Computational Design

Adeno-associated virus (AAV) is a viral delivery harness used to package and express CRISPR genome-editing components in vivo. In the cited literature, AAV supports single-vector delivery when smaller Cas9 orthologues and their chimeric guide RNAs fit within AAV packaging constraints, enabling robust in vivo genome editing.

Chimeric antigen receptor natural killer (CAR-NK) cells represent a promising "off-the-shelf" alternative to CAR-T cells.

Next-generation CAR designs, such as cytokine-armed CAR-T cells, may enhance T cell infiltration and persistence despite the suppressive TME.

Subsequently, we delve into cutting-edge applications of nanoparticles to enhance immune protection, including mosaic and cocktail nanoparticle vaccines, surface-modified targeting strategies, and the integration of mRNA technology with virus-like particles (VLPs).

AsLOV2 is the light-oxygen-voltage 2 photosensory domain from Avena sativa phototropin 1 used as a blue-light-responsive actuator in engineered fusion proteins. Blue-light activation drives allosteric conformational extension involving sequential unfolding of the N-terminal A'α helix and the C-terminal Jα helix, enabling conformational uncaging and related optogenetic control.

This review examines recent advancements in nanoparticle( s) (NPs) delivery systems, with a focus on ... lipid nanoparticles (LNPs)... We discussed various NP platforms and their applications, such as ... dry powder formulations of mRNA-loaded LNPs for pulmonary delivery, and LNP-mediated siRNA delivery for respiratory infections.

Deep brain stimulation (DBS) is an established neuromodulation method used as an add-on treatment for severe Parkinson's disease and other chronic neurological conditions. In the cited review, DBS is presented primarily as the clinical benchmark for comparison with optogenetic neuromodulation.

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

The CRISPR/Cas9 system is a multi-component genome engineering platform derived from a bacterial defense system that uses Cas9 and guide RNA to manipulate genomic loci in living cells. It has been widely adopted for mutagenesis and genome research, with reported applications spanning basic biology, biotechnology, agriculture, medicine, epigenetic perturbation, and disease models.

Engineered cellular therapies include chimeric antigen receptor T (CAR-T) cells

DNA nanostructures, such as DNA origami, provide nanoscale spatial precision for regulating receptor valency and oligomerization.

UNC10245092 is a previously identified linear peptide inhibitor that binds calcium and integrin binding protein 1 (CIB1). It has been used as a reference peptide in structural and in silico studies of CIB1-targeting decoy peptide design.

CRISPR/Cas9 is a bacterial type II genome editing system repurposed as a programmable nuclease for target DNA cleavage and site-specific genome modification. The supplied evidence states that it was engineered for gene editing in mammalian cells by 2013 and is used to interrupt gene expression through cleavage of target DNA.

iLID/SspB is a blue-light-inducible heterodimerization system built from an engineered iLID module and the SspB binding partner. It is used to reversibly recruit proteins in cells for control of localization and signaling, including membrane recruitment, neurotrophin receptor construction, microtubule plus-end targeting, and perturbation of small GTPase pathways.

Various CRISPR delivery systems, including viral vectors, nanocarriers, and extracellular vesicles, play crucial roles in the effective access of this tool to neural cells.

Functional magnetic resonance imaging (fMRI), exploiting the blood oxygen level-dependent (BOLD) contrast, is the most widely used technique to study brain function. Combined with tools from biotechnology, molecular biology, and genetics, preclinical fMRI offers unparalleled opportunities to experimentally test causal hypotheses that are beyond the reach of human research.

Key methodological parameters such as adeno-associated virus (AAV) serotype, actuator drug, dose, and application routes were investigated by measuring the food-intake-reducing effect of chemogenetic inhibition of the lateral hypothalamus (LH) by hM4D(Gi) designer receptor stimulation.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

PpSB2-LOV is a compact "short" light, oxygen, voltage (LOV) photosensory protein from Pseudomonas putida KT2440. It forms a light-induced LOV photoadduct and exhibits rapid dark-state thermal recovery, with a reported recovery time of 3.5 min at 20 °C, making it a candidate building block for genetically encoded photoswitches.

