Toolkit Items

Beggiatoa photoactivated adenylyl cyclase (bPAC) is a blue light-activated optogenetic adenylyl cyclase used to generate cyclic AMP in cells. The cited studies used it to drive cAMP-dependent signaling, including PKA activation, to increase endogenous cortisol in a blue light-dependent manner, and to localize cAMP production to defined subcellular compartments such as the cilium.

The engineered GEF-Pak1 interaction is a rewired Cdc42 positive-feedback construct in Schizosaccharomyces pombe in which a guanine nucleotide exchange factor is engineered to interact with the Cdc42 effector p21-activated kinase 1 (Pak1). This engineered coupling supports scaffold-mediated positive feedback, promotes active Cdc42 zone formation, and enables rod-shape polarization.

Archaerhodopsin-3 (Arch) is a light-sensitive microbial rhodopsin proton pump used as an optogenetic inhibitory tool. The supplied evidence identifies Arch as a previously available optogenetic tool and specifically as an ion-pumping rhodopsin.

Photoactivated adenylyl cyclases are light-responsive adenylyl cyclase protein domains used as optogenetic tools to modulate intracellular cAMP levels. Reported effects include light-induced CREB signaling and Cox-2/prostaglandin E2 upregulation in HEK-293T cells, and altered starvation-induced development in Dictyostelium discoideum.

Here, we developed an all-optical platform to examine less invasive defibrillation strategies.

This tool is a tunable optogenetic, light-inducible gene expression system used to control morphogen production in vitro. It was reported to generate long-range Sonic hedgehog (Shh) gradients that pattern neural progenitors into spatially distinct progenitor domains resembling vertebrate neural tube organization in vivo.

This tool is a genetically encoded optogenetic switch that uses light to regulate biological function. The supplied evidence supports its use to control central metabolic flux in Escherichia coli and to drive spatiotemporally controlled shape change in yeast with pulses of dim blue light.

optofYap is an optogenetic YAP construct reported in EMBO Reports (2022) for light-responsive control of YAP function in zebrafish embryos. The supplied evidence indicates that it can modulate target gene expression in vivo, but does not provide construct architecture or photoreceptor details here.

Opto-PIP3 is an optogenetic construct used to elevate or spatially pattern PI(3,4,5)P3 signaling in cells. In adipocytes, its activation largely mimicked the maximal effect of insulin on IRAP-pHluorin translocation, supporting the sufficiency of PI3K-generated PIP3 for much of this membrane-trafficking response.

we performed patch-clamp recordings from basal amygdala (BA) neurons in brain slices from mice with channelrhodopsin genetically targeted to 5-HT neurons

Optical VTA stimulation in ChR2+ mice during continuous, steady-state general anesthesia (CSSGA) with isoflurane produced behavioral and EEG evidence of arousal and restored the righting reflex.

We transduced rat LC neurons by direct injection of a lentiviral vector expressing channelrhodopsin2 under the control of the PRS promoter.

All-optical approaches with the opportunity to write complex three dimensional patterns into neuronal networks have recently emerged.

Fetal neuroblasts are transplanted donor cells used to replace neurons in damaged basal ganglia circuits. The review describes their use in early rodent studies of circuitry repair.

Recent progress in the generation of striatal and nigral progenitors from pluripotent stem cells have provided compelling evidence that they can survive and mature in the lesioned brain and re-establish afferent and efferent axonal connectivity with a remarkable degree of specificity.

Updating these findings leads us to propose that the rodent pilocarpine model continues to represent a valuable tool for identifying the basic pathophysiology of MTLE.

Recent progress in the generation of striatal and nigral progenitors from pluripotent stem cells have provided compelling evidence that they can survive and mature in the lesioned brain and re-establish afferent and efferent axonal connectivity with a remarkable degree of specificity.

However, the use of transgenic mice has revealed novel information regarding this animal model.

Automated optogenetic feedback control is an engineering method that combines light-driven optogenetic regulation with a feedback loop to control gene expression and cell growth. The available evidence supports it as a control framework for precise and robust regulation rather than as a single molecular reagent.

Clustering Indirectly using Cryptochrome 2 (CLICR) is a genetically encoded optogenetic method for spatiotemporal control of endogenous transmembrane receptor activation. It uses engineered Arabidopsis Cry2 to regulate target receptor clustering through noncovalent interactions, thereby activating downstream signaling.

Light-controlled nuclear localization is an optogenetic engineering method reported for constructing repressors of gene expression in yeasts. It uses light to regulate nuclear localization, thereby controlling transcriptional repression.

Midbrain organoids (MOs), three-dimensional (3D) stem cell-derived neuronal structures mimicking midbrain architecture, have emerged as transformative tools for modelling PD.

we created a modular light-controlled skeletal muscle-powered bioactuator that can generate up to 300 µN (0.56 kPa) of active tension force in response to a noninvasive optical stimulus

This entry describes an optogenetic engineering method applied to identify a rapid eye movement sleep modulatory circuit in the hypothalamus. The available evidence supports only that light-based circuit interrogation was used in this neurobiological context.

Optogenetically driven exocyst-mediated vesicle tethering is a light-controlled perturbation method that acutely promotes exocytosis by driving exocyst-dependent vesicle tethering. In epithelial cells, this manipulation is linked to increased plasma membrane PI(3,4,5)P3 and activation of the EGFR/PI-3K/AKT pathway.

Optogenetically driven repositioning of lysosomes is a light-controlled perturbation method used to move lysosomes and test their causal role in endoplasmic reticulum remodeling. In the cited 2020 study, chemo- and optogenetically driven lysosome repositioning was used to validate a causal link between lysosome positioning and ER network organization.

