Toolkit Items

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.

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.

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 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.

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.

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.

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.

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.

Transcription activator-like effector nucleases (TALENs) are programmable site-specific nucleases used for genome editing. The supplied evidence describes them as artificial systems with customizable DNA-binding motifs that can be designed to target specific genomic loci, bind practically anywhere in the genome, and cleave double-stranded DNA.

Zinc finger nucleases (ZFNs) are programmable site-specific nucleases that use customizable DNA-binding motifs to target specific genomic loci for genome manipulation. The supplied evidence also places ZFNs among molecular tools used to alter gene expression and documents their use for gene knockout in sea urchins.

Chemogenetics is an engineering method in which target proteins are genetically engineered to interact with a designed chemical partner with high selectivity. It is used as a chemical-input strategy to manipulate protein or receptor function in cells and has also been used alongside optogenetics to perturb cellular structures such as specific microtubule subtypes.

nano is the wild-type SspB protein used as the binding partner for iLID in a blue-light-responsive dimerization system. In the cited work, the iLID–nano pair is used to control protein interactions and localization with light.

PpSB1-LOV is a bacterial short LOV photosensory domain from Pseudomonas putida KT2440 with a light-induced flavin-cysteinyl photo-adduct and exceptionally slow dark recovery. It has been characterized as a compact LOV building block whose photocycle kinetics can be tuned by conserved hydrophobic-pocket mutation, including the I48T variant that accelerates adduct rupture while remaining structurally and mechanistically benign.

Optical imaging methods covered in this review include... Raman spectroscopy for early-stage cancer detection.

Stimulated depletion quenching (SDQ) is a nonlinear optical control method, described as similar to STED, for improving photoactivation selectivity in bidirectional photoswitches. It has been developed and implemented as a photoswitching strategy and applied to the Cph8 optogenetic switch to shift photoequilibrium beyond what is achievable with continuous-wave illumination.

Many draw inspiration from widely successful fluorescence-based techniques such as stimulated emission depletion (STED) microscopy, photoactivated localization microscopy (PALM), and stochastic optical reconstruction microscopy (STORM).

Despite the great success that chimeric antigen receptor (CAR) T-cells have had in patients with B-cell malignancies and multiple myeloma, they continue to have limited efficacy against most solid tumors.

All-atom replica exchange discrete molecular dynamics is a computational docking method used to generate structural models of calcium and integrin binding protein 1 (CIB1) bound to α-integrin cytoplasmic tails. In the cited CIB1 study, it predicted that multiple α-integrin tails engage the same hydrophobic binding pocket on CIB1.

The web research summary identifies CAR-T as explicitly supported by the anchor review figures/text and by multiple discovered reviews centered on synthetic-biology engineering of CAR-T cells.

FRASE-bot is an in silico fragment-based hit-finding method for drug discovery against unconventional therapeutic targets. It mines thousands of 3D protein-ligand complex structures to build a fragment-in-structural-environment database, matches target protein environments to that database, and uses machine learning to prioritize seeded fragments as candidate binders.

GUBS (Genomic Unified Behavior Specification) is a domain-specific, rule-based declarative language for behavioral specification of synthetic biological devices. It represents device programs as behavioral specifications for open systems rather than as complete closed-system descriptions.

Lipid-polymer hybrid nanoparticles (LPHNPs) are the next-generation nanocarriers that integrate the mechanical strength and sustained-release capacity of polymeric cores with the biocompatibility and high drug-loading efficiency of lipid shells.

Mathematical modeling is a computational method used to guide the rational design of synthetic gene circuits. The cited literature also places it alongside live-cell imaging and within quantitative model systems used to study microbial drug resistance and spatial-temporal features of cancer in mammalian cells.

Molecular dynamics simulation is a computational method for modeling atomistic conformational dynamics of proteins and analyzing residue fluctuations and vibrational behavior. In the cited studies, it was used as a noninvasive approach to validate dynamic behavior and to compare PAS-domain dynamics across functional groups.