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

PMC text for the anchor paper explicitly states that intraneural AAV6-hSyn-SwiChR-eYFP expression enabled transdermal optogenetic inhibition and sustained post-light inhibition of pain behaviors.

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.

Genetic code expansion is an engineering method that enables incorporation of non-physiological amino acids into proteins. In the supplied evidence, it was used to design efficient incorporation systems in Bacillus subtilis and to generate a Cas9 variant that became full-length and active in cultured somatic cells only after BOC exposure.

The split Cas9 logic gate is a synthetic multi-component circuit that uses split Cas9 halves to sense biological events through conditional reconstitution of Cas9 activity. In the reported 2023 implementation, self-assembling inteins reconstituted split Cas9 and enabled reporter activation only when specified transcriptional or cell-state inputs were present.

AcrIIC3-LOV2 is an engineered light-switchable anti-CRISPR protein formed by fusing the Neisseria meningitidis Cas9 inhibitor AcrIIC3 to the Avena sativa LOV2 blue-light sensory domain. In mammalian cells, two reported hybrids strongly inhibit NmeCas9 in the dark and allow robust genome editing under blue-light irradiation.

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.

We selected a clone, designated CardioProtect, whose sensitivity was optimized to detect human AMI-relevant cTnI levels.

Single exosomes are detected via surface-enhanced Raman scattering (SERS) due to electromagnetic field accumulation on a specially designed flexible metasurface.

Lastly, a human designed MORp (hMORp) efficiently transduced macaque cortical OPRM1+ cells.

AAV2-hSyn-hM3Dq-mCherry, a viral vector that has been shown to preferentially transduce LDAFs

Adeno-associated virus (AAV) particles were used as a delivery harness for the BphP1-QPAS1-based TA optogenetic system in neurons. In the cited ChemBioChem study, this application was enabled by the small size of the QPAS1 component.

Based on the developed PABs, we present the inducer-free allulose-mediated auto-inducible protein expression system.

The alpha-helical domain linker is a construct pattern in which a rigid alpha-helical segment is placed between fused protein domains to couple their functions. In the cited design context, it is proposed to act as a helical allosteric lever arm that transmits conformational information between domains.

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 Anderson-Darling test is a nonparametric computational method applied in genome-wide association studies of complex quantitative traits. In an enlarged maize association panel, it identified loci across 17 agronomic traits, including both previously known loci and additional candidate loci detected only by this test.

Emerging therapeutic strategies aim to counteract these processes through antisense oligonucleotide-mediated splicing correction

Artificial Intelligence (AI)-have emerged as transformative tools to accelerate nanocarrier design and optimise their properties... AI-driven models accelerate the discovery of lipid-based nanoparticle formulations by analysing vast chemical datasets and predicting optimal structures for gene delivery and vaccine development

This Bayesian computational approach is a data-analysis method developed to improve prediction of split protein behavior by contextualizing errors inherent to experimental procedures. In the cited study, it was applied to pooled, sequencing-based screening data from split Cre recombinase constructs generated with optogenetic dimers, enabling comprehensive analysis of split sites across the protein.

The binding equilibrium model is a computational modeling approach used to quantitatively describe how proteins partition into engineered synthetic condensates. In the reported synthetic membraneless organelle framework, it supports prediction of condensate composition based on affinity-dependent recruitment.

Recently, several novel resistance strategies, including the bioengineering of immunoreceptors... have enabled the customized development of disease resistance traits.

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.

BROAD is a computational protein design method that combines Rosetta-based structure modeling, machine learning, and integer linear programming to improve design search beyond Rosetta sampling alone. It was demonstrated in antibody design to increase the predicted HIV neutralization breadth of VRC23 across a panel of 180 divergent viral strains.

This review systematically introduces the concept of CAR-b3b4 T cells as programmable innate immune sentinels.

its cognate stem-loop RNA (Cas6 binding site, termed CBS)

Caspase-2 active-site mutants are engineered variants of human Caspase-2 designed in silico to broaden substrate recognition at the substrate N-terminal amino acid position. In vitro experiments confirmed that two proposed mutants showed enhanced promiscuity, including increased recognition of branched amino acids relative to unmutated Caspase-2.

