Selection / Enrichment

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.

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.

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.

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.

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.

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.

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.

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.

incorporated into second-generation chimeric antigen receptor (CAR) constructs that were termed sherpabody-guided CARs (SbCAR)

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.

Chrimson is a red light-activated channelrhodopsin with a reported crystal structure. It provides red-shifted optogenetic excitation and has been used with Chronos to support two-color activation of independent neural populations in mouse brain slice without detectable cross-talk.

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

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.

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

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

our optimized prime editing strategy provides a highly efficient and versatile framework for genome engineering in vitro

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 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.

Amine functionalization of the membrane pore with a hydrogel exhibited >70 % retention of 20 nm negatively charged particles even when λ>40 and 80 % retention of DNA and protein when λ>160.

The CpbHLH gene family is the set of basic helix-loop-helix transcription factor genes identified in Chimonanthus praecox. A genome-wide study reported 131 CpbHLH genes distributed across 11 chromosomes and characterized their expression across tissues and flower developmental stages.

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

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.

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).

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.

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.

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

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.

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

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.

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.

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

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.

A functional lentiviral vector, LV_EF1α_GBA_Opt, was generated at a titer of 7.88 × 108 LV particles/mL as determined by qPCR.

we developed a biosensor based on turn-on fluorescent protein, named LV-EcpG

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

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.

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.

Among them, paper-based biosensors have emerged as a promising platform due to their low fabrication cost, simplicity, biodegradability, and compatibility with point-of-care (POC) testing.

PHPLCδ1 is a phosphoinositide-binding pleckstrin homology domain used as a membrane-associated fluorescence probe. In the cited 2019 C. elegans zygote study, its reported PIP2 signal was interpreted as reflecting general plasma membrane localization rather than selective enrichment in a distinct PIP2 microdomain.

Product Nkabinde (PN), a polyherbal formulation derived from traditional medicinal plants, has recently demonstrated significant potential in the treatment of HIV.

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.

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.

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.

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.

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 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.

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

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.

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.

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

We then focus on bottlenecks such as target selection strategies, engineering design, and TME-driven issues like phenotypic inactivation and antigen escape, discussing corresponding optimization approaches like armoring modifications, logic-gated designs, and convection-enhanced delivery.

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.

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.

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 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.

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.

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.

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.

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.

High-signal enrichment leads were found primarily in PubMed/PMC and ClinicalTrials sources, with strongest support for EBV gp350/LMP1-directed CARs.

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.

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.

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

High-signal enrichment leads were found primarily in PubMed/PMC and ClinicalTrials sources, with strongest support for HBV HBsAg-directed CARs. Explicitly supported related components/tools include HBV-directed binders/constructs (HBsAg, PreS1, 4D06, 4D08).

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.

High-signal enrichment leads were found primarily in PubMed/PMC and ClinicalTrials sources, with strongest support for HIV Env/bNAb-based CARs. Explicitly supported related components/tools include HIV bNAb-derived CAR binders (VRC01, 3BNC117, 10-1074).

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.

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.

We firstly discuss the development of microelectrodes and strategies for their flexibility, which is mainly represented by the selection of flexible substrates and new electrode materials.

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.

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.

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.

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.

sgRNA (single-guide RNA) is the RNA guide element in CRISPR systems that directs sequence-specific targeting for RNA or DNA manipulation. In the cited review, sgRNA design and modification are highlighted as central determinants of effective virus-targeted gene knock-in, gene knock-out, and CRISPR/Cas mutation efficiency.

This review will give an overview about aptamers interacting with small molecules and their selection.

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

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 supplied web research summary states that the CaMKIIα promoter is explicitly discussed in the anchor review as a cell-type-enrichment promoter for viral opsin delivery.

Recommendations regarding the initial management of thyroid cancer include those relating to screening for thyroid cancer, staging and risk assessment, surgical management, radioiodine remnant ablation and therapy, and thyrotropin suppression therapy using levothyroxine.

C. flexa RhPDE1 (CfRhPDE1) revealed the highest cGMP affinity and the most pronounced light regulation

The web research summary states that the anchor paper full text explicitly names CheRiff as the engineered channelrhodopsin actuator spectrally orthogonal to QuasAr indicators.

