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      Optophysiology: Illuminating cell physiology with optogenetics

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          Abstract

          Abstract

          Optogenetics combines light and genetics to enable precise control of living cells, tissues, and organisms with tailored functions. Optogenetics has the advantages of noninvasiveness, rapid responsiveness, tunable reversibility, and superior spatiotemporal resolution. Following the initial discovery of microbial opsins as light-actuated ion channels, a plethora of naturally occurring or engineered photoreceptors or photosensitive domains that respond to light at varying wavelengths has ushered in the next chapter of optogenetics. Through protein engineering and synthetic biology approaches, genetically encoded photoswitches can be modularly engineered into protein scaffolds or host cells to control a myriad of biological processes, as well as to enable behavioral control and disease intervention in vivo. Here, we summarize these optogenetic tools on the basis of their fundamental photochemical properties to better inform the chemical basis and design principles. We also highlight exemplary applications of opsin-free optogenetics in dissecting cellular physiology (designated “optophysiology”) and describe the current progress, as well as future trends, in wireless optogenetics, which enables remote interrogation of physiological processes with minimal invasiveness. This review is anticipated to spark novel thoughts on engineering next-generation optogenetic tools and devices that promise to accelerate both basic and translational studies.

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          Cleavage of GSDMD by inflammatory caspases determines pyroptotic cell death.

          Inflammatory caspases (caspase-1, -4, -5 and -11) are critical for innate defences. Caspase-1 is activated by ligands of various canonical inflammasomes, and caspase-4, -5 and -11 directly recognize bacterial lipopolysaccharide, both of which trigger pyroptosis. Despite the crucial role in immunity and endotoxic shock, the mechanism for pyroptosis induction by inflammatory caspases is unknown. Here we identify gasdermin D (Gsdmd) by genome-wide clustered regularly interspaced palindromic repeat (CRISPR)-Cas9 nuclease screens of caspase-11- and caspase-1-mediated pyroptosis in mouse bone marrow macrophages. GSDMD-deficient cells resisted the induction of pyroptosis by cytosolic lipopolysaccharide and known canonical inflammasome ligands. Interleukin-1β release was also diminished in Gsdmd(-/-) cells, despite intact processing by caspase-1. Caspase-1 and caspase-4/5/11 specifically cleaved the linker between the amino-terminal gasdermin-N and carboxy-terminal gasdermin-C domains in GSDMD, which was required and sufficient for pyroptosis. The cleavage released the intramolecular inhibition on the gasdermin-N domain that showed intrinsic pyroptosis-inducing activity. Other gasdermin family members were not cleaved by inflammatory caspases but shared the autoinhibition; gain-of-function mutations in Gsdma3 that cause alopecia and skin defects disrupted the autoinhibition, allowing its gasdermin-N domain to trigger pyroptosis. These findings offer insight into inflammasome-mediated immunity/diseases and also change our understanding of pyroptosis and programmed necrosis.
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            Pattern recognition receptors and inflammation.

            Infection of cells by microorganisms activates the inflammatory response. The initial sensing of infection is mediated by innate pattern recognition receptors (PRRs), which include Toll-like receptors, RIG-I-like receptors, NOD-like receptors, and C-type lectin receptors. The intracellular signaling cascades triggered by these PRRs lead to transcriptional expression of inflammatory mediators that coordinate the elimination of pathogens and infected cells. However, aberrant activation of this system leads to immunodeficiency, septic shock, or induction of autoimmunity. In this Review, we discuss the role of PRRs, their signaling pathways, and how they control inflammatory responses. 2010 Elsevier Inc. All rights reserved.
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              Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

