Toolkit Items

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 ...)

Non-invasive brain stimulation (NIBS) techniques, such as ... transcranial ultrasound stimulation (TUS), have emerged as promising alternatives.

Multi-locus sequencing, multiplex PCR, and next-generation sequencing refined the identification of fungal and bacterial pathogens.

Subset-specific ICOS expression was evaluated using multiplex pseudocolored immunohistochemistry in 10 representative cases selected from the ICOS+ TIL-high group and validated using a publicly available single-cell RNA-seq dataset.

Subset-specific ICOS expression was evaluated using multiplex pseudocolored immunohistochemistry in 10 representative cases selected from the ICOS+ TIL-high group and validated using a publicly available single-cell RNA-seq dataset.

Contrast-enhanced ultrasound (CEUS), utilizing microbubbles (MBs) and nanobubbles (NBs) to target vascular biomarkers, significantly enhances tumor visualization and demonstrates high sensitivity in molecular imaging.

functional near-infrared spectroscopy was used to detect functional connections between regions of interest and the whole brain in individuals with ASD

Lattice lightsheet microscopy (LLSM) is a modified light-sheet imaging platform used for three-dimensional optogenetic activation with subcellular resolution. In the cited 2022 study, it enabled high-spatiotemporal-resolution manipulation of cellular behavior, including membrane ruffling and guided cell migration.

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

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).

The supplied source summary states that the review explicitly covers SIM and includes linear and nonlinear SIM.

functional magnetic resonance imaging (MRI) methods such as diffusion-weighted imaging

Using electrochemical impedance spectroscopy, the device exhibits a linear response over the range of 62.5-1000 nM tetracycline.

These neuromodulations include electroconvulsive therapy (ECT)...

Electromyography (EMG) recordings are utilized to analyze the effects of temporal interference (TI) ultrasound and single-frequency ultrasound stimulation on contralateral limb movements in mice.

we multiplexed fast-scan cyclic voltammetry (FSCV) and genetically encoded fluorescence sensors to simultaneously measure adenosine, dopamine, and glutamate

Lipid uptake and localization was studied by flow cytometry and confocal laser scanning microscopy (CLSM) and revealed a rapid uptake by bacteria within 5 min.

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.

Isothermal titration calorimetry (ITC) is a thermal biophysical assay that quantifies binding-associated heat changes under isothermal conditions. In the cited study, ITC was used to support thermodynamic analysis of binding between CIB1 and α-integrin cytoplasmic tails.

The anchor paper explicitly reports super-resolution imaging under a PALM setup.

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.

Systematic in situ hybridization mapped specific clusters to the principal DR, caudal DR, or MR.

α-integrin cytoplasmic tails are short intracellular integrin tail domains that bind calcium and integrin binding protein 1 (CIB1). Evidence indicates that multiple α-integrin cytoplasmic tails engage a shared hydrophobic pocket on CIB1 through a consensus binding site and can compete for CIB1 binding in vitro.

TiGGER is a 240 GHz time-resolved Gd-Gd electron paramagnetic resonance assay for tracking inter-residue distances during a protein mechanical cycle in the solution state. It was demonstrated on the light-responsive AsLOV2 domain to resolve time-dependent structural separation and relaxation after photoactivation.

We produced and verified a novel virus-like particle (VLP) by incorporating the neutralizing epitope 1134SVQSFDGKL1142 into a recombinant hepatitis B virus core antigen (HBcAg) scaffold.

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.

Anchor paper verified: the 2021 Nature Communications article reports mid-infrared modulation (MIM) as an opsin-free, noninvasive/thinned-skull-capable optical neuromodulation method that elevated cortical firing, activated a subset of cortical neurons, and accelerated auditory associative learning in mice.

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