CARs capable of secreting enzymes, such as catalase to reduce oxidative stress in situ

Cell-free systems (CFSs) have become powerful tools in synthetic biology, enabling the creation of fast, modular, and customizable biosensors without relying on living cells.

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.

CIB1-targeting decoy peptides are computationally modeled peptide variants intended to bind calcium and integrin-binding protein 1 (CIB1) and inhibit its function. A 2023 in silico study reported that top-ranked second-generation mutant peptides had greater predicted inhibitory potential than the reference peptide UNC10245092.

This review systematically evaluates several spatial engineering platforms for biocatalytic process control... and scaffoldless assemblies (membraneless organelles and coacervates)-designed to reconfigure metabolic landscapes in cellular or cell-free contexts.

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)

This computational design strategy combines in silico design with biophysical experiments to improve the response kinetics of protein conformational switches. In the cited 2018 Nature Communications study, it was applied to an engineered protein-based Ca2+ sensor and rationally accelerated its response into the range of fast physiological Ca2+ fluctuations.

Computational protein design is an engineering methodology described in a 2018 review as a next-generation tool for expanding synthetic biology applications. The supplied evidence frames it as a design approach used alongside phage display and high-throughput binding assays rather than as a single molecular reagent.

Conventional replica exchange molecular dynamics (REMD) is a molecular simulation method used for statistical sampling of biomolecular conformational ensembles. In the cited evidence, it functions as the benchmark comparator against two coarse kMC-based replica exchange methods.

Designed decoy peptides targeting CIB1 are in silico engineered variants of the reference peptide UNC10245092 generated by residue scan methodology to bind CIB1. In the reported computational study, top candidates were prioritized by predicted binding free energy, evaluated by AMBER molecular dynamics simulations, and were predicted to interfere with RAF–CIB1 binding; mutant 2 showed stronger predicted interactions with CIB1 than the reference peptide.

Directed evolution is an engineering method that improves biological tool performance by iteratively selecting functional protein variants. In the cited split fluorescent protein study, it was demonstrated as one of two approaches used to improve split fluorescent proteins, contributing to brighter split sfCherry3 variants.

Here, we describe an inducible and drug-selectable acoustic reporter gene system that can enable gas vesicle expression in mammalian cell lines, which we demonstrate using HEK293T cells.

DUAL CARs ... are some of the most advanced instances.

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).

Dynamic multiplexing is a computational design principle for synthetic gene networks that encodes and decodes time-varying inputs into distinct gene expression states. In the cited 2021 study, it increased information transmission from signal to gene expression and enabled dynamic signal decoding using engineered regulators with different response kinetics.

The elastic network model (ENM) is a computational method for analyzing protein structural dynamics from an elastic network representation. In the cited PAS domain superfamily study, ENM was used to quantify residue fluctuations and vibrational patterns and to relate these dynamic features to sequence conservation, structural features, and biological function.

Engineered bacteriophages are emerging as a promising class of precision antimicrobials... Advances in synthetic biology and nanotechnology have made it possible to redesign phages with enhanced specificity, expanded functionality, and improved stability, positioning them as versatile tools for microbiota-centered therapies.

Through the integration of computational structural biology and enzyme channel engineering, this study successfully elucidated the key intermediates in the stepwise hydroxylation-cleavage catalytic process of Digitalis purpurea-derived DlCYP87A enzyme. Building on this foundation, we implemented structure-guided rational design to precisely engineer the substrate channel and catalytic pocket.

Engineered virus-like particles (eVLPs) have emerged as a promising class of delivery systems for genome editing agents.

The Escherichia coli-based biosensor harbors a plasmid-based fusion of a gene promoter, acting as the sensing element, to a microbial bioluminescence gene cassette as the reporter.

Exo-nanomaterials, hybrids that fuse EV membranes with synthetic cores, aim to unite EV biocompatibility and trafficking with the loading capacity, modularity and stimulus-responsiveness of engineered nanomaterials.

Feedback linearisation control is an engineering control method designed to regulate an in-wheel motor drive system. In the cited study, it is implemented within a DSP-based control architecture for a light electric vehicle drive using a six-phase permanent magnet synchronous motor.