Chronos is a channelrhodopsin construct used for optical excitation of neurons. In the cited 2014 Nature Methods work, it is presented with Chrimson as a complementary optogenetic pair for two-color activation of distinct neural populations, enabling independent spiking and downstream synaptic transmission in mouse brain slice without detectable cross-talk.

The droplet microfluidic platform is an assay method for screening and separating cell populations based on the in vivo fluorescence response of expressed biosensors after addition of an exogenous analyte. It was applied to HeLa-cell genetic linker libraries for genetically encoded Zn2+ sensors to assess library diversity and detect response heterogeneity.

FLIPR (Fluorometric Imaging Plate Reader) is a fluorescence-analysis instrument used as a miniaturized optogenetic assay platform in 384-well plates. In the cited study, FLIPR LEDs provided optical modulation to support recombinant cellular assays, including Channelrhodopsin-2 control of CaV1.3.

Fluorescence recovery after photobleaching (FRAP) is proposed as a functional assay readout for liquid-like molecular mobility within the pathological condensate termed the addivosome. In this context, FRAP is intended to detect restoration of mobility, or reliquefaction, during compound screening.

Fluorescent polarization is an assay method provided as a protocol for validating, improving, and using newly designed photoswitches in the context of LOV2-based optogenetic engineering. In the cited source, it is presented alongside phage display and microscopy as part of the experimental toolkit for photoswitch development.

The establishment of in vivo optogenetics could provide for high-impact independent research projects for upper-level undergraduate students.

KillerRed is a genetically encoded protein photosensitizer used to generate singlet oxygen upon light irradiation for photodynamic perturbation. In the cited study, plasma-membrane-targeted KillerRed activated cholecystokinin 1 receptor (CCK1R) signaling in AR4-2J cells, producing persistent calcium oscillations consistent with permanent photodynamic receptor activation.

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

Microscopy is a protocolized assay method included alongside fluorescent polarization and phage display in a 2020 methods source on engineering and applying LOV2-based photoswitches. In that context, it is used as part of the experimental workflow for validating, improving, and using light-responsive optogenetic switches built on the LOV2 domain.

Midbrain organoids (MOs), three-dimensional (3D) stem cell-derived neuronal structures mimicking midbrain architecture, have emerged as transformative tools for modelling PD.

miniSOG is a genetically encoded protein photosensitizer described as a mini singlet oxygen generator. In the cited AR4-2J cell study, plasma-membrane-targeted miniSOG generated singlet oxygen upon light irradiation and produced photodynamic activation of cholecystokinin 1 receptor (CCK1R), leading to persistent calcium oscillations.

The open-source microplate reader is a low-cost, open-source assay platform for automated plate-based measurements. It was designed, constructed, validated, and benchmarked to support full-spectrum absorbance detection, fluorescence emission detection, in situ optogenetic stimulation, and stand-alone touch screen programming of assay protocols.

Herein, we validated polyvinyl alcohol (PVA) as a single-molecule environment to efficiently quantify the photoswitching properties of fluorophores... Defining PVA as a fluorophore photoswitching screening platform will facilitate SMLM fluorophore development and optimal image buffer assessment through facile and accurate photoswitching property characterization, which translates to SMLM fluorophore imaging performance.

The pooled library approach is an engineering method for rapid generation and parallel screening of nearly all possible split-protein constructs, with sequencing-based readout. In the cited application, it was used with optogenetic dimers to comprehensively map split-site behavior across Cre recombinase and support inducible post-translational control design.

The supplied source summary states that the review explicitly covers STED/RESOLFT and references RESOLFT in relation to photoswitching-based resolution enhancement.

Innovative platforms like plant cell packs and self-sustained bioluminescence systems facilitate rapid prototyping of gene circuits, enabling high-throughput screening and optimization.

Finally, we emphasize the critical value of integrating high-dimensional tools such as spatial transcriptomics, single-cell profiling, and machine learning to refine ACT design, identify biomarkers of response, and support patient selection and stratification.

SIBR-Cas, termed Self-splicing Intron-Based Riboswitch-Cas, is a multi-component bacterial CRISPR genome engineering system that provides inducible control over CRISPR-Cas counterselection. It is reported to delay counterselection to permit editing events and has been applied to gene knockout in bacteria with poor homologous recombination systems.

Focal depolarization via optogenetics biased pseudopod selection and triggered new protrusions, which depended on Gα signaling. Global hyperpolarization caused neutrophils to stall migration.

