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.

LiCre is a single-chain light-inducible Cre recombinase optogenetic switch. The supplied evidence supports that blue light can activate Cre-dependent recombination outputs, including induction of antibiotic resistance gene expression in Escherichia coli.

FUN-LOV is a fungal light-oxygen-voltage optogenetic switch for yeast built from Neurospora crassa photoreceptors WC-1 and VVD. It uses the photon-regulated interaction of these components to drive light-dependent target gene activation, including GPD1 and ADH1 expression in a wine yeast strain.

Focused ultrasound (FUS) is a noninvasive physical delivery and control modality that penetrates deep biological tissues and induces confined mild hyperthermia to activate heat-sensitive genetic modules. In the cited 2023 study, FUS was coupled to heat-sensitive CRISPR, CRISPRa, and CRISPRi systems to enable remote spatiotemporal regulation of genome and epigenome function in live cells and animals.

Single-cell RNA sequencing (scRNA-seq) is a transcriptomic assay method that measures RNA molecules in individual cells by sequencing-based transcript detection. In the cited application, it detected FLiCRE transcripts within the endogenous transcriptome, enabling simultaneous readout of cell type and calcium activation history.

Adeno-associated virus (AAV) is a viral delivery harness used to package and express CRISPR genome-editing components in vivo. In the cited literature, AAV supports single-vector delivery when smaller Cas9 orthologues and their chimeric guide RNAs fit within AAV packaging constraints, enabling robust in vivo genome editing.

Chimeric antigen receptor natural killer (CAR-NK) cells represent a promising "off-the-shelf" alternative to CAR-T cells.

As a tool component, CIB1 is most directly supported as the cryptochrome-interacting bHLH partner used with CRY2 to create blue-light-controlled protein association systems. In these systems, CIB1 is typically fused to localization, transcriptional, or enzymatic modules so that blue light drives CRY2–CIB1 binding and light withdrawal reverses the interaction.

Next-generation CAR designs, such as cytokine-armed CAR-T cells, may enhance T cell infiltration and persistence despite the suppressive TME.

Subsequently, we delve into cutting-edge applications of nanoparticles to enhance immune protection, including mosaic and cocktail nanoparticle vaccines, surface-modified targeting strategies, and the integration of mRNA technology with virus-like particles (VLPs).

AsLOV2 is the light-oxygen-voltage 2 photosensory domain from Avena sativa phototropin 1 used as a blue-light-responsive actuator in engineered fusion proteins. Blue-light activation drives allosteric conformational extension involving sequential unfolding of the N-terminal A'α helix and the C-terminal Jα helix, enabling conformational uncaging and related optogenetic control.

This review examines recent advancements in nanoparticle( s) (NPs) delivery systems, with a focus on ... lipid nanoparticles (LNPs)... We discussed various NP platforms and their applications, such as ... dry powder formulations of mRNA-loaded LNPs for pulmonary delivery, and LNP-mediated siRNA delivery for respiratory infections.

qRT-PCR is a quantitative reverse-transcription PCR assay used to measure transcript abundance, here applied to GFP mRNA during light-controlled gene expression in Synechococcus sp. PCC 7002. In the cited study, it quantified transcriptional activation and deactivation kinetics of optogenetic systems under green/red and light/dark illumination cycles.

RNA sequencing (RNA-seq) is a transcriptomic assay method that quantifies gene-expression changes by sequencing RNA-derived libraries. In the cited study, it was used on adult rat amygdala tissue to detect subtle expression changes associated with development, cellular function, and nervous system disease after gestational high-THC cannabis smoke exposure.

Cry2 is a blue-light photoreceptor cryptochrome from Arabidopsis used as a light-responsive multi-component optogenetic switch. The supplied evidence supports blue-light-dependent photoactivation linked to regulation of transcription factor control and to CRY2 degradation.

