Toolkit Items

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.

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.

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

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.

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.

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.

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

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.

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.

This study aimed to use dynamic light scattering (DLS) for monitoring EV71 particle size... The DLS technique was validated.

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.

Light-induced Fourier transform infrared (FTIR) difference spectroscopy is an assay method for detecting light-triggered structural changes associated with signaling-state formation in photoreceptor proteins. In the cited literature, it was applied to blue-light sensing LOV and BLUF/FAD systems to measure protein- and chromophore-associated spectral changes after illumination.

Light-sheet microscopy, also termed single plane illumination microscopy, is an in vivo fluorescence imaging method tailored to larval research and embryonic imaging. The supplied evidence indicates that it can capture the full course of embryonic development from egg to larva and has been coupled with optogenetic perturbation to study Wnt signaling during embryogenesis.

Microarray gene expression profiling is a transcriptome-scale assay method used in Arabidopsis seedlings to measure genome-wide expression changes under genetic and light-regulated perturbations. In the cited studies, it was applied to define how COP/DET/FUS loci and COP1 regulate light-responsive gene expression and seedling development.

AF4-MALS was shown to be a suitable surrogate for nanoparticle tracking analysis, as the 90° light scattering peak area exhibited a strong linear correlation with total particle concentration.

OptoAssay is a light-controlled dynamic bioassay that integrates optogenetic switches to regulate assay behavior. It was introduced as the first light-controlled assay for wash- and pump-free point-of-care diagnostics and enables wavelength-dependent, reversible control of assay components.

Phage display is an assay and selection method used during engineering workflows for light-responsive protein tools. In the cited context, it is applied alongside computational protein design and high-throughput binding assays in development of LOV2-based optogenetic systems such as improved light-induced dimers.

Recent technological innovations, including ... super-resolution and photoacoustic imaging ... have created new opportunities for investigating the cellular and molecular basis of VDs.

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).

This review highlights the latest cutting-edge technologies driving progress in the field, including ... single-cell sequencing...

fenestrations were only discernible with EM, but now they can be visualized ... in fixed cells using single molecule localization microscopy (SMLM) techniques such as direct stochastic optical reconstruction microscopy

Time-resolved EPR is an assay method used to investigate light-triggered functional dynamics in the AsLOV2 photosensory domain at high magnetic fields. The supplied evidence supports its use as a light-responsive biophysical readout for AsLOV2.

Time-resolved infrared spectroscopy, also termed transient infrared spectroscopy, is a light-triggered functional assay that monitors vibrational and structural dynamics of LOV photoreceptors on picosecond-to-microsecond timescales. In the cited studies, it resolved FMN triplet-state progression to cysteinyl-FMN adduct formation and subsequent protein conformational changes, including Jα helix unfolding.

Time-resolved serial oscillation crystallography is a synchrotron-based, room-temperature X-ray diffraction method that collects, processes, and merges monochromatic oscillation data from fewer than 100 crystals. It was used to follow light-driven structural changes in a blue-light photoreceptor domain with 63 ms time resolution and to visualize time-dependent rearrangements of both the protein and its chromophore.