Chimeric antigen receptor macrophages (CAR-M) therapy presents a promising new avenue for GBM treatment, leveraging its inherent tumor-homing capacity, TME reprogramming function, and potential to bridge innate and adaptive immunity.

The web research summary identifies albumin-bound paclitaxel as an exemplar nanomedicine modality already used or tested clinically and explicitly names nab-paclitaxel as a clinically relevant nanomedicine example.

The web research summary states that PubMed indexes the review with MeSH terms spanning reporter genes and that additional enrichment leads strongly supported by source-associated literature cluster around reporter-gene imaging.

Comprehensive insertion libraries are a high-throughput engineering method in which many insertion variants are generated and screened. In the cited context, they are discussed as an approach that could accelerate creation of stimulus-responsive receptor–protein chimeras.

Genetic screens in Arabidopsis thaliana are a plant genetics method used to identify components of light-responsive signal transduction pathways. The cited evidence states that several laboratories devised such screens to dissect pathways associated with various photoreceptor systems.

The different luciferin-luciferase pairs have different light emission wavelengths and hence are suitable for various applications.

NCBI sequence screening for 2A/2A-like occurrence is a computational survey method that updates the distribution of viral 2A and 2A-like sequences by screening sequences deposited in the National Center for Biotechnology Information database. In the cited 2021 review, this approach identified 69 newly reported 2A-like occurrences across multiple virus groups.

Dynamic control over SAMs for cell adhesion provides an additional handle to direct and study the attachment of cells to surfaces... recent developments in cell adhesion of mammalian cells to SAM-modified surfaces, the physical properties of which can be controlled by an external stimulus, e.g. by light, electrochemistry, etc., are discussed.

To bridge this gap, we use touchscreens to permit greater flexibility in stimulus presentation and task design, track key dependent measures, and minimize experimenter involvement. Touchscreens offer a valuable tool for creating rodent cognitive tasks that are directly comparable to tasks used with humans.

Here we report ChReef, an improved variant of the channelrhodopsin ChRmine.

Multi-electrode array recording is an electrophysiological assay method that measures extracellular action potential firing from the retinal ganglion layer. In the cited study, it was used with the array in contact with the retinal ganglion layer to detect light-evoked responses.

The nMag/pMag photodimerization system, also called Magnets photosensors, is a light-controlled protein-domain pair that mediates heterodimerization. Reported engineering work altered its light sensitivity and tuned its light-activity dose-response behavior through directed evolution and high-throughput screening.

High-signal enrichment leads and related item candidates identify a photoactivable/photoconvertible CMA reporter built around a KFERQ-targeting motif fused to PA-mCherry1, and explicitly name the reporter variant as KFERQ-PA-mCherry1.

Light-activated MLKL is an engineered optogenetic MLKL system that undergoes rapid light-triggered oligomerization and plasma membrane recruitment, causing rapid cell death. A re-engineered variant blocks the cell-killing activity while retaining light-mediated membrane recruitment, enabling single-component control of protein function at the plasma membrane.

The CRISPR/Cas system is a multi-component genomic engineering platform composed of clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins. It is described as a versatile and powerful genetic tool for genome manipulation, with reported applicability across essentially any organism and cell type.

Split Gal4 is a Drosophila multi-component genetic system used for neural circuit mapping. The cited review describes its use to map and functionally characterize specific neuronal populations in the fly brain and to support behavioral circuit studies.

Self-assembled proteomimetic (SAP) is a multi-component binding scaffold built from short PNA-peptide conjugates that assemble into a proteomimetic three-helix-bundle-like architecture. In the cited study, SAPs were generated against HER2 and the SARS-CoV-2 spike receptor-binding domain, and an RBD-targeting SAP inhibited viral entry with an IC50 of 2.8 nM.

Phytochrome-based reporters and biosensors are construct designs derived from phytochrome systems for near-infrared sensing applications. They have been described for detecting protein-protein interactions, proteolytic activities, and posttranslational modifications, particularly in contexts relevant to mammalian cells and in vivo use.

Corelets is a biomimetic optogenetic multicomponent switch designed to control intracellular phase separation with light-activated multivalent seeds. It was used to induce condensate formation and to map intracellular phase behavior, including regimes of nucleation-and-growth and spinodal decomposition.