Deep brain stimulation (DBS) is an established neuromodulation method used as an add-on treatment for severe Parkinson's disease and other chronic neurological conditions. In the cited review, DBS is presented primarily as the clinical benchmark for comparison with optogenetic neuromodulation.

CLSM and super-resolution fluorescence imaging by direct stochastic optical reconstruction microscopy demonstrated homogeneous distribution of ceramide analogs in the bacterial membrane.

The LOV2 domain of Avena sativa phototropin 1 is a blue-light-responsive protein domain that uses an FMN-dependent photocycle to reversibly switch between dark and lit states through formation and decay of a flavin-cysteinyl adduct. It has been repurposed as a modular photoswitch to control nuclear import/export motif exposure and to generate light-dependent inhibitory peptides.

The CRISPR/Cas9 system is a multi-component genome engineering platform derived from a bacterial defense system that uses Cas9 and guide RNA to manipulate genomic loci in living cells. It has been widely adopted for mutagenesis and genome research, with reported applications spanning basic biology, biotechnology, agriculture, medicine, epigenetic perturbation, and disease models.

Here, the latest research progresses in AAV-mediated gene editing and silencing strategies to modify that the genetic ocular diseases are systematically outlined, especially by base editing and prime editing.

CRY2/CIB1 is a blue-light-inducible multi-component interaction switch composed of the photoreceptor CRY2 and its interacting partner CIB1. It is used for acute light-dependent protein recruitment, including plasma-membrane recruitment and clustering, to control protein localization and downstream signaling with high spatial and temporal resolution.

CARmacrophages (CAR-M) ... not only phagocytose tumor cells and present antigens but also remodel the immunosuppressive tumor microenvironment

Key innovations in engineered NK cell therapies-including CAR-NK, cytokine armoring (e.g., IL-15), and bispecific/trispecific NK cell engagers (NKCEs)-are critically evaluated.

Engineered cellular therapies include chimeric antigen receptor T (CAR-T) cells

DNA nanostructures, such as DNA origami, provide nanoscale spatial precision for regulating receptor valency and oligomerization.

UNC10245092 is a previously identified linear peptide inhibitor that binds calcium and integrin binding protein 1 (CIB1). It has been used as a reference peptide in structural and in silico studies of CIB1-targeting decoy peptide design.

SOUL is an engineered step-function opsin with ultra-high light sensitivity for optogenetic control of neuronal activity. It was reported to enable activation and modulation of neurons with external light delivery, including use in mice and macaque cortex.

Cryptochrome 1 (CRY1) is an Arabidopsis UV-A/blue-light photoreceptor protein implicated in regulation of chalcone synthase (CHS) gene expression. The supplied evidence supports a role for CRY1 in a distinct cry-mediated light signaling pathway that interacts with UV-B and phytochrome signaling networks.

synaptoPAC is a presynaptically targeted version of the photoactivated adenylyl cyclase bPAC developed as a light-responsive optogenetic tool for induction of presynaptic plasticity. It is reported to increase action potential-evoked transmission in some neuronal contexts, but this potentiation was not observed in non-granule hippocampal cultures or at Schaffer collateral synapses in CA1 acute slices.

CRISPR/Cas9 is a bacterial type II genome editing system repurposed as a programmable nuclease for target DNA cleavage and site-specific genome modification. The supplied evidence states that it was engineered for gene editing in mammalian cells by 2013 and is used to interrupt gene expression through cleavage of target DNA.

EL222 is a blue light-activated LOV-HTH transcription factor from the marine bacterium Erythrobacter litoralis HTCC2594 that functions as a light-dependent DNA-binding protein for optical control of transcription. Its flavin mononucleotide chromophore photodynamics have been characterized in free solution and when embedded in EL222 variants.

iLID/SspB is a blue-light-inducible heterodimerization system built from an engineered iLID module and the SspB binding partner. It is used to reversibly recruit proteins in cells for control of localization and signaling, including membrane recruitment, neurotrophin receptor construction, microtubule plus-end targeting, and perturbation of small GTPase pathways.