Nanobody-based CAR-T cells further expand design versatility, offering improved stability, tumor penetration, and reduced immunogenicity compared with single-chain variable fragment constructs.

Emerging synthetic biology tools, such as CRISPR-based transcriptional control, high-throughput screening, and machine learning-assisted promoter design, are enabling the creation of tunable, orthogonal promoters suited for complex multigene expression.

EGxxFP is a Cas9 reporter construct used in split-Cas9 synthetic circuits to convert successful Cas9 reconstitution into a fluorescent readout. In the cited 2023 Scientific Reports study, it reported cellular states and events including cancer epithelial origin, epithelial-to-mesenchymal transition, and cell-cell fusion.

Melanopsin (Opn4) is a light-responsive opsin used as an optogenetic protein domain to activate Gq-linked signaling. Supplied evidence indicates that melanopsin can be functionally linked to an NFAT control circuit and that light-driven activation in cardiomyocytes modulates beating rate and local pacemaker activity.

Spatial transcriptomics is a transcriptomic assay method identified in the supplied review as a recent methodological advance. In that evidence, it is presented as part of a broader technology set that enables easier and more accurate visualization of cell behavior and qualitative and quantitative analysis of cell-cell interactions.

the molecular mechanism of bacteriorhodopsin, a light-driven H+ pump and the best studied microbial rhodopsin, is described.

This tool comprises designer mammalian cells engineered to express human placental secreted alkaline phosphatase (SEAP) under control of a benzoate-/vanillate-responsive mammalian gene switch. It functions as a small-molecule-regulated reporter system for monitoring inducible and repressible transgene expression in vitro and in implanted mice.

Smart RNA guides (SmartGuides) are engineered CRISPR-Cas9 guide RNAs that become active only in the presence of a specific RNA opener. They provide conditional RNA-responsive control of guide function and were reported in miRNA-responsive formats and Boolean logic circuit compositions.

These tools include quantitative behavioral assays, calcium imaging, optogenetics and transgenics.

Computational modeling was used to analyze how promoters decode light-driven transcription factor nuclear translocation dynamics. In the cited work, the modeling identified promoter kinetic regimes that enable efficient expression under short light pulses and proposed a multi-stage, thresholded activation scheme to explain opposite promoter-response phenotypes.

Electrophysiology is used as a functional assay in a multimodal study of gasdermin D pore behavior, alongside optogenetic tools and live-cell fluorescence biosensing. In the cited work, it supports measurement of pore conductance dynamics and the conclusion that gasdermin pores show phosphoinositide-dependent, repeated fast opening-closing behavior.

We focus primarily on three techniques, optogenetic manipulation, fiber photometry and microendoscopic imaging

Iris is an intuitive web tool for programming light signals in optogenetics and photobiology experiments. In the supplied evidence, it is linked to programming illumination for BphP1-QPAS1-based systems, including the iRIS platform for light-controlled protein localization.

increasing clinical experience with in-vivo editing - particularly using lipid nanoparticle (LNP) and adeno-associated virus (AAV)-based platforms - that has also revealed important safety considerations

Molecular dynamics simulations were used as a computational design method to guide construction of the PiL[D24] photoswitchable mPKM2-LOV2 fusion reported in the 2017 FEBS Journal study. In that context, the simulations supported engineering of a light-responsive pyruvate kinase chimera that preserved LOV2 photoreactivity and showed illumination-dependent changes in enzyme activity.

The one-dimensional active gel model is a theoretical computational framework for contractile cell migration that incorporates the tendency of myosin II to assemble into minifilaments. It predicts bistability between sessile and motile cell states and models how optogenetic activation or inhibition of contractility can switch between these states.

OptoSTIM1 is an optogenetic protein tool engineered by combining the STIM1 SOAR region with a plant photoreceptor LOV2 domain. It manipulates intracellular Ca2+ levels by light-dependent activation of endogenous Ca2+-selective CRAC channels.