FUN-LOVSP-Hph is a blue-light-responsive yeast optogenetic switch variant of FUN-LOVSP that includes a hygromycin resistance cassette for selection after genome integration. It drives light-induced reporter expression and was reported to outperform the original FUN-LOV system in BY4741 yeast while remaining functional in a wine yeast strain.

FUN-LOVSP-Nat is a blue-light-responsive yeast optogenetic switch variant derived from the FUN-LOVSP system and carrying a nourseothricin resistance marker. In BY4741 yeast, it supported blue-light-induced luciferase expression that exceeded the original FUN-LOV system in both episomal and genome-integrated formats.

Human Neuropsin (hOPN5) is a light-responsive optogenetic switch used to selectively control Gq signaling. It has been reported to support specific and repetitive manipulation of this pathway in vitro and in vivo with high spatiotemporal resolution.

The light-inducible split Cre recombinase is an optogenetic multi-component switch in which split Cre recombinase fragments are coupled to light-inducible dimerization modules to achieve inducible post-translational control of Cre activity. It was characterized by comprehensive screening of split sites across the Cre protein using a pooled, sequencing-based domain insertion profiling approach.

Light-switchable transcription factors are multi-component optogenetic regulators reported in a 2023 Nature Communications study. The available evidence indicates that they were obtained by direct screening in mammalian cells and are designed to enable light-dependent control of transcription factor activity.

LOV-Turbo is a light-regulated proximity-labeling system generated by installing a light-sensitive LOV domain into the biotin ligase TurboID. It provides rapid and reversible control of biotin-labeling activity with low-power blue light and can also be activated by luciferase-derived BRET for interaction-dependent proximity labeling in living cells.

OptoORAI1 is a photoswitchable CRAC channel engineered from ORAI1 by insertion of a LOV2 photosensory domain into an ORAI1 loop region. In this design, LOV2 functions as an allosteric light-responsive switch that opens the channel, enabling optical control of calcium signaling.

The DMNP-EDTA-Cu system is a light-activated, photocaged Cu2+ induction method for controlling transcription. Illumination releases Cu2+, which activates the Cu2+-responsive pCUP1 promoter from Saccharomyces cerevisiae to drive gene expression.

The strongest enrichment set includes primary in vivo studies on cognition, sleep/memory, motor coordination, and circuit-level behavioral control, plus one methods-focused review on genetic targeting strategies.

3D pharmacophore models are three-dimensional ensembles of chemically defined interactions of a ligand in its bioactive conformation.

Using the 2020 review on intersectional AAV targeting as the anchor, the strongest enrichment leads are the primary method papers that the review explicitly builds on: the engineered retrograde capsid AAV2-retro (Tervo et al., 2016).

By harnessing our newly developed Acousto-Optogenetics Bandpass Stabilizer, we transform phototoxicity into a tunable parameter, thereby enabling artifact-free drug response analysis.

In this review, we summarize the main approaches that have been developed to face such bottlenecks, including the adapter CAR (AdCAR) system...

The paper explicitly defines adaptive multiplicative superlets as a frequency-dependent order selection variant.

Here, we introduce AdaptUC, a computational framework that demonstrates how the fraction of biomass precursors synthesized from unadapted carbon sources governs both the evolutionary driving force and the minimal substrate requirement.

Artificial intelligence (AI) has emerged as a powerful tool to address these challenges, accelerating the design and optimization process of LNPs. AI-guided approaches can improve the efficiency of lipid structure and formulation screening by rapidly identifying key design parameters and employing predictive modeling to optimize LNP properties.

The anchor paper and official vignette identify AUCell as the regulon/gene-set activity scoring step used by SCENIC.

To address these limitations, we employ base-editing-mediated mutagenesis followed by several rounds of functional selection and screening. This directed protein evolution generates several gain-of-function OsTIR1 variants, including S210A, that significantly enhance the overall degron efficiency.

We also incorporate strategies for iterative biopanning and bioinformatic refinement to improve sensitivity and accuracy.

Here, we developed BlueGENEs, a set of optimized optogenetic gene switches.

High-signal enrichment leads found around this anchor cluster into ... opsin-engineering papers explicitly tied to SGN/oCI performance, especially CatCh, Chronos, and red-shifted Chrimson-family work.

