Functional Assay

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.

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.

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

This method primarily utilizes genetically encoded calcium indicators (GECIs) or synthetic fluorescent dyes to detect physiologically relevant calcium dynamics.

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.

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.

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).

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

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

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.

Light-controlled crRNA is a chemically modified CRISPR guide RNA in which vitamin E is attached to the 5' terminus through a photolabile linker, creating a caged crRNA that inactivates CRISPR/Cas9 until light exposure. Upon irradiation, this design restores CRISPR/Cas9 activity and supports genome editing of VEGFA and knockdown of EGFP expression in human cells.

Optogenetic or chemogenetic manipulation of NTLS neurons and their downstream connections modulates social interaction and social reward.

Here we develop a proteomic kinase activity sensor technique (ProKAS) for the analysis of kinase signaling using mass spectrometry.

The photoactivatable CRISPR/Cas12a system is a light-gated nucleic acid sensing platform that integrates photoactivation with CRISPR/Cas12a for DNA and RNA detection. It has been used in visual assay formats, including HPV16 detection and biomarker imaging, to provide spatiotemporal control over Cas12a-based sensing.

The study aimed to evaluate the accuracy of... apparent diffusion coefficient (ADC) maps... Diffusion restriction was observed on DWI and ADC map sequences in 43 (86%) of the cases.

This study reports the construction and validation of a CAFLUX (Chemically Activated Fluorescent Expression) HepG2 reporter cell line engineered to express a histone H2B-green fluorescent protein (H2B-GFP) fusion protein under the control of a dioxin-responsive cytochrome P450 1A1 (CYP1A1) promoter.

Of particular interest is offline 5 Hz repetitive TUS (5 Hz-rTUS), originally reported by Zeng et al. (2022) to elicit lasting corticospinal excitability increases, with large effect sizes.

ProKAS is based on a tandem array of peptide sensors with amino acid barcodes that allow multiplexed analysis for spatial, kinetic, and screening applications. We engineered a ProKAS module to simultaneously monitor the activities of the DNA damage response kinases ATR, ATM, and CHK1 in response to genotoxic drugs.

The study aimed to evaluate the accuracy of... T1-weighted imaging (T1WI). On T1WI, cancerous lesions were isointense in 47 (94%) cases and moderately hyperintense in three (6%) cases, particularly in lesions larger than 8 mm in diameter.

The study aimed to evaluate the accuracy of T2-weighted imaging (T2WI)... On T2WI, the lesions appeared hypointense in 46 (92%) of the 50 cases. The findings of this study confirm the high accuracy of T2WI in diagnosing malignant prostate lesions.

We conducted comprehensive longitudinal assessments using ... electroencephalogram (EEG) to analyze neurophysiological dynamics.

Fast volumetric ultrasound facilitates high-resolution 3D mapping of tissue compartments.

Blood samples were collected on day 21 to measure hemagglutination inhibition (HI) and virus-neutralizing (VN) antibody responses.

Blood samples were collected on day 21 to measure hemagglutination inhibition (HI) and virus-neutralizing (VN) antibody responses.

and (14)C content in human cadaver brains

Jin et al. report a framework to obtain the intrinsic dipole moment and radiative lifetime of excitions in monolayer WSe2 from absorption measurement.

and employs acoustic feedback via cavitation-induced subharmonics to guide real-time energy delivery

Among different sensory modalities, acoustic stimulation is the most effective in increasing the magnitude of slow waves.

By using brain-wide analysis of activity-dependent labeling, we next pin-pointed the medial preoptic area as a brain region strongly activated during the post-ejaculatory period.

The allelic series of Cry mutants is a panel of 22 cryptochrome variants, each carrying a single amino acid substitution identified by random mutagenesis and a cell-based screen. The series was used to generate diverse deficiencies across CRY functions and to identify residues involved in protein-protein interaction and CRY2-specific repression.

Genetically encoded indicators and antineoepitope antibodies should improve spatial and temporal resolution of the in vivo activity of proteases that locally erode PNN.

The web research summary states that the source paper explicitly names ASTM D695-15 as the compression standard.

The review title directly names atomic force microscopy, and the supplied summary states that the review emphasizes AFM modalities for mapping dynamic mechanical properties of biological samples.

Through the use of atomic force microscopy (AFM) we were able to show that AAV binds to alginate and we quantified the force and frequency of the interaction.

we report a broadly compatible barcoded Cre recombinase mRNA barcode platform that enables multiplexed LNP tracking in vivo in tdTomato reporter mice

BH3 profiling (a functional assay measuring proximity to the mitochondrial apoptotic threshold and identifying BCL-2 family dependencies)

Optical imaging methods covered in this review include... bioluminescence imaging...

This tool is a bioreactor-based assay platform coupled to automated cytometry measurements for monitoring intracellular protein levels and secretory stress during production of hard-to-secrete proteins. It was reported as a real-time measurement platform to identify an optimal secretory-stress regime during protein production.

Biosensors have shown potential for success in diagnostic testing due to their ease of use, inexpensive materials, rapid results, and portable nature. Biosensors can be combined with nanomaterials to produce sensitive and easily interpretable results.

Both multiparametric MRI and biparametric MRI (bpMRI) are currently in use. This study aims to evaluate the role and accuracy of bpMRI in patients with prostate cancer.

Bisulfite pyrosequencing is an assay method used to quantify promoter CpG DNA methylation after bisulfite treatment. In the cited study, it was used to measure methylation in the CAMK1D, CRY2, and CALM2 promoter regions in peripheral blood from patients with type 2 diabetes and matched healthy controls.

functional magnetic resonance imaging (MRI) methods such as diffusion-weighted imaging, blood oxygen level-dependent MRI

utilizes acoustic feedback from cavitation-induced subharmonics to guide real-time energy delivery

Based on these findings, CBN was selected for formulation into soy lecithin liposomes. The resulting CBN-loaded liposomes displayed favorable colloidal properties, with an average size of approximately 122.9 ± 0.4 nm.

Here, we developed a genetically encoded biosensor, cdiGEBS, based on the transcriptional activity of the c-di-GMP-responsive transcription factor MrkH.

Cell-free chromatin immunoprecipitation (cfChIP) is an assay method that immunoprecipitates histone mark-associated cell-free chromatin from blood plasma. In the cited study, cfChIP targeting H3K36me3-associated cfDNA was used with droplet digital PCR to infer transcriptional activity of specific genes, including EGFR, in the cells that released the cfDNA.

The development of the cell-free system (CFS) is transforming the manufacturing landscape of biomolecules with therapeutic value by providing a flexible and convenient alternative to cell-based expression systems.

This chapter explores the principles, platforms, and applications of CFS-based HTS... Altogether, CFS-based HTS offers a flexible, rapid, and accessible approach for next-generation biomolecular screening and therapeutic development.

cfDNA fragmentomics evaluation is an assay method that analyzes plasma cell-free DNA fragment length distributions and fragment end motifs to identify signatures associated with active gene expression. In a 2024 study, integrating short-fragment frequency with end-motif information improved enrichment for highly expressed genes in plasma samples from lung cancer patients and healthy individuals.

The supplied review summary explicitly mentions CLARITY for correspondence between CBV-weighted signal spread and microvascular architecture.

the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS)

Here, we introduce an approach for visualizing individual microrobots in real time with color flow mapping ultrasound imaging based on acoustically induced structural oscillations of the microrobot generating a pseudo-Doppler signal.

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.

The CRY2-lacZ gene fusion is a Saccharomyces cerevisiae reporter construct used to measure how CRY2 sequence features regulate reporter expression. It was applied to identify cis-acting elements involved in repression of CRY2, linking CRY2-derived nucleotide information to lacZ output.

Cryogenic-temperature ENDOR spectroscopy is a spectroscopic assay method applied to LOV domains to interrogate the local environment of the flavin mononucleotide (FMN) cofactor. It does so by measuring temperature-dependent hyperfine couplings associated with hindered rotation of the methyl group attached at C(8) of the FMN isoalloxazine ring.

dcFCCS is a dual-color fluorescence cross-correlation spectroscopy assay method used to quantify interactions relevant to cGAS phase separation. In the cited study, it was applied to systematically examine binding among cGAS, double-stranded DNA, and accessory proteins in relation to condensate formation and enzymatic activity.

Differential Pulse Voltammetry (DPV) measurements showed satisfactory stability over 12 days

Measurements of domain mobility indicated the presence of 120 nm wide ordered and 40 nm wide disordered domains.

We report a novel dual-receptor lateral flow biosensor (LFB) for the rapid, sensitive, and visual detection of MCF-7 breast cancer cells as a model for circulating tumor cells (CTCs).

The studies reported here suggest that the Edelhoch method is the best method for measuring epsilon for a protein.

The source lead states that the paper used EEG/SEP readouts.

The elevated plus maze is a widely used behavioral assay for rodents...

EndoV-seq is an assay method reported for genome-wide profiling of adenine base editor specificity. The available evidence supports its use as a functional assay to identify where adenine base editing occurs across the genome.

This Perspective synthesizes recent evidence (2020-2025) on three modalities that together form a regenerative triad: extracorporeal shockwave therapy (ESWT), high-intensity laser therapy (HILT), and ultrasound-guided mechanical needling with sterile water injection (SWI). ESWT promotes mechanotransduction, angiogenesis, and ECM remodeling.