Optogenetic control of apical constriction is an engineering method that uses light to drive apical constriction and thereby induce synthetic morphogenesis in mammalian tissues. The available evidence supports this method as a light-responsive approach for reshaping tissue architecture.

Optogenetic control of contractility is a light-based engineering method proposed to spatially modulate cellular contractility and thereby influence cell migration behavior. In a one-dimensional active gel model, optogenetic activation or inhibition of contractility is predicted to switch cells between sessile and motile states at realistic parameter values.

Optogenetic control of mitochondria-lysosome contacts is an engineering method that uses light to modulate contacts between mitochondria and lysosomes. In the cited 2022 Nature Communications study, this manipulation enabled light-activated mitochondrial fission.

Optogenetic inhibition of Delta is a light-controlled perturbation method reported in a 2019 EMBO Reports study to inhibit the Notch ligand Delta during tissue differentiation. The study links this intervention to revealing digital Notch signalling output.

The optogenetic inhibitor of c-Jun NH2-terminal kinase (JNK) is a light-controlled construct used to inhibit JNK signaling. In the cited eNeuro study, it was used to interrogate local JNK function in dendritic spine heads and to modulate stress-associated AMPAR internalization, actin reorganization, and spine structural remodeling.

Optogenetic-mediated acute inhibition of myosin is a light-controlled perturbation method used during Drosophila mesoderm invagination to acutely inhibit myosin-dependent contractility. In the cited 2021 gastrulation study, it was applied to test how myosin activity contributes to mesoderm invagination and epithelial buckling.

This engineering method is an optogenetic system for light-triggered ligand secretion, demonstrated for chemokine release. It combines UV-conditioned endoplasmic reticulum-to-Golgi trafficking with a furin-processing step to enable regulated secretion.

Optogenetic modulation is an engineering method used in the cited study to control locus coeruleus neurons with light in order to tune arousal. The available evidence establishes the application context but does not specify the opsin, construct design, or stimulation regime.

Optogenetic protein clustering is a light-controlled engineering method reported in mammalian cells to induce protein clustering and activate signaling. The available evidence identifies it as an optogenetic approach for regulating signaling with light input.

Optogenetic stimulation is a light-based engineering method used to activate defined neuronal populations. In the cited 2012 Nature study, optogenetic stimulation of a hippocampal engram was sufficient to activate fear memory recall.

This optogenetic method regulates endogenous nuclear formin mDia by photoreactive release of formin autoinhibition. In the cited Science study, mDia activation induced rapid and reversible nuclear actin network assembly, followed by MAL nuclear accumulation and SRF activity.

Optogenetic transcriptional control is a light-responsive gene regulation approach used in an integrative cell-ablation strategy in zebrafish embryos. The available evidence indicates that it enabled targeted cell elimination with spatial and temporal precision.

We used a mouse model of temporal lobe epilepsy, on-line seizure detection, and responsive optogenetic intervention to investigate the potential for cerebellar control of spontaneous temporal lobe seizures.

Reversible optogenetic unmasking-masking of carboxy-terminal residues is an engineering method used to probe how exposed versus occluded C-terminal sequence features affect prenylation and membrane interactions of prenylated proteins. In the cited work, it was applied to G protein gamma (Gγ) C-terminal residues to enable light-controlled interrogation of their functional contribution.

Venus iLID is an optogenetic improved Light Inducer Dimer system used to impose light-controlled protein proximity. In the cited application, a Venus iLID-based strategy was developed to bring αvβ3 integrin and ALK3 into proximity, and this was sufficient to induce cell spreading on a soft substrate.

Here, we present an optogenetics-integrated gut organ culture system that enables real-time, whole-tissue stimulation of defined ENS lineages, and detailed analysis of their functional impact.

The light directed protein kinase A optogenetic switch analog is a multi-component light-controlled system reported in cardiac cells for directing PKA activity and retention to specific intracellular subdomains. It was used with optogenetic cAMP signaling to interrogate localized signaling behavior in myocytes.

The merging of optogenetics and optical mapping techniques for 'all-optical' electrophysiology marks a significant step forward. This combination allows for the contactless actuation and sensing of cardiac electrophysiology, offering unprecedented spatial-temporal resolution and control.

Light-activated ion channels are optogenetic protein tools used in neuroscience to control action potential generation with light. The supplied evidence places them within a broader class of optogenetic actuators but does not specify a particular channel family or construct.

We particularly focus on light-based defibrillation strategies that represent one of the latest achievements in this field.

Light-regulated phosphodiesterases are optogenetic protein tools that use light input to directly control phosphodiesterase activity and thereby manipulate cAMP hydrolysis. They are described as part of the toolkit for spatiotemporally precise interrogation of cAMP signaling in subcellular domains.

Optogenetic regulation is a light-input engineering method used to manipulate cellular signaling with spatiotemporal precision. In the cited review, it is specifically described as providing insights into the spatiotemporal control of RAS/MAPK and phosphoinositide-3 kinase (PI3K) pathways.

Organelle-targeting strategies are optogenetic engineering approaches that use light to direct proteins to specific subcellular compartments and regulate subcellular organization. Reported applications include manipulation of nuclear translocation, plasma membrane morphology, and control over assembly of synthetic organelles.

Synthetic organelles are engineered multienzyme assemblies formed inside microbial cells that behave as independent subcellular entities. Reported examples can be optogenetically controlled during assembly and, in some cases, isolated from cells to catalyze biosynthetic reactions ex vivo.