              Current genome-editing technologies introduce double-stranded (ds) DNA breaks at a target locus as the first step to gene correction. 1,2 Although most genetic diseases arise from point mutations, current approaches to point mutation correction are inefficient and typically induce an abundance of random insertions and deletions (indels) at the target locus from the cellular response to dsDNA breaks. 1,2 Here we report the development of base editing, a new approach to genome editing that enables the direct, irreversible conversion of one target DNA base into another in a programmable manner, without requiring dsDNA backbone cleavage or a donor template. We engineered fusions of CRISPR/Cas9 and a cytidine deaminase enzyme that retain the ability to be programmed with a guide RNA, do not induce dsDNA breaks, and mediate the direct conversion of cytidine to uridine, thereby effecting a C→T (or G→A) substitution. The resulting “base editors” convert cytidines within a window of approximately five nucleotides (nt), and can efficiently correct a variety of point mutations relevant to human disease. In four transformed human and murine cell lines, second- and third-generation base editors that fuse uracil glycosylase inhibitor (UGI), and that use a Cas9 nickase targeting the non-edited strand, manipulate the cellular DNA repair response to favor desired base-editing outcomes, resulting in permanent correction of ∼15-75% of total cellular DNA with minimal (typically ≤ 1%) indel formation. Base editing expands the scope and efficiency of genome editing of point mutations.
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                Author and article information

                Journal
                Physiol Rev
                Physiol Rev
                PHYSREV
                Physiological Reviews
                American Physiological Society (Rockville, MD )
                0031-9333
                1522-1210
                1 July 2022
                24 January 2022
                24 January 2022
                : 102
                : 3
                : 1263-1325
                Affiliations
                [1] 1Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University , Houston, Texas
                [2] 2Klarman Cell Observatory, Broad Institute of MIT and Harvard , Cambridge, Massachusetts
                [3] 3Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University , Houston, Texas
                [4] 4Department of Translational Medical Sciences, College of Medicine, Texas A&M University , Houston, Texas
                Author notes
                [*]

                P. Tan and L. He contributed equally to this work.

                Correspondence: Y. Zhou ( yubinzhou@ 123456tamu.edu ); Y. Huang ( yun.huang@ 123456tamu.edu ).
                Author information
                https://orcid.org/0000-0001-6992-9000
                https://orcid.org/0000-0001-7962-0517
                Article
                PRV-00021-2021 PRV-00021-2021
                10.1152/physrev.00021.2021
                8993538
                35072525
                64080a72-8083-44a4-874e-a33e17c7a018
                Copyright © 2022 The Authors

                Licensed under Creative Commons Attribution CC-BY 4.0. Published by the American Physiological Society.

                History
                : 12 July 2021
                : 13 December 2021
                : 14 January 2022
                Funding
                Funded by: American Cancer Society (ACS), doi 10.13039/100000048;
                Award ID: RSG-16-215-01-TBE
                Award Recipient : Yubin Zhou
                Funded by: American Cancer Society (ACS), doi 10.13039/100000048;
                Award ID: RSG-18-043-01-LIB
                Award Recipient : Yun Huang
                Funded by: Cancer Prevention and Research Institute of Texas (CPRIT), doi 10.13039/100004917;
                Award ID: RP210070
                Award Recipient : Yubin Zhou
                Funded by: HHS | NIH | National Cancer Institute (NCI), doi 10.13039/100000054;
                Award ID: R01CA232017
                Award Recipient : Yubin Zhou
                Funded by: HHS | NIH | National Institute of General Medical Sciences (NIGMS), doi 10.13039/100000057;
                Award ID: R01GM112003
                Award Recipient : Yubin Zhou
                Funded by: HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI), doi 10.13039/100000050;
                Award ID: R01HL134780
                Award ID: R01HL146852
                Award Recipient : Yun Huang
                Funded by: HHS | NIH | National Cancer Institute (NCI), doi 10.13039/100000054;
                Award ID: R01CA240258
                Award Recipient : Yun Huang
                Funded by: Welch Foundation (The Welch Foundation), doi 10.13039/100000928;
                Award ID: BE-1913-20190330
                Award Recipient : Yubin Zhou
                Categories
                Review

                cellular physiology,nanophotonics,optogenetics,signal transduction,synthetic biology

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