Field-domain rapid-scan EPR at 240 GHz is a high-frequency electron paramagnetic resonance assay method reported for studying protein functional dynamics at room temperature. The available evidence identifies it specifically as a field-domain rapid-scan EPR approach operating at 240 GHz.

Especially the image processing package Fiji is a valuable and powerful extension of ImageJ.

Fluorescence line narrowing (FLN) is a spectroscopic assay method used in the cited study to interrogate the electronic structure of flavin mononucleotide (FMN) within phototropin LOV2 domains. In this context, FLN was applied to support mechanistic analysis of how the conserved cysteine near FMN perturbs the chromophore ground state and promotes photochemistry.

Fluorescence microscopy is an imaging assay method used to detect and localize fluorescent signals in living biological specimens. In the supplied evidence, it is described for larval zebrafish as a means to achieve subcellular fluorescence localization and real-time monitoring of cell identity, fate, physiology, and organ pathophysiology.

Fluorescence resonance energy transfer-fluorescence lifetime imaging microscopy (FRET-FLIM) is an assay method that combines fluorescence resonance energy transfer with fluorescence lifetime imaging to detect molecular proximity in living cells. In the cited Arabidopsis study, it was used to support a physical interaction between CRY2 and SPA1 in nuclei.

Focused transcranial ultrasound stimulation (fTUS) has emerged as a novel noninvasive technique with promising therapeutic potential for various neurological and psychiatric conditions.

technologies based on molecular forces, such as atomic force microscopy (AFM) and force spectroscopy, have been recently refined to enable sensitive characterization of biomolecular interactions, folding- and unfolding pathways, and single molecule imaging

Vibrational spectroscopies, such as Fourier transform infrared (FTIR) and Raman, are powerful tools that are sensitive to the secondary structure of proteins and have been widely used to investigate protein misfolding and aggregation.

FRASE, also described as FRASE-bot, is a computational fragment-based ligand discovery method that mines 3D ligand–protein complex structures to build a database of fragments in structural environments. It screens this database against a target protein, seeds the target structure with relevant ligand fragments, and uses a neural network to prioritize fragments with the highest likelihood of being native binders.

Furthermore, using freely moving in vivo calcium imaging to compare the neural activity of inhibitory and excitatory neurons in the medial preoptic area, we revealed that a subset of the neurons in this region responds significantly and specifically to male ejaculation but not to female-to-male sniffing or to male mounting.

The FRET-based RhoA biosensor is an assay method developed to visualize RhoA activity during optical control experiments using photoswitchable RhoGEF (psRhoGEF). The available evidence supports its use for monitoring RhoA signaling in the context of endogenous RhoA manipulation.

Full-length transcriptome analysis is an assay method used to examine transcriptomic features associated with shade-induced promotion of tuber production in Pinellia ternata. The available evidence supports its application in this specific plant developmental context, but does not provide methodological detail beyond the study focus.

EPR imaging further demonstrated superior diffusion of liposomal CBN through a gelatin-based semi-solid model compared to the control solution. While the current model does not replicate skin architecture, it provides a cost-effective and reproducible platform for early-stage screening of formulation mobility.

Genetically encoded indicators and antineoepitope antibodies should improve spatial and temporal resolution of the in vivo activity of proteases that locally erode PNN.

In this study, we screened a panel of 11 CjCas9 orthologous using a GFP activation assay and identified seven active nucleases.

Glass nanopipette-based single-cell extraction is an ex situ single-cell sampling method that removes material from individual cells for downstream analysis. In the cited Chemical Science study, it was coupled to SiNx solid-state nanopores to identify LOV2 and monitor its conformational changes from single-cell extracts.

GntR is a gluconate-responsive transcriptional repressor from Escherichia coli that has been repurposed as a protein domain for synthetic gene-control switches. Reported designs use GntR to construct gluconate-regulated transcriptional systems in mammalian cells, including rewired OFF/ON transcriptional architectures and a split transcriptional activator.

The groovDB database (https://groov.bio) was launched in 2022 with the goal of organizing information on prokaryotic ligand-inducible transcription factors (TFs). Uniquely, groovDB contains stringently curated, literature-referenced data on both TF:DNA and TF:ligand interactions.

H3K36me3 cell-free chromatin immunoprecipitation sequencing (cfChIP-seq) is a plasma-based assay that establishes a personal gene expression profile from cell-free chromatin. In the cited study context, it functions as a reference enrichment assay for active genes in liquid biopsy samples.

H3K36me3 cfChIP followed by droplet digital PCR is a cell-free chromatin immunoprecipitation assay that enriches plasma cfDNA associated with the transcription-linked histone mark H3K36me3 and then quantifies specific alleles by ddPCR. In a 2021 NSCLC study, it detected greater enrichment of EGFR-L858R fragments than EGFR wild-type fragments, providing proof of principle for identifying tumor-specific transcriptional activity of mutated alleles.

we developed a simple, rapid, and efficient system based on hairy root transformation to evaluate somatic genome editing efficiency in plants

Our findings reveal that harmonic cross-propagating wave AM (HxAM) imaging markedly surpasses traditional xAM in isolating GVs' nonlinear acoustic signature.

High-throughput screening is an assay method cited in microbial biotechnology literature as part of the CRISPR/Cas toolbox for evaluating variants generated by multiplexed engineering. In the supplied evidence, it is presented as a screening approach associated with CRISPR/Cas-based metabolic engineering and with development of new dynamic systems.

A detailed functional characterization of electrogenic cells, such as neurons and cardiomyocytes, by means of high-density microelectrode arrays (HD-MEAs) has emerged as a powerful approach for inferring cellular phenotypes and elucidating fundamental mechanisms underlying cellular function.

This Perspective synthesizes recent evidence (2020-2025) on three modalities that together form a regenerative triad: extracorporeal shockwave therapy (ESWT), high-intensity laser therapy (HILT), and ultrasound-guided mechanical needling with sterile water injection (SWI). HILT enhances mitochondrial bioenergetics and downregulates inflammatory pathways.

Lipopeptides (surfactin and fengycin) were extracted and quantified at multiple time points (up to 48 h) via high-performance thin-layer chromatography (HPTLC).

adjusting the sample composition based on measurements of the extrusion stability taken with a high-speed camera setup

The high-throughput online monitoring system with an LED array is an assay platform for screening light-controlled gene expression conditions by individually illuminating each well in a multiwell format. In the cited yeast study, it was used with photocaged Cu2+ to regulate the Cu2+-inducible pCUP1 promoter from Saccharomyces cerevisiae and monitor eYFP expression.

We outline how synthetic promoters are designed and validated via high-throughput reporter assays.

Higher-energy collisional dissociation (HCD) is a top-down mass spectrometry fragmentation method referenced in a study characterizing covalent insulin dimers. The supplied evidence identifies HCD by name, but does not describe its specific analytical role, performance, or outcomes in that study.

ImageJ is a versatile and powerful tool for quantitative image analysis in microscopy.

Using in vivo bimolecular fluorescence complementation, we find that Wbm0152 interacts with the Vps2p subunit of the ESCRT-III subcomplex as well as the Vps2p ortholog (BmVps2, Bm6583b) from a Wolbachia host nematode, Brugia malayi.

In vivo PET with [(11)C]-PE2I is a radiotracer imaging assay used to assess dopamine degeneration in MPTP-treated non-human primates. In the cited study, it was applied alongside post-mortem tyrosine hydroxylase and dopamine transporter quantification.

The in-gel assay is a functional assay method used to detect protein kinase activity within a gel matrix. In the cited Arabidopsis study, it was used to show that OST1 is an abscisic acid (ABA)-activated protein kinase involved in stomatal signaling.

In this work, we present "inkube", an incubation system that has been combined with an electrophysiology setup and a fully automatic perfusion system.

The web research summary states that the anchor full text explicitly names inkulevel as the culture-medium volume sensing subsystem based on a laser and camera sensor, relevant to automated osmolarity and medium-level control.

This chapter offers a detailed examination of the design, functionalities, and constraints of automated cell-free systems, emphasizing technologies such as microfluidic devices, liquid handling robots, and integrated analytical platforms.

We describe an extension of our programs MntJULiP and Jutils for differential splicing detection and visualization from RNA-seq data that accounts for covariates. Jutils visualizes alternative variation with heatmaps, sashimi plots, Venn diagrams, and, reported here, PCA maps.

While histopathology and LANA staining remain diagnostic standards... Current diagnosis of KS still relies primarily on histopathology and LANA immunostaining, which remain the gold standard

LC-MS analysis of fittest binders is an assay method used with small combinatorial libraries of self-assembled proteomimetics (SAPs) to identify enriched target binders after affinity selection by liquid chromatography–mass spectrometry. In the cited SAP study, this workflow was applied in the context of target-directed selection from self-assembled PNA-peptide conjugate libraries.

the potential of lipid nanoparticle (LNP)-based messenger RNA (mRNA) vaccines to revolutionize HIV prevention

The localized GEF recruitment assay system is an optogenetic functional assay that uses blue light-inducible cryptochrome- and LOV-domain dimerization to recruit guanine nucleotide exchange factors with spatiotemporal precision. It is used to probe how local network activation drives changes in cell polarity and directed migration.

functional magnetic resonance imaging (MRI) methods such as diffusion-weighted imaging, blood oxygen level-dependent MRI, magnetic resonance elastography

This study aimed to correlate micro-CT and MRI images of the middle and caudal abdominal regions with corresponding anatomical sections in Syrian hamsters (SHs).