Fernando's model is a computational model of a synthetic molecular circuit designed to mimic Hebbian learning in a neural network architecture. It is described as one of the earliest models in this area to use Hill equation-based regulatory modeling, and computational analysis indicated that a reinforcement effect can be obtained with appropriate parameter choices.

The biosensors (termed FLIPs) offer an extremely simple design, high sensitivity, multiplexing capability, ratiometric readout, and other advantages, without requiring modifications to their targets.

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.

Free-energy calculations are an in silico prediction method used in the rational design of human Caspase-2 mutants. In the cited study, they were applied alongside sequence and structural comparisons of Caspase-2 and Caspase-3 to predict effects of active-site mutations on substrate recognition and to support engineering of broader amino-acid acceptance.

Here, we design and fabricate a frequency-adjustable ferroelectric heterojunction based on the developed K0.5Na0.5NbO3 piezoelectric ceramics...

NoV Virus-like particles (VLPs) composed of the major capsid protein VP1 (~60 kDa) are essential for vaccine development... VP1 from four epidemiologically relevant GI genotypes was expressed using the silkworm-baculovirus system.

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.

heparanase to promote infiltration by degrading the extracellular matrix

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.

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

The inducible gRNA (gRNAi) AAV vector is an adeno-associated viral construct that places a CRISPR guide RNA under an H1/TO promoter and co-expresses Tet repressor (TetR) for doxycycline-dependent control of gRNA expression. In the cited 2016 study, related H1/TO and U6/TO promoter configurations supported doxycycline-dependent DNA editing in vitro, and the system was described for inducible in vitro and in vivo genome editing.

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.

Integrated Classification Pipeline (ICP) is a computational method developed to decompose and categorize CRISPR/Cas9-generated mutations at genomic target sites in complex multicellular insects. It classifies mixed DNA double-strand break repair outcomes, including non-homologous end joining and homology-directed repair events within the same samples.

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.

The development of KEAP1-recruiting PROTACs utilizing ligands derived from different classes of known KEAP1 inhibitors-including short peptides, covalent small molecules (e.g., CDDO derivatives), and non-covalent inhibitors (e.g., KI696)-is discussed.

Likelihood maximization analysis is a computational method for selecting reaction coordinate models for individual substeps of a conformational transition and inferring tentative transition states. In the cited application, it was applied to transition path sampling data from explicit-solvent molecular dynamics of the millisecond partial unfolding transition in the photoactive yellow protein photocycle.

Linkage disequilibrium mapping is a computational genetic association method used here in Arabidopsis thaliana to connect natural CRY2 sequence variation with flowering-time phenotypes. In the cited study, it identified strong haplotype-phenotype associations under short-day photoperiod and implicated a candidate serine substitution linked to early flowering.

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

An ingenious logic DNAzyme system consists of Chain 1 (C1)/Chain 2 (C2) and endogenous lncRNA is designed.

This review systematically evaluates several spatial engineering platforms for biocatalytic process control... and scaffoldless assemblies (membraneless organelles and coacervates)-designed to reconfigure metabolic landscapes in cellular or cell-free contexts.

Innovations in AAV engineering, such as capsid modification (chemical conjugation, rational design, directed evolution), self-complementary genomes, and tissue-specific promoters (e.g., MHCK7), enhance muscle tropism while mitigating immunogenicity and off-target effects.

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 mixed linear model (MLM) is a computational genome-wide association study method applied in an enlarged maize association panel. In the cited 2014 study, MLM identified ten loci across five agronomic traits at a Bonferroni-corrected significance threshold of -log10(P) > 5.74.

Concurrently, advanced immune cell therapies, including modified natural killer (NK) cells and CAR-T cells, are being designed to eradicate tumor clones that evade standard therapeutic approaches.

Molecular dynamics simulations combined with Markov state modeling were used to characterize blue-light-induced conformational switching in the Avena sativa LOV2 (AsLOV2) domain. This computation method resolved C-terminal Jα-helix unfolding into seven structurally distinguishable steps spanning initiