work, we exploit a combination of recently developed [...] Read more.
Recent improvements in optical tools that can perturb brain activity and simultaneously reveal the elicited alterations in the associated regions offer an exceptional means to understand and map the connectivity of the brain. In this work, we exploit a combination of recently developed optical tools to monitor neural population at the meso-scale level and to mould the cortical patterns of targeted neuronal population. Our goal was to investigate the propagation of neuronal activity over the mouse cortex that is triggered by optogenetic stimulation in the contralateral hemisphere. Towards this aim, we developed a wide-field fluorescence microscope that is characterized by a double illumination path allowing for the optogenetic stimulation of the transfected area in the left hemisphere and the simultaneous recording of cortical activity in the right hemisphere. The microscope was further implemented with a custom shutter in order to split the LED illumination path, resulting in a half-obscured field of view. By avoiding the spectral crosstalk between GCaMP6f and channelrhodopsin 2 (ChR2), this system offered the possibility of simultaneous “pumping and probing” of inter-hemispheric functional connectivity on Thy1-GCaMP6f mice. Full article
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Open AccessTechnical Note
A Software Architecture to Mimic a Ventricular Tachycardia in Intact Murine Hearts by Means of an All-Optical Platform
Methods Protoc. 2019, 2(1), 7; https://doi.org/10.3390/mps2010007
Received: 29 November 2018 / Revised: 29 December 2018 / Accepted: 4 January 2019 / Published: 8 January 2019
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Abstract
Optogenetics is an emerging method that uses light to manipulate electrical activity in excitable cells exploiting the interaction between light and light-sensitive depolarizing ion channels, such as channelrhodopsin-2 (ChR2). Initially used in the neuroscience, it has been adopted in cardiac research where the [...] Read more.
Optogenetics is an emerging method that uses light to manipulate electrical activity in excitable cells exploiting the interaction between light and light-sensitive depolarizing ion channels, such as channelrhodopsin-2 (ChR2). Initially used in the neuroscience, it has been adopted in cardiac research where the expression of ChR2 in cardiac preparations allows optical pacing, resynchronization and defibrillation. Recently, optogenetics has been leveraged to manipulate cardiac electrical activity in the intact heart in real-time. This new approach was applied to simulate a re-entrant circuit across the ventricle. In this technical note, we describe the development and the implementation of a new software package for real-time optogenetic intervention. The package consists of a single LabVIEW program that simultaneously captures images at very high frame rates and delivers precisely timed optogenetic stimuli based on the content of the images. The software implementation guarantees closed-loop optical manipulation at high temporal resolution by processing the raw data in workstation memory. We demonstrate that this strategy allows the simulation of a ventricular tachycardia with high stability and with a negligible loss of data with a temporal resolution of up to 1 ms. Full article
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