Additional high-signal leads cluster into four enrichment themes explicitly aligned to that scope... ectonucleotidase control via CD39 and CD73.

Additional high-signal leads cluster into four enrichment themes explicitly aligned to that scope... ectonucleotidase control via CD39 and CD73.

Cell-free protein synthesis (CFPS) has been used as a transformative technology in synthetic biology, providing a programmable, scalable, and automation-compatible platform for biological engineering.

We overcame this challenge using methods based on compressed sensing to efficiently determine the roles of individual neuron types in learned avoidance behavior.

Personalization using advanced technologies like CRISPR screening and single-cell RNA sequencing can enhance durability and effectiveness of treatments for heavily pretreated patients

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.

Data-driven AAV engineering, integrating machine learning and high-throughput screening, has significantly accelerated the development of next-generation vectors.

This review summarizes current evidence on mRNA melanoma vaccines, focusing on two leading delivery platforms: lipid nanoparticles (LNPs) and dendritic cell (DC) vaccines.

Flash nanoprecipitation (FNP) has emerged as a transformative technique in the preparation of nanoparticles for targeted drug delivery.

FLP/FRT and CRISPR/Cas9 homology-directed repair (HDR) strategies, as well as their combinations, are currently the most effective for SSTI in maize.

Here, we report on the discovery of ligands for the DNA binding domain of MITF, using fragment-based screening (FBS) by nuclear magnetic resonance (NMR).

Here, we present a novel formulation to calculate genetic Minimal Intervention Sets, gMISs, which incorporate both gene knockouts and knock-ins.

The anchor paper and PubMed record explicitly describe GENIE3 as the co-expression/network inference component used in SCENIC.

This review summarizes current research on innovative molecular approaches, including... genomic selection (GS)... for soybean improvement.

We compared three manufacturing methods for diclofenac-loaded liposomes: probe sonication, microfluidic mixing, and a high-turbulence microreactor.

By delivering light into deep tissue via these devices, novel applications including biological sensing, stimulation and therapy can be realized. Therefore, implantable fibers ... in biocompatible formats with versatile functionalities are highly desirable.

We also incorporate strategies for iterative biopanning and bioinformatic refinement to improve sensitivity and accuracy.

lentiviral delivery of pegRNAs, ensuring robust, ubiquitous, and sustained expression of both prime editors and pegRNAs

Here, we present LncExpDB 2.0 ... with significant updates and enhancements

Low-Intensity Focused Ultrasound Stimulation (LIFU) is a noninvasive and nondestructive neuromodulatory method with growing evidence for the safe and effective treatment of chronic pain.

Low-intensity transcranial ultrasound stimulation (LITUS) is an emerging non-invasive neuromodulation technique for pain treatment, with the unique ability to modulate deep brain nuclei associated with pain.

Finally, we emphasize the critical value of integrating high-dimensional tools such as spatial transcriptomics, single-cell profiling, and machine learning to refine ACT design, identify biomarkers of response, and support patient selection and stratification.

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.

This review summarizes current research on innovative molecular approaches, including marker-assisted selection (MAS)... for soybean improvement.

Microfluidics has emerged as a set of powerful tools that have greatly advanced some areas of biological research, including research using C. elegans... provide guides for the design, fabrication, and use of microfluidic devices for C. elegans research studies.

We compared three manufacturing methods for diclofenac-loaded liposomes: probe sonication, microfluidic mixing, and a high-turbulence microreactor.

Additionally, we summarize recent applications of cutting-edge technologies in the enhancement of heat-tolerant rice varieties, including multi-omics integration, CRISPR/Cas9 genome editing, marker-assisted selection (MAS), and rational design breeding.

This force is generated by Epsin-mediated endocytosis of the ligand into the signal-sending cell and results in the extracellular cleavage of the force-sensing negative regulatory region (NRR) of the receptor by an ADAM10 protease on the signal-receiving cell.

Here, we introduce nf-core/crisprseq, a Nextflow DSL2 pipeline for the assessment of CRISPR gene editing and screening assays. The workflow is written in a modularized fashion to allow the easy incorporation of new steps.

Additional high-signal enrichment leads cluster into: (1) foundational optogenetic condensate tool papers, especially Cry2-based optoDroplets

The web research summary states that the anchor paper explicitly names Optopatch as the coexpression vector/platform enabling cross-talk-free genetically targeted all-optical electrophysiology.

The supplied web research summary states that organoid-on-chip and microfluidic integration are strongly supported enrichment themes repeatedly linked to this review topic, and explicitly lists organoids-on-chip as a related item candidate.

Emerging therapeutic strategies aim to counteract these processes through antisense oligonucleotide-mediated splicing correction, pharmacologic modulation of splicing regulators, and isoform-selective antibody or CAR-T designs.

stable genomic integration of prime editors via the piggyBac transposon system

Of particular importance is the polymer encapsulated nanoparticles containing ... fluorogens with aggregation induced emission (AIE) characteristics as the core, which have shown significant advantages in terms of tunable brightness, superb photo- and physical stability, good biocompatibility, potential biodegradability and facile surface functionalization.

Of particular importance is the polymer encapsulated nanoparticles containing conjugated polymers (CP) ... as the core, which have shown significant advantages in terms of tunable brightness, superb photo- and physical stability, good biocompatibility, potential biodegradability and facile surface functionalization.

Polymer encapsulated organic nanoparticles have recently attracted increasing attention in the biomedical field because of their unique optical properties, easy fabrication and outstanding performance as imaging and therapeutic agents.

We compared three manufacturing methods for diclofenac-loaded liposomes: probe sonication, microfluidic mixing, and a high-turbulence microreactor.

The review explicitly centers optogenetic/all-optical electrophysiology for phenotypic screening, especially the Optopatch platform pairing CheRiff with QuasAr voltage indicators.

Additionally, we summarize recent applications of cutting-edge technologies in the enhancement of heat-tolerant rice varieties, including multi-omics integration, CRISPR/Cas9 genome editing, marker-assisted selection (MAS), and rational design breeding.

The anchor paper and official package documentation identify RcisTarget as the motif-enrichment and direct-target pruning component within SCENIC.

We developed REDAC, a web-based R application that offers an interactive platform designed to simplify and enhance RNA-seq expression data exploration and analysis.

The review discusses the prospects of using rhodopsin as an optogenetic tool for prosthetics of degenerative (blind) eye retina.

We present SCENIC, a computational method for simultaneous gene regulatory network reconstruction and cell-state identification from single-cell RNA-seq data.

We evaluate accumulation and degradation kinetics of mRNA encapsulated in Selective Organ Targeting (SORT) LNPs in the liver, lung, and spleen

we introduce sherpabodies, engineered from a human SH3 domain scaffold, as a class of antibody-mimetic proteins capable of precise tumor-associated antigen (TAA) recognition

Additional high-signal enrichment leads cluster into four useful categories: foundational CALI methodology, mechanistic papers explaining ROS-mediated inactivation, genetically encoded photosensitizer/tool-development papers (notably KillerRed, miniSOG, SuperNova), and representative application papers in neurons, mitochondria, nuclei, and whole-animal cell ablation.

We demonstrate the toxicity of CRISPRa vectors expressing the activation domains (ADs) of the transcription factors p65 and HSF1, components of the synergistic activation mediator (SAM) CRISPRa system.

Synthetic suppressor T cells are a customizable platform to potentially treat autoimmune diseases, organ rejection, and CAR T cell toxicities with spatial precision.

Key points such as patient selection, skull density ratio, monitoring, thermal effects and tractography are discussed.

High-signal enrichment leads include earlier domain reviews that frame psychiatric LIFU/tFUS and summarize human parameterization. Explicitly supported related component/tool names in discovered sources include transcranial focused ultrasound/transcranial ultrasound stimulation (tFUS/TUS).

From screenings of more or less specific candidates to broader studies based on transcriptome analysis, our understanding of the genetic control behind LTM has expanded exponentially in the past years.

we introduce TripleMatcher, which searches for a triple-helix pattern, filters candidates by C1'-C1' distance thresholds, and merges overlaps into region-level zones

we also summarize recent developments in zebrafish genetics and small molecule screening, which markedly enhance the disease modelling and the discovery of novel drug targets.

The zebrafish (Danio rerio) is increasingly utilized as a powerful animal model in neuropharmacology research and in vivo drug screening... we also summarize recent developments in zebrafish genetics and small molecule screening, which markedly enhance the disease modelling and the discovery of novel drug targets.