ReaChR is the light-sensitive opsin used in this study to evoke visual responses in the inner retina after photoreceptor degeneration. The paper compares its effects when expressed in ON bipolar cells versus retinal ganglion cells.

Immunohistochemistry is an antibody-based tissue staining assay used in the cited stroke study alongside transcriptomics and real-time polymerase chain reaction to examine post-stroke tissue in aged rats and post-stroke patients. In that context, it supported assessment of angiogenesis-related histological features such as vascular density after stroke.

SspB is the binding partner used in the iLID blue-light-inducible dimerization system. Upon blue-light activation of iLID, the exposed SsrA peptide binds SspB, enabling light-controlled recruitment and localization of SspB-fused cargo proteins.

Chimeric antigen receptor T (CAR-T) cell therapy is an innovative and promising approach to treat cancer.

CRY1 is a blue-light-sensing cryptochrome protein from the Arabidopsis cryptochrome family, and the name cry1 is also used for a Drosophila-like insect cryptochrome gene family. The supplied evidence indicates that CRY1 mediates blue light responses, contributes to regulation of early blue light-induced genes, and has functional overlap with CRY2.

Channelrhodopsin-2 (ChR2) is a light-activated ion channel used as an optogenetic switch to depolarize membranes and activate electrically excitable cells. The supplied evidence also indicates that light-activated ChR2 can modulate CaV1.3 calcium channel activity.

Prime editing is mentioned in the cited review as part of the broader set of genome-editing approaches considered in bacterial genome engineering. The supplied evidence does not describe its molecular architecture, target scope, or editing outcomes.

Three-dimensional (3D) bioprinting is a rapidly evolving technology that uses complementary biomaterials to emulate native extracellular matrices, enabling the generation of finely patterned, multicellular tissue architectures.

CAR-Tregs are presented as an emerging CAR-based cell therapy approach for autoimmune diseases. In the abstract's framing, CAR-based strategies can help restore immune homeostasis.

Key ACT modalities include chimeric antigen receptor (CAR) T cells, tumor-infiltrating lymphocytes (TILs), and T cell receptor (TCR)-engineered T cells.

Chimeric antigen receptor T-cell (CAR-T) therapy is a novel form of adoptive cellular immunotherapy that involves modifying autologous T cells to recognize and target tumor-associated antigens (TAAs) on malignant cells, independent of major histocompatibility complex (MHC) restriction.

Chromatin immunoprecipitation sequencing (ChIP-seq) is an assay method that combines chromatin immunoprecipitation with sequencing-based genomic localization to map protein-associated genomic regions. In the cited study, it was used to identify genome-wide ZFHX3-binding sites in suprachiasmatic nucleus chromatin, revealing occupancy concentrated near transcription start sites and co-localization with known histone modifications.

Various CRISPR delivery systems, including viral vectors, nanocarriers, and extracellular vesicles, play crucial roles in the effective access of this tool to neural cells.

Functional magnetic resonance imaging (fMRI), exploiting the blood oxygen level-dependent (BOLD) contrast, is the most widely used technique to study brain function. Combined with tools from biotechnology, molecular biology, and genetics, preclinical fMRI offers unparalleled opportunities to experimentally test causal hypotheses that are beyond the reach of human research.

Key methodological parameters such as adeno-associated virus (AAV) serotype, actuator drug, dose, and application routes were investigated by measuring the food-intake-reducing effect of chemogenetic inhibition of the lateral hypothalamus (LH) by hM4D(Gi) designer receptor stimulation.

Live-cell imaging is an assay method used in neurons in culture and brain slices to observe dynamic cellular processes in real time. The cited studies applied it to visualize minute-scale membrane PI(3,4,5)P3 fluctuations and microtubule retrograde flow during neuronal polarization-related dynamics.

We have developed a novel "real time" quantitative PCR method.

The three considered modalities were... central neuromodulation (... transcranial electrical stimulation ...)