Mass spectrometric analysis revealed a substantial decrease in contaminants, with VLP-specific proteins comprising >90% of the final product.

Screening of antioxidant properties of compounds needs appropriate methods including metal chelating assay.

This study aimed to correlate micro-CT and MRI images of the middle and caudal abdominal regions with corresponding anatomical sections in Syrian hamsters (SHs).

Microelectrode arrays (MEAs) provide scalable access to population spiking activity, yet they lack the spatial resolution and molecular specificity to precisely dissect synaptic mechanisms.

Microfluidic single-cell analysis is an assay method used during microfluidic cultivation to quantify growth behavior and expression phenotypes at single-cell resolution. In the cited 2016 E. coli study, it was applied comparatively across PT7lac/LacI, PBAD/AraC, and Pm/XylS expression systems to reveal dynamic and spatiotemporal heterogeneity in recombinant protein production.

The review integrates data from in vitro, in silico, and clinical studies, including both classical detection strategies and emerging technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based modulation, biosensors, and microfluidics.

The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles ("MISEV") guidelines for the field in 2014. We now update these "MISEV2014" guidelines based on evolution of the collective knowledge in the last four years.

The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.

MR-guided focused ultrasound has emerged as an incisionless and minimally invasive neurofunctional treatment.

Using multi-tracer positron emission tomography imaging, we detected DREADD expression in vivo, which was confirmed in nigrostriatal dopamine neurons by immunohistochemistry, as well as by assessed activation of the SN following agonist administration.

Multicomponent, ligand-functionalized microarrays are a patterned substrate assay method for individual living cells that spatially segregates distinct ligand presentations to enable simultaneous monitoring of receptor activation and downstream signaling. The method was developed to probe clustering-dependent EphA2 signal transduction.

This study shows that multiplexing FSCV and fluorescence sensors (iGluSnFR3.v857) allows simultaneous monitoring of multiple neurotransmitters

The NanoLuc luciferase reporter assay is a bioluminescent functional reporter assay used to test guide RNA efficiency. In the cited study, it served as a pre-screening step to identify optimal guide RNAs before downstream cell-based experiments with an optogenetic CRISPR-dCas9 LITE system.

Optical imaging methods covered in this review include fluorescence imaging in the near-infrared (NIR) region...

Nonlinear sound-sheet microscopy: Imaging opaque organs at the capillary and cellular scale. ... we applied nondiffractive ultrasound beams in conjunction with a cross-amplitude modulation sequence and nonlinear acoustic reporters to enable fast and volumetric imaging of targeted biological functions.

Li et al. reviews various optical techniques employed to determine the thickness of 2DLMs.

Pseudovirus technology, which uses single-round infectious viral particles lacking replication competence, has thus gained prominence as a safe and versatile tool for antiviral research.

This directed protein evolution generates several gain-of-function OsTIR1 variants, including S210A, that significantly enhance the overall degron efficiency.

Additionally, acoustic emissions, recorded via passive cavitation detection, increased with both pressure and pulse number but decreased in droplets with higher bulk boiling points.

The plasmid toolkit for CeLINC is a construct set that extends the CeLINC optical binary protein-protein interaction assay in Caenorhabditis elegans by enabling custom promoter usage or substitution of CRY2 variants. It is intended to increase flexibility of a CRY2/CIB1-based in vivo colocalization assay for testing whether two proteins interact in vivo.

The PORC promoter is an Arabidopsis promoter element that functions as an in vivo binding target of the scarecrow-like transcription factor SCL27. Available evidence indicates that SCL27 binds GT cis-elements within this promoter and regulates PORC promoter activity, with DELLA proteins reducing SCL27 promoter binding.

Promoter fusion is a reporter construct pattern used in Saccharomyces cerevisiae to assay cis-regulatory activity associated with CRY2 repression. In the cited 1995 study, promoter fusions were analyzed alongside CRY2-lacZ gene fusions to identify cis-acting elements involved in regulation of CRY2 expression.

Proximity labeling is described here as a methodological approach proposed to define state-specific proteomic and post-translational signatures in studies evaluating the addivosome pathological condensate model. The supplied evidence does not identify a specific proximity-labeling enzyme, chemistry, or construct design.

Most of these drawbacks can be circumvented with the use of pseudotyped viruses, which are surrogate, non-pathogenic recombinant viral particles bearing the surface envelope protein of a virus of interest.

Lifetimes of PNN vs. intrasynaptic components would be compared with pulse-chase (15)N labeling in mice

we developed assays on three-dimensional (3D) graphene foam electrodes by functionalising them with a 1-Pyrenebutyric acid N-hydroxysuccinimide ester (Pyr-NHS) to enable effective antibody immobilisation for the detection of amyloid beta peptides (Aβ42 and Aβ40)

Quantitative chromatin immunoprecipitation (qChIP) is an assay method for measuring protein association with specific chromatin regions. In the cited Ustilago maydis study, qChIP analysis supported direct binding of the UPR regulator Cib1 to UPRE-containing promoter fragments of pit2 and tin1-1.

Finally, we explore emerging biotechnological strategies... such as... quantitative m6A profiling at single-base resolution.

Receptor-antibody sandwich assays are assay methods established for detection of Bacillus thuringiensis Cry1 and Cry2 toxins. The reported assays are described as broadly detecting toxins within the Cry1 and Cry2 groups.

Reverse cross-saturation NMR methodology is an NMR assay approach that maps the binding interface on a larger binding partner by applying selective radio-frequency irradiation to a smaller binding partner. In the cited study, irradiation of the αIIb peptide enabled detection of the interaction surface on Ca2+-bound CIB1.

Accurately quantifying total RNA concentration in complex formulations is challenging, often requiring expensive, low-throughput methods or fluorescence-based assays like RiboGreen that rely on effective NP disruption.

RNA interference (RNAi) was used in the Madeira cockroach to reduce expression of the circadian clock genes per, tim1, and cry2 by dsRNA injection. In this study, single injections produced persistent target mRNA knockdown within about two weeks and enabled analysis of resulting locomotor rhythm phenotypes.

Here, by using a self-paced mating assay, we first demonstrate that female mice show decreased sexual motivation acutely after experiencing male ejaculation.

The 3D intertwining of PNN and synapses would be imaged by serial-section EM.

imaging modalities including novel ultrasound techniques, shear wave elastography

To simplify measurements of fluorescence intensity in a complex tissue we developed software that allows simultaneous analyses of fluorescence intensities of several neighbouring cells.

Single cell FRET measurements with Rho GTPase biosensors are a quantitative cell-based assay used in primary human endothelial cells to monitor guanine nucleotide exchange factor activity toward Cdc42 and Rac1. In the cited study, the method was applied to compare the cellular activities of overexpressed endothelial GEFs.

Single pass tangential flow filtration (SPTFF) was implemented at bench scale ... At pilot scale, a multi-membrane staged SPTFF module was designed ...

In case the transfer process does not involve stable or transient paramagnetic species or states, site-directed spin labeling with suitable nitroxide radicals still allows EPR techniques to be used for studying structure and conformational dynamics of the proteins in action.

The solid-phase competitive binding assay is an in vitro binding assay used to test whether α-integrin cytoplasmic tails compete for association with CIB1. In the cited 2020 study, it supported the conclusion that multiple α-integrin tails can compete with the αIIb cytoplasmic tail for a shared CIB1-binding site.

We present a cheap, rapid, and versatile assay called SOSHI-seq (Screening of Self-transcribed Hormone Inducible response elements coupled to sequencing).

Split-protein complementation assays (PCAs), where a reporter protein is divided into two inactive fragments, have evolved from simple reporters of biological events into an increasingly important tool in modern virology.

The supplied source summary states that the review explicitly covers SMLM, including STORM/dSTORM.

Stroke transcriptomics is a gene-expression profiling assay applied to post-stroke tissue and combined with immunohistochemistry in aged rats and post-stroke patients. In the cited study, it was used to characterize post-stroke angiogenesis-associated transcriptional programs and relate them to vascular density differences across age groups.

SUMO urban mobility simulator assessment is a simulation-based functional assay used to evaluate a multi-intersection traffic management system. In the cited 2024 study, it assessed a visible light communication-enabled, learning-driven traffic signal control approach and reported reduced waiting time and travel time in multi-intersection scenarios.

The paper explicitly introduces super-linear excitation-emission (SEE) microscopy.

Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed.

Data obtained with SFAS were compared to fluorescent-based assays utilizing RiboGreen and SYTO 9 dyes, which bind to RNA in free or encapsulated forms, respectively.

The method measures PCR product accumulation through a dual-labeled fluorogenic probe (i.e., TaqMan Probe).

Thioflavine T (ThT) associates rapidly with aggregated fibrils ... giving rise to a new excitation maximum at 450 nm and enhanced emission at 482 nm ... This fluorometric technique should allow the kinetic elucidation of the amyloid fibril assembly process as well as the testing of agents that might modulate their assembly or disassembly.

Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed.

Touchscreen-equipped operant conditioning chambers are a behavioral assay platform for measuring visual pairwise discrimination and reversal learning. In the cited 2023 study, they were used to quantify cognitive performance in Sprague Dawley rat offspring after gestational exposure to high-THC cannabis smoke.

TR-FRET assay is a time-resolved fluorescence resonance energy transfer binding assay used in the cited study to confirm binding of a small-molecule ligand to CIB1. In this evidence set, it functions as a chemical-input assay for ligand-binding confirmation.

It is possible to enhance sleep slow waves in humans using transcranial direct-current stimulation.

It is possible to enhance sleep slow waves in humans using transcranial magnetic stimulation.

Transcription factor-based biosensors (TFBs) are powerful tools in microbial biosensor applications, enabling dynamic control of metabolic pathways, real-time monitoring of intracellular metabolites, and high-throughput screening (HTS) for strain engineering.

Further progress in transparent MEAs and hybrid optical-electrical systems has bridged the divide between electrophysiology and optical control, allowing simultaneous, bidirectional interaction with biological neural networks (BNNs) and real-time feedback modulation of activity patterns.

In combination with an original tri-scanning linear dichroism confocal microscope, FLIPs allow unparalleled imaging of activity of nonmodified, endogenously expressed G proteins.

To this end, we adapted a GFP-based calcium reporter to luciferase that was expressed in small subsets of circadian neurons. This Tric-LUC reporter allowed a direct comparison of luciferase activity with locomotor activity, which was assayed in the same flies with video recording.

Two-dimensional transient absorption (2D-TA) is a transient absorption spectroscopy assay used with a streak camera to search for short-lived photochemical intermediates in LOV domain photocycles. In the cited study, it was applied extensively and did not detect an intermediate with a rate constant between fluorescence decay and triplet-state decay.

We employed ultra-high-speed brightfield [10 million frames per second (Mfps)], fluorescence (2 Mfps), and confocal microscopy (1 fps) to capture ADV and real-time payload release in fibrin-based hydrogels.

We employed ultra-high-speed brightfield [10 million frames per second (Mfps)], fluorescence (2 Mfps), and confocal microscopy (1 fps) to capture ADV and real-time payload release in fibrin-based hydrogels.

An ultrafast wide-field macroscope was developed to optically map action potential propagation with a red-shifted voltage sensitive dye in whole mouse hearts.

The review also highlights the pros and cons of ultrasound imaging in early-stage cancer detection.

This Perspective synthesizes recent evidence (2020-2025) on three modalities that together form a regenerative triad: extracorporeal shockwave therapy (ESWT), high-intensity laser therapy (HILT), and ultrasound-guided mechanical needling with sterile water injection (SWI). SWI disrupts fibrosis and calcification while restoring neurovascular dynamics.

an untargeted metabolomics analysis via liquid chromatography-mass spectrometry (LC-MS)

The paper uses the upconversion-specific term uSEE microscopy when SEE microscopy is implemented with upconversion nanoparticles.

In this work, we developed a vertically deployed surface acoustic wave (VD-SAW) platform that generates 30 MHz focused ultrasound wave for mechanical stimulation of single cells.

Furthermore, a preliminary indirect ELISA method was established based on this VLP for AKAV detection... The developed VLP-based indirect ELISA method successfully identified AKAV antibody-positive serum, with a detection sensitivity of up to a 1:1600 serum dilution.

VNAR-based CAR-T cells targeting PD-L1 demonstrated strong anti-tumor effects in preclinical assays

Whole-brain axonal projection mapping revealed that DR serotonin neurons co-expressing vesicular glutamate transporter-3 preferentially innervate the cortex, whereas those co-expressing thyrotropin-releasing hormone innervate subcortical regions in particular the hypothalamus.

Here, we present an alternative tool for AC detection using a whole-cell bacterial biosensor, which utilises the YwbIR transcriptional regulator from Bacillus subtilis.

Determination of the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) demonstrated that short-chain ceramides and a ω-azido-functionalized C6-ceramide were active against Neisseria meningitidis and N. gonorrhoeae.

Sensitive detection of tobamoviruses in the field with minimal sample preparation can be achieved using latest technologies such as isothermal amplification, CRISPR/Cas-hybrid assays or next-generation sequencing.

Interactomic techniques such as yeast two-hybrid screening and affinity purification-mass spectrometry further map host-pathogen protein-protein interactions, highlighting key immune nodes such as receptor-like kinases, R proteins, and effector-targeted complexes.

We present translational routes, sentinel epimarkers (bisulfite amplicons, CUT&Tag)

Murray et al. broke the acoustic diffraction limit by implementing a blind speckle illumination and block-FISTA reconstruction algorithm and achieved a resolution close to the acoustic speckle size

Catharanthus roseus Extract-Loaded Zn-Substituted Hydroxyapatite Nanocomposites as a Multifunctional Antioxidant and Anticancer Therapeutic Applications

Condensate-specific lifetimes were used to track protein-protein interactions by measuring FLIM-Förster resonance energy transfer (FRET). We used condensate FLIM-FRET to evaluate whether mRNA decapping complex subunits can form decapping-competent interactions within P-bodies.

we applied nondiffractive ultrasound beams in conjunction with a cross-amplitude modulation sequence and nonlinear acoustic reporters

Our findings reveal that harmonic cross-propagating wave AM (HxAM) imaging markedly surpasses traditional xAM in isolating GVs' nonlinear acoustic signature.

We present translational routes, sentinel epimarkers (bisulfite amplicons, CUT&Tag)

Emerging CRISPR-based diagnostics (e.g., SHERLOCK and DETECTR)

We used DNA array technology to decipher the interplay between these responses in P. putida KT2440 subjected to a short challenge (15 min) with toluene.

By using viral-mediated gene transfer to overexpress a dominant-negative mutant of DVL in NAc... we show that blockade of DVL function renders mice more susceptible to social defeat stress

we emphasize a FRET-based immunological synapse biosensor as a powerful system that directly assesses CAR activation upon antigen binding. This platform offers significant advantages in speed and scalability for predicting CAR-T cell functionality.

This review covers latest approaches, such as genome editing with CRISPR, targeting susceptibility genes

Here we used differently colored dyes as reporters for the registration of both ordered and disordered lipids from the two leaves of a freestanding bilayer.

It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions.

MINFLUX nanometer-scale 3D imaging and microsecond-range tracking on a common fluorescence microscope

advanced tools such as next-generation sequencing (NGS), direct stochastic optical reconstruction microscopy (dSTORM), or multiparametric flow cytometry are helping to identify novel tumor-specific targets and improve therapy designs

Here, we present a multiparametric imaging system that simultaneously records four wavelengths to visualize cAMP activity alongside real-time transmembrane potential and intracellular Ca2+ in intact hearts from a cardiac-specific cAMP reporter mouse.

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

Here, we report NMR-based kinetic and selectivity studies on representative 1-amino-but-3-enes

It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions.

Many tools have been developed to interrogate particular aspects of AMPAR signaling, including compounds that selectively inhibit CPARs, raising exciting translational possibilities.

Emerging CRISPR-based diagnostics (e.g., SHERLOCK and DETECTR)

Here, we implement a single unique molecular identifier strategy that reduces sequencing artifacts and achieves an error rate of ~10⁻⁵, enabling single-particle-level quantification of quasi-species diversity.

Small RNA profiling and network analyses of viral movement proteins reveal complex mechanisms of immune evasion and resistance breakdown.

The protocol is an adaptation of the STARR-seq method, which allows testing the capacity of thousands of synthetic DNA sequences to act as hormone-response elements.

Surface plasmon resonance (SPR) ... makes it possible to measure accurately the adsorption of molecules on the metal surface and their eventual interactions with specific ligands.

tangential flow filtration (TFF) serving as a critical unit operation for vector concentration, impurity reduction, and buffer exchange while maintaining viral functionality

a tandem mass tag (TMT)-labeled quantitative proteomics analysis

Using a transfection-infection assay (T-I assay), the AcMNPV gp64 gene was targeted at six different locations to evaluate the effects of single and multiple targeting sites

Interactomic techniques such as yeast two-hybrid screening and affinity purification-mass spectrometry further map host-pathogen protein-protein interactions, highlighting key immune nodes such as receptor-like kinases, R proteins, and effector-targeted complexes.

LOV2-based photoswitches are optogenetic switches engineered from the LOV2 photoreceptor domain to control biological activities with light. They repurpose endogenous light-induced conformational changes in LOV2 to generate new cellular outputs and have been developed on the basis of detailed biophysical characterization of the isolated domain.

LOVpep/ePDZb is a blue-light-inducible heterodimerization system examined as one of three optogenetic dimer variants in a comparative cellular optogenetics study. It mediates light-dependent protein association that was used to control cellular localization and activity in assays including transcription, intracellular localization, and GTPase signaling.

OST1 is an Arabidopsis thaliana protein kinase domain identified by positional cloning as an abscisic acid (ABA)-activated kinase expressed in stomatal guard cells and vascular tissue. Genetic and physiological evidence places OST1 as a regulator of stomatal movement, acting upstream of reactive oxygen species production and interacting genetically with HT1 during red light- and CO2-responsive stomatal responses.

Electrochemical techniques such as impedance spectroscopy, cyclic voltammetry, chronoamperometry, and scanning electrochemical microscopy are central to probing electron transfer mechanisms, tuning redox potentials, and analyzing protein-electrode interactions.

Electrochemical techniques such as impedance spectroscopy, cyclic voltammetry, chronoamperometry, and scanning electrochemical microscopy are central to probing electron transfer mechanisms, tuning redox potentials, and analyzing protein-electrode interactions.

Impulsivity was modeled by the subjects' inability to maintain hold of a touch-sensitive bar until presentation of an imperative signal.

Here, we review the theory and development of the ultrasound brain functional imaging and its applications.

Electrochemical techniques such as impedance spectroscopy, cyclic voltammetry, chronoamperometry, and scanning electrochemical microscopy are central to probing electron transfer mechanisms, tuning redox potentials, and analyzing protein-electrode interactions.

Electrochemical techniques such as impedance spectroscopy, cyclic voltammetry, chronoamperometry, and scanning electrochemical microscopy are central to probing electron transfer mechanisms, tuning redox potentials, and analyzing protein-electrode interactions.

Using a spectral imaging system based on liquid crystal tunable filters, we were able to separate individual spectral species on a pixel-by-pixel basis.

We then use Tope-seq to screen epitope libraries against a model therapeutic candidate TCR.

we introduce latest advancements in ultrasound brain modulation and its applications in rodents, primates, and human; its mechanism and closed-loop ultrasound neuromodulation based on electroencephalograph are also presented.

Blood oxygenation level-dependent functional magnetic resonance imaging (BOLD-fMRI) revealed abnormal activity in a region of interest (ROI) that responded to analgesic medication adjustments.

Both vesicle fluid culture and next-generation sequencing (NGS) of blood samples confirmed the presence of Escherichia coli.

Both vesicle fluid culture and next-generation sequencing (NGS) of blood samples confirmed the presence of Escherichia coli.

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.

The three considered modalities were... peripheral neuromodulation (afferent stimulation and vibration).

Innovations such as AI-assisted monitoring, 4D printing, and advanced drug delivery systems represent transformative approaches to overcome current therapeutic limitations.

Functional annotation combined eggNOG-mapper, InterProScan and BLASTp searches against UniProtKB/Swiss-Prot

BUSCO analyses indicate high completeness of the assembly gene space and completeness of the predicted proteome (74.6%)

These were confirmed by Cryo-EM.

Diagnostic imaging, particularly ultrasonography, plays a central role in detection.

double retrograde tracing demonstrated that LS- and mPFC-projecting cells represent two largely anatomically distinct cell groups

evaluated by structural characterization, DPPH antioxidant assay, antibacterial testing against Staphylococcus aureus and Escherichia coli, and MTT cytotoxicity testing

The web research summary lists electrophoretic tissue clearing (ETC) as an explicitly supported related component/tool name and describes it as an active lipid-removal component in the original/Advanced CLARITY workflow.

Here, we monitor genetically encoded DA and calcium indicators as well as cFos in mice

Using genetically encoded voltage indicators, we observed oscillating hyperpolarization during tail retraction in zebrafish neutrophils, with Kir7.1 required for depolarization toward the chemokine source.

Granger causality analysis revealed a controlling role for temporally defined leaders

Optical methods such as ... hyperspectral imaging (HSI) enable real-time, noninvasive monitoring of microbes.

The web research summary states that the anchor paper describes a whole-mouse-brain spatial cell atlas built with MERFISH and integrated with whole-brain scRNA-seq.

evaluated by structural characterization, DPPH antioxidant assay, antibacterial testing against Staphylococcus aureus and Escherichia coli, and MTT cytotoxicity testing in MG-63/HOS osteosarcoma cells

Optical methods such as ... multiwavelength fluorescence spectroscopy (MFS) ... enable real-time, noninvasive monitoring of microbes.

Here, we conducted a pre-registered replication of this protocol that benefited from three additional features: double-blind application of TUS, neuronavigation for consistent TMS positioning, and individualised 3D acoustic simulations to assess M1 target exposure to TUS.

We found that AgRP1 neuron activation in transgenic larvae led to a significantly higher food-consumption behavior than wildtype larvae when analyzed using Particle Image Velocimetry (PIV) to calculate the food particle velocity initiated by larval suction behavior.

This case report describes a 29-year-old pregnant woman at 22 weeks' gestation who was incidentally diagnosed with two large hepatic hydatid cysts during a routine ultrasound.

The source lead states that the paper used EEG/SEP readouts.

The three considered modalities were... central neuromodulation (... and transcutaneous spinal cord stimulation)...

Diagnostic imaging, particularly ultrasonography, plays a central role in detection, while treatment decisions are complicated by the lack of standardized guidelines and the need to balance maternal-fetal safety.

The three considered modalities were... peripheral neuromodulation (afferent stimulation and vibration).

Explicitly supported component/tool names from the sources include zinc-substituted hydroxyapatite (Zn-HA), hydroxyapatite (HA/HAp), Catharanthus roseus extract, DPPH assay, MTT assay, MG-63/HOS cells, XRD, and tuna/fish-bone-derived hydroxyapatite.

cLIPS2 is a light-responsive multi-component switch identified from small libraries of cLIPS1 variants in a higher-throughput yeast screen. It binds human eIF4E in a light-dependent manner in vitro and inhibits translation in vivo in yeast harboring human eIF4E, with improved optical control relative to screened cLIPS1 variants.

Using dexamethasone-inducible overexpression lines, transcriptomic profiling, and chromatin immunoprecipitation, we identified 142 GIS2- and 138 ZFP8-associated candidate genes involved in sterol metabolism, senescence, and stress responses. Chromatin immunoprecipitation and DEX-CHX experiment confirmed GIS2 binding to SQE5 and SEN1 promoters at conserved C2H2 motifs.

Here we show that the five-choice serial reaction time task has greatly facilitated the study of the neural circuits underlying attention in a well-controlled setting.

Finally, quercetin and abscisic acid were quantified to complete the data by HPLC-DAD.

Here we show an imaging-based method that profiles protein-protein interactions (PPIs) through phase-separated condensates.

The web research summary states that the paper studies human supragranular glutamatergic neuron diversification using multimodal Patch-seq on neurosurgical tissue and that the abstract explicitly states the multimodal Patch-seq framework.

ErbB2 activation, identified by IHC with an antibody against phosphorylated ErbB2

we have super-resolution microscopy techniques such as STED, PALM and STORM able to achieve 10 to 20 nm spatial resolution in single molecule localisation

The title explicitly names live-cell STED nanoscopy of mitochondrial cristae.

Functional ultrasound imaging (fUSi) is an emerging neuroimaging technique that can be used to transcranially detect changes in cerebral blood volume following introduction of a stimulus.

Photoablation of zebrafish leader cells disrupted pan-islet signalling, identifying these as likely pacemakers.

The A2A selective agonist [3H]-CGS 21680... has also been used by Varani et al. (1994) in human platelet membranes... although CGS 21680 interacts with the platelet A2A adenosine receptor, like NECA, it proved to be unsatisfactory for the characterization of A2A human platelet receptors... in the purified protein preparation [3H]-CGS 21680 interacts with one recognition site only, with an affinity in the nanomolar range.

The non-selective agonist NECA (A1, A2A, A2B, A3) was the first pharmacological tool to be used for labelling the A2A receptor in the rat brain but it was also found to bind to different affinity states and subtypes of adenosine receptors... the majority of the [3H]-NECA binding to human platelet membranes is to non-receptor sites.

The tritium-labelled form, [3H]-SCH 58261, has been found to label A2A receptors... On the basis of this pharmacological profile [3H]-SCH 58261 has been used to characterize A2A receptors in human platelet membranes... Thus, [3H]-SCH 58261 is the first radioligand that has allowed the binding characterization of the A2A receptor subtype in human platelets.

The A1-selective antagonist [3H]-XAC, having high levels of non-specific binding (Ukena et al., 1986), does not permit satisfactory binding studies of A2A receptors.

2A is a short viral oligopeptide sequence that mediates a ribosome skipping effect during translation, causing co-translational cleavage of polyproteins. It is used in heterologous co-expression systems to separate proteins of biotechnological interest from a single coding sequence.

Is there any method which can reliably be used as a measure of intracellular O·̄2? There is and it is based on the rapid inactivation of [4Fe-4S]-containing dehydratases, such as aconitase... The balance between these opposing processes can be used as a measure of O·̄2 and has been so used in E. coli and in mammalian cells.

The sensitivity of DNA in situ to denaturation, was increased in apoptotic and necrotic cells. This feature, probed by staining with AO at low pH, provided a sensitive and early assay to discriminate between live, apoptotic and necrotic cells, and to evaluate the cell cycle phase specificity of these processes.

The ATP-dependent lysosomal proton pump, tested by the supravital uptake of acridine orange (AO) was also preserved in apoptotic but not necrotic cells.

Particular emphasis is placed on the integration of advanced imaging for precise lesion assessment, improved patient selection, and the use of combination strategies in complex cases.

The web research summary states that the review strongly emphasizes alternative test systems relevant to neurotoxicity-focused ecotoxicology assessment.

Animal whole-brain functional magnetic resonance imaging (fMRI) provides a non-invasive window into brain activity.

The autodisplay system was developed on the basis of the natural Escherichia coli autotransporter protein AIDA-I (adhesin involved in diffuse adherence). Autodisplay has been used for the surface display of random peptide libraries to successfully screen for novel enzyme inhibitors. The autodisplay system was also used for the surface display of functional enzymes... Autodisplay of epitopes on the surface of attenuated Salmonella carriers has also provided a novel way to induce immune protection after oral vaccination.

The web research summary states that the review places strong emphasis on behavior and argues for neurotoxicity-focused assessment frameworks beyond conventional lethality and morphology endpoints.

Using biochemical purification and functional reconstitution techniques, multiple transporters have been identified and characterized.

Biosensing is mentioned only as an emerging assay-related strategy expected to shape future directions in the field. The supplied evidence does not define a specific biosensor modality, analyte, or experimental implementation.

In combination with calcium and fluorescent imaging, functional alterations caused by mutations in epilepsy genes can be traced.

The supplied review summary explicitly emphasizes CBV-weighted fMRI as central to layer-specific fMRI and laminar activity mapping.

The so-called Cholinergic REM Induction Test revealed that REM sleep abnormalities can be mimicked by administration of cholinomimetic agents.

Chromatin in vivo imaging is identified in a 2018 review as a CRISPR/Cas9-based epigenetic technique for imaging chromatin in living systems. The supplied evidence supports its existence as a method category within the CRISPR/Cas9 epigenetics toolkit, but does not describe a specific construct, protocol, or performance profile.

These label-free techniques span a variety of different approaches, including structured illumination, transient absorption, infrared absorption, and coherent Raman spectroscopies.

Emerging targets such as B7-H3, Claudin 18.2, and MUC1, along with advancements in companion diagnostics, are reshaping the landscape of CAR-T therapy by enabling more precise patient selection and real-time therapeutic monitoring.

The combination of several complementary techniques in one instrument has increasingly become a vital approach to investigate the details of the interactions among molecules and molecular dynamics. In this review, we reported the principles of AFM and optical microscopy ... and focused on the development and use of correlative AFM and optical microscopy.

These reporters support real-time tracking of infection dynamics and host-virus interactions and power diagnostic platforms including reporter viruses, CRISPR-based assays, and nanotechnology-enhanced biosensors.

protons in lipids and proteins have been selectively replaced by deuterons and the resultant deuterium NMR spectrum analyzed to give structural and dynamic information about the molecular associations between a range of membrane components

DNA synthesis is presented as an engineering method that supports the development of new dynamic metabolic engineering systems. In the cited review, advances in DNA synthesis are identified as a factor that will continue to drive innovation in responsive cell factory design.

The supplied source summary states that the review explicitly covers SMLM, including STORM/dSTORM.

Dynamic metabolic engineering is an engineering strategy that uses dynamic regulation of gene expression to build responsive cell factories. It is described as enabling metabolic flux rebalancing under changing cellular or fermentation conditions while managing trade-offs between growth and production.

By virtue of smart MIT, new formatted MIPs gain popularity for versatile applications, including ... chemical/biological sensing (electrochemical sensing, fluorescence sensing, etc.).

However, electrophysiological analysis is necessary to understand their functional characteristics and complexity.

The endometrial receptivity assay (ERA) is a clinical assay intended to assess endometrial receptivity during the window of implantation. The supplied evidence indicates that, as a current test of the window of implantation, it does not consistently improve clinical outcomes measured by live birth rates.

Endometrial thickness measurement is a current clinical assay method used as a marker of the window of implantation and endometrial receptivity. The cited evidence indicates that, as a current test of the window of implantation, it does not consistently improve clinical outcomes measured by live birth rates.

Epigenetic element screening is described in a 2018 review as a CRISPR/Cas9-based epigenetic technique. The supplied evidence establishes only that it belongs to the set of CRISPR/Cas9-enabled approaches used in epigenetics, without further methodological detail.

Epigenome editing is a CRISPR/Cas9-based engineering approach that regulates the epigenomic state of a target genomic region to control the associated gene while causing minimal or no modification of genomic DNA. The cited literature presents it as a novel epigenetic technique and a potential therapeutic modality.

Furthermore, epitope analysis reveals that linear, as opposed to conformational epitopes, are prominent; however, single amino-acid substitutions of IgE-binding sites often lead to a loss of binding to these epitopes, a finding with obvious therapeutic implications.

the abstract states that full potential of fast optical neural circuit control will depend crucially on fast, intact-circuit readout technology and that millisecond-scale optical control will be best leveraged with simultaneous millisecond-scale optical imaging.

This has been circumvented by exploiting its reaction with various “detector” molecules such as ferricytochrome c...

The fluorescence method is a signal transformation modality used in CRISPR-Cas pathogen nucleic acid diagnostic platforms. In the cited context, Cas effector proteins recognize and cleave specific DNA or RNA targets, and fluorescence is combined with signal amplification and transformation technologies to report detection.

By virtue of smart MIT, new formatted MIPs gain popularity for versatile applications, including ... chemical/biological sensing (electrochemical sensing, fluorescence sensing, etc.).

Fluorescent probes are described as an expanding assay toolbox that can be combined with larval zebrafish for real-time in vivo monitoring of cell identity, cell fate, and physiology. In the cited review, this use context is framed for organ pathophysiology studies, including the pancreas and islets of Langerhans.

Fluorescent-protein-based methods are assay approaches discussed for evaluating the efficacy of CRISPR-based genome-editing systems in bacteria. The available evidence supports their use as fluorescence-based functional readouts of bacterial editing performance, but does not specify particular reporter proteins, construct architectures, or assay workflows.

In the forced swim test (FST) rodents progressively show increased episodes of immobility if immersed in a beaker with water from where escape is not possible.

Imaging molecular interactions in living cells by FRET microscopy. FRET imaging provides information about all these molecular processes with high specificity and sensitivity via probes expressed by or introduced from the external medium into the cell, tissue or organism.

From a variety of initial designs two have emerged as promising prototypes for further optimization: FRET (Förster Resonance Energy Transfer)-based sensors and single fluorophore sensors of the GCaMP family.

From a variety of initial designs two have emerged as promising prototypes for further optimization: FRET (Förster Resonance Energy Transfer)-based sensors and single fluorophore sensors of the GCaMP family.

The supplied source summary states that the review explicitly covers SMLM, including GSDIM.

The histology of the main organs was examined using conventional haematoxylin-eosin stained sections.

When combined with other methods like optical imaging and high-field functional magnetic resonance imaging, the translation of optical stimulation to clinical practice adds high value.

High-resolution electrocorticography is presented as a recording approach enabled by conformal electrodes in epilepsy surgery.

High-resolution live imaging is cited as a methodological approach that provides new opportunities to study branching morphogenesis in living systems. The supplied evidence identifies it only at the level of a general live-imaging assay and does not specify the imaging modality, reporter strategy, or biological model.

In the context of pharmaceutical research, hPSC-derived cellular models now underpin high-throughput drug screening and mechanistic toxicological assays, offering superior human relevance compared to traditional animal models.

The hypocotyl elongation screen for ethylene-insensitive Arabidopsis mutants is a phenotypic assay based on ethylene-mediated inhibition of hypocotyl elongation in dark-grown seedlings. Arabidopsis mutants that remain tall despite treatment with high concentrations of ethylene are identified as ethylene-insensitive.

By using soy-absorbed, peanut-allergic patient sera on two-dimensional immunoblots and N-terminal amino-acid sequencing, about 30 protein fractions were shown to be isoforms, or fractions, of the three major peanut proteins.

In this review, we discuss some significant biological insights in plant growth and development, breakthroughs and limitations of various microscopic applications and the exciting possibilities offered by emergent in vivo live imaging and fluorescent protein engineering technologies.

These label-free techniques span a variety of different approaches, including structured illumination, transient absorption, infrared absorption, and coherent Raman spectroscopies.

Lateral flow technology is a signal transformation format used within CRISPR-Cas pathogen nucleic acid diagnostic platforms. In the supplied evidence, it functions alongside Cas protein-based sequence recognition and cleavage and with signal amplification approaches for rapid molecular diagnosis.

Studies utilizing electron microscopy and live fluorescence microscopy have significantly enhanced our understanding of the molecular mechanisms that regulate junctional dynamics...

We outline the technical developments that have led to the emergence of localization microscopy techniques from single-molecule spectroscopy.

An example is the luminescence that can be elicited from lucigenin... the use of lucigenin as a “specific” detector of O·̄2 continues... lucigenin was shown to function, much as does paraquat, to increase intracellular O·̄2 production.

Another luminescent method that is misused to measure O·̄2 is based on luminol... Luminol luminescence thus can be caused by a variety of oxidants and in all cases SOD inhibits.

Recently, magnetic resonance-guided focused ultrasound has emerged as an alternative to surgical procedures, offering incisionless lesioning of the thalamus, resulting in immediate and sustained tremor reduction.

Here, we review a broad spectrum of single-molecule tools and techniques such as optical and magnetic tweezers...

In the context of pharmaceutical research, hPSC-derived cellular models now underpin high-throughput drug screening and mechanistic toxicological assays, offering superior human relevance compared to traditional animal models.

Microelectrode arrays and microprobes have been widely utilized to measure neuronal activity, both in vitro and in vivo. The key advantage is the capability to record and stimulate neurons at multiple sites simultaneously.

Microelectrode arrays and microprobes have been widely utilized to measure neuronal activity, both in vitro and in vivo.

By virtue of smart MIT, new formatted MIPs gain popularity for versatile applications, including sample pretreatment/chromatographic separation (solid phase extraction, monolithic column chromatography, etc.)

FX has been identified in HbRC cores by EPR and Mössbauer spectroscopy, and shown to be a [4Fe-4S]1+,2+ cluster with a ground spin state of S=3/2.

Multiplexed engineering refers here to the use of the CRISPR/Cas toolbox for simultaneous genome engineering tasks in microbial biotechnology. The cited review places this approach in the context of metabolic engineering and high-throughput screening for production of chemicals and natural compounds.

Specific linear IgE-binding epitopes have recently been identified, and mutational analysis is underway.

Here, we review a broad spectrum of single-molecule tools and techniques such as ... nanopore tweezers...

These reporters support real-time tracking of infection dynamics and host-virus interactions and power diagnostic platforms including reporter viruses, CRISPR-based assays, and nanotechnology-enhanced biosensors.

One additional artifactual detector of O·̄2 needs to be mentioned because of its widespread misuse, and that is nitroblue tetrazolium... many aerobic tetrazolium reductions are inhibitable by SOD even though O·̄2 was not being produced in the system in the absence of the tetrazolium.

Nitrogen vacancy (NV) diamond centers are described as a methodological approach for following cryptochrome magnetic field sensitivity in vivo. In the cited review, they are presented as an assay-related innovation for studying magnetically sensitive cryptochrome biology.

Noncoding RNA manipulation is identified in a 2018 review as a CRISPR/Cas9-based epigenetic technique. The supplied evidence establishes only that it falls within the review’s scope and that CRISPR/Cas9 opened new routes into epigenetics.

Novel positron emission tomography ligands are presented as an emerging imaging innovation in epilepsy management.

behavioral measures in rodents, like prepulse inhibition of the acoustic startle and open-field locomotion, which are commonly used along with neurochemical approaches or drug challenge designs

In hypothalamic slice preparations in vitro, electrical stimulation of the optic nerves induces release of glutamate and aspartate, and glutamate antagonists block field potentials in the SCN evoked by stimulation of the optic nerve.

Optical mapping, using fluorescent probes and high-speed cameras, offers detailed insights into cardiac activity and arrhythmias by analysing electrical signals, calcium dynamics, and metabolism.

This review focuses on the recent advances in optoacoustic imaging assisted by smart molecular labeling and dynamic contrast enhancement approaches that enable new types of multiscale dynamic observations not attainable with other bio-imaging modalities.

Bock & Atkins ( 18) followed 32 peanut-allergic children (confirmed by double-blind, placebo-controlled oral food challenges)...

Orthogonal degrons are bacterial construct patterns used in tunable degradation systems to direct targeted proteolysis of proteins of interest. The cited literature places them among recent advances that enable large screens and functional interrogation through regulated protein degradation.

Human BAT can be detected using PET.

While these methods, like polymerase chain reactions or whole-genome sequencing, are considered the "gold standard" for diagnostics, the development of inexpensive, rapid diagnostic assays is necessary for effective AMR detection and management.

The introduction of polysomnography into psychiatric research confirmed a disturbance of sleep continuity in patients with depression...

A major challenge for such applications is the need to track the location and function of chemogenetic receptors and opsins in vivo, and new developments in positron emission tomography (PET) imaging techniques offer promising solutions.

Using the pressure jump relaxation technique in combination with time-resolved synchrotron X-ray diffraction, the kinetics of different lipid phase transformations was investigated.

The combination of PI followed by Hoechst 33342 proved to be an excellent probe to distinguish live, necrotic, early- and late-apoptotic cells.

Highly purified AQP1 protein from human red cells reconstituted with pure phospholipid yielded proteoliposomes of approximately 100 nm in diameter. The change in volume of AQP1 proteoliposomes was compared to liposomes containing no reconstituted protein by measuring quenching of internal carboxyfluorescein.

The upstream web research summary identifies the Psychomotor Vigilance Test (PVT) as the core assay for vigilant attention under sleep loss and as the operational assay in closely related review and primary sources aligned to this review's abstract focus on vigilant attention and vigilance decrement.

facilitating diagnosis via gold nanoparticles (AuNPs) and magnetic nanoparticle biosensors, quantum dots, and artificial intelligence-integrated nanosensors

Using RAST and RAST inhibition, Barnett et al. ( 1) showed that peanut-allergic individuals had extensive IgE binding to other legumes, including soy.

The recent introduction of fluorescence-based kinetic RT-PCR procedures significantly simplifies the process of producing reproducible quantification of mRNAs and promises to overcome these limitations.

These reporters support real-time tracking of infection dynamics and host-virus interactions and power diagnostic platforms including reporter viruses, CRISPR-based assays, and nanotechnology-enhanced biosensors.

Furthermore, rescue experiments can clarify the phenotypic capabilities of CALI after the depletion of endogenous targets.

The reverse transcription polymerase chain reaction (RT-PCR) is the most sensitive method for the detection of low-abundance mRNA, often obtained from limited tissue samples. However, it is a complex technique, there are substantial problems associated with its true sensitivity, reproducibility and specificity and, as a quantitative method, it suffers from the problems inherent in PCR.

Mitochondrial transmembrane potential, assayed by retention of rhodamine 123 was preserved in apoptotic but not necrotic cells.

The web research summary states that the anchor review groups RiboTag with TRAP as a ribosome-tagging strategy for cell-type-specific translation profiling in memory studies.

To evaluate the risk of bias, the RoB2 tool was used for randomized studies

the ROBINS-I tool for non-randomized studies.

We suggest that rodent self-grooming may be a useful measure of repetitive behaviour in such models, and therefore of value to translational psychiatry. Assessment of rodent self-grooming may also be useful for understanding the neural circuits that are involved in complex sequential patterns of action.

Root-specific transcriptomic dataset comparison is a comparative transcriptomic assay approach used to identify transcripts that respond consistently to elevated ethylene across multiple root datasets. In the cited review, this approach defined a core set of 139 ethylene-responsive root transcripts.

Screening based on selective labeling is identified in a 2023 review as an available genetic engineering tool within Aspergillus genome engineering workflows. The supplied evidence supports only that it is used as a screening approach associated with Aspergillus genetic technology, without operational or performance details.

Sequencing-based solutions are proposed assay methods for detecting large-scale CRISPR-associated genomic alterations. In the cited review, they are positioned as potential approaches to identify rare events such as translocations, inversions, deletions, and chromothripsis that can be missed by current workflows.

Single-cell measurements are assay methods used to study cellular dynamics at the level of individual cells. The supplied evidence indicates that technological improvements have increased their throughput and capabilities.

Single-molecule fluorescence provides high resolution spatial distributions of ribosomes and RNA polymerase (RNAP) in live, rapidly growing Escherichia coli.

Here, we review a broad spectrum of single-molecule tools and techniques such as ... single-molecule fluorescence resonance energy transfer (smFRET)...

Single-molecule imaging enables biophysical measurements devoid of ensemble averaging, gives enhanced spatial resolution beyond the diffraction limit, and permits superresolution reconstructions.

For more than 20 years, single-molecule spectroscopy has been providing invaluable insights into nature at the molecular level.

Today, single molecule super-resolution imaging is routinely used in the study of macromolecular function and structure in the cell.

We cover commonly used techniques such as spatial point pattern analysis, colocalization, and protein copy number quantification but also describe more advanced techniques such as structural modeling, single-particle tracking, and biosensing.

Since there are homologous proteins in peanut and soy, it is not uncommon to find positive tests for IgE antibody to both of these foods in individuals who are clinically reactive to one or the other.

We describe an animal model of social defeat as a possible model for human depression. We discuss the paradigm, behavioral correlates to depression, and potential underlying neurobiological mechanisms with an eye toward possible future therapies.

By virtue of smart MIT, new formatted MIPs gain popularity for versatile applications, including sample pretreatment/chromatographic separation (solid phase extraction, monolithic column chromatography, etc.)

A dedicated home-built fluorescence microscope records spectrally resolved images to measure the QCSE induced spectral shift at the single-particle level.

Studies using spin-polarized EPR transients and spectra to investigate the electron transfer pathway and kinetics are also reviewed.

This has been circumvented by exploiting its reaction with various “detector” molecules such as ferricytochrome c or spin-trapping agents.

The supplied source summary states that the review explicitly covers major modality families including STED/RESOLFT.

These label-free techniques span a variety of different approaches, including structured illumination, transient absorption, infrared absorption, and coherent Raman spectroscopies.

Single-molecule imaging enables biophysical measurements devoid of ensemble averaging, gives enhanced spatial resolution beyond the diffraction limit, and permits superresolution reconstructions.

targeted proteomics have produced long lists of proteins potentially regulated by Cys oxidation/thioredoxin, Met-SO formation, phosphorylation, or Lys acetylation

Tension sensors are assay methods cited as emerging tools for studying branching morphogenesis. In the supplied evidence, they are presented as part of a methodological set that can create new opportunities for future research.

Advances in targeting, thermometry and other biological effects such as histotripsy could expand accessibility and indications.

Analysis of time-resolved images of the nucleoid spatial distribution after treatment with the transcription-halting drug rifampicin and the translation-halting drug chloramphenicol shows that both drugs cause nucleoid contraction on the 0-3 min timescale.

Using the pressure jump relaxation technique in combination with time-resolved synchrotron X-ray diffraction, the kinetics of different lipid phase transformations was investigated.

This entry refers broadly to imaging-oriented tools and sensors associated with bacterial degron and degrader concepts. The supplied evidence only states that bacterial degrons can be used to interrogate and control protein function and mentions “tools and sensors for imaging,” without defining a specific construct, sensor architecture, or imaging readout.

These label-free techniques span a variety of different approaches, including structured illumination, transient absorption, infrared absorption, and coherent Raman spectroscopies.

The web research summary identifies TRAP as a primary-paper-supported activity-dependent genetic access method aligned with the review's coverage of activity-driven genetic targeting.

Our review discusses emerging perspectives on: (iii) classical and new techniques to monitor vesicle fusion in cultured astrocytes

In this Review, we explore new insights from studies using super-resolution and volume electron microscopy into the nanoscale organization of these junctional complexes...

In particular, wavelength-tunable FSRS exploits dynamic resonance conditions to track transient-species-dependent vibrational motions, enabling rational design to alter functions.

Whole-genome screening of gene knockout mutants in Toxoplasma gondii is a CRISPR/Cas9-based assay method for generating and interrogating genome-scale loss-of-function mutant populations. The cited review identifies this as a recent use of CRISPR/Cas9 in an apicomplexan parasite.

The Xenopus oocyte expression system has proven to be a valuable method for functional analysis of candidate water channel RNAs, since the oocytes normally exhibit low membrane water permeability.

Zebrafish spinal cord injury paradigms are experimental assay methods used to study central nervous system axon regeneration and functional recovery in zebrafish. The cited review presents these paradigms as a framework for investigating the strong regenerative capacity observed in fish after spinal cord injury.

The all-optical framework for functional testing of opsin responsiveness in cardiac fibroblasts is an assay method described to evaluate whether virally introduced optogenetic actuators are functionally responsive in primary cFB. In the cited study, it provides an optical functional readout for opsin-expressing cardiac fibroblasts and is associated with co-culture conditions that can yield a light-sensitive excitable cardiac syncytium.

The web research summary states that the anchor paper uses 3D-dSTORM and specifically astigmatism-based 3D-dSTORM for single-particle localization measurements on nanoparticles.

Atomic force microscopy under physiological conditions and tracer particle microrheology are modern methods to determine gel modulus and viscoelastic properties in spatial resolution.

Human brain tissue was obtained postmortem from patients who had been treated with the thymidine analog, bromodeoxyuridine (BrdU), that labels DNA during the S phase. Using immunofluorescent labeling for BrdU and for one of the neuronal markers, NeuN, calbindin or neuron specific enolase (NSE), we demonstrate that new neurons ... are generated from dividing progenitor cells in the dentate gyrus of adult humans.

Using the TBK1 inhibitor, BX795, we discovered that HBsAg-enhanced TBK1 dimerization, promoting sequestosome-1 (p62) phosphorylation, was necessary for HBV-induced autophagy and HBV replication.

Using a closed-loop system, GSWDs were detected and stopped within 500 milliseconds.

Chromatin immunoprecipitation and DEX-CHX experiment confirmed GIS2 binding to SQE5 and SEN1 promoters at conserved C2H2 motifs.

The title names droplet based microfluidics as the method used to investigate host-microbiome interactions.

The mapping was aided by an engram index, which identified 117 cFos+ brain regions holding engrams with high probability

Within the bouquets, expansion microscopy resolved many individual striosomal fibers tightly intertwined with the dopamine-containing dendrites and also with afferents labeled by glutamatergic, GABAergic, and cholinergic markers and markers for astrocytic cells and fibers and connexin 43 puncta.

We use focused ion beam (FIB) milling and scanning electron microscopy (SEM) to directly evaluate changes in 3D pore structure in a Viresolve® Pro membrane due to fouling by human serum immunoglobulin G.

We also review tools to measure pHlys, ranging from fluorescent dyes to genetically encoded biosensors and nanomaterial-based probes...

We here provide evidence for such a regionalization of the output from the cerebellar cortex by genetically encoded transneuronal mapping of efferent circuits of zebrafish Purkinje neurons.

Subsequent optoactivation of the LC evoked repeatable, robust, antinociceptive (+4.7°C ± 1.0, p < 0.0001) or pronociceptive (-4.4°C ± 0.7, p < 0.0001) changes in hindpaw thermal withdrawal thresholds.

Recent breakthroughs in redox biosensors (i.e., redox-sensitive fluorescent proteins, HyPer variants, and peroxiredoxin-FRET constructs) enable precise, real-time ROS imaging across subcellular compartments.

mRNA-sequencing of OX lines revealed substantial upregulation of Pi starvation-responsive genes, including SPX1, PS2/PECP2, and SRG3/GDPD1.

Multimodal ultrasound (MU), incorporating techniques such as elastography and automated breast volume scanning (ABVS), achieves improved diagnostic accuracy when combined with MRI/CT.

Finally, we also demonstrated that nano flow cytometry is a powerful tool for assessing cell-free EV engineering efficiency.

We also review tools to measure pHlys, ranging from fluorescent dyes to genetically encoded biosensors and nanomaterial-based probes...

PAIR (puncture, aspiration, injection, re-aspiration) was contraindicated due to multivesicular bone and spinal cysts.

Here, we define the tension response of mechanosensitive K2Ps using patch-clamp recording and imaging.

Retrograde tracing showed that these clustered cell bodies in turn project to the striatum as part of the classic nigrostriatal pathway.

Single-nucleus and spatial atlases anchor these circuits in cell types and microenvironments relevant to stress and symbiosis.

small RNA-sequencing identified the downregulation of miR399 and miR827, which are involved in the Pi starvation response.

Protocol explicitly linked from the anchor Nature article’s associated content and relevant because the anchor study used SNARE-seq2 nuclei profiling for joint RNA/chromatin accessibility measurements in M1.

Single-nucleus and spatial atlases anchor these circuits in cell types and microenvironments relevant to stress and symbiosis.

Three-dimensional structured illumination microscopy (3D-SIM) demonstrated a network of channels and wider lacunas, called the interchromatin compartment (IC).

Atomic force microscopy under physiological conditions and tracer particle microrheology are modern methods to determine gel modulus and viscoelastic properties in spatial resolution.

Imaging morphology was consistent with the WHO-IWGE (Informal Working Group on Echinococcosis) CE1-CE3 hydatid cysts.

Retrograde transsynaptic tracing using pseudorabies virus (PRV) was employed to identify central amygdala (CeA) involvement in gastric-related neural circuits.

The supplied review summary explicitly emphasizes BOLD as a central comparison contrast in the review's discussion of layer-specific fMRI.

When combined with concurrent brain imaging, such stimulation methods can reveal patterns of neuronal activity responsible for regulating simple and complex behaviours at the level of local circuits and across widespread networks.

the methods for evaluating lower urinary tract function in rodents are discussed

These target T cells were protected from programmed cell death by preincubation of T cells with a Fas-blocking monoclonal antibody (mAb)...

These target T cells were protected from programmed cell death by ... preincubation ... of myeloma cells with a FasL-neutralizing mAb.

Recommendations related to long-term management of differentiated thyroid cancer include those related to surveillance for recurrent disease using imaging and serum thyroglobulin

With intracoronary imaging (intravascular ultrasound and optical coherence tomography), peri-procedural success for treating calcified lesions has increased significantly.

The supplied review summary explicitly describes line-scanning fMRI as a high spatiotemporal-resolution approach for early laminar BOLD dynamics.

novel magnetic resonance imaging applications combined with pupillometry have opened the way to evaluate LC activity in vivo

With intracoronary imaging (intravascular ultrasound and optical coherence tomography), peri-procedural success for treating calcified lesions has increased significantly.

We will review some of the novel tools that have been developed for the observation of cellular activity and then discuss the recent breakthroughs in optical super-resolution microscopy that allow for optical observations beyond the diffraction limit.

The supplied review summary explicitly lists patch clamp as a complementary method integrated with AFM.

More recently, with the use of long-range PCR, denaturing HPLC (DHPLC), and the protein truncation test, mutations in the duplicated region of the PKD1 gene have been identified

novel magnetic resonance imaging applications combined with pupillometry have opened the way to evaluate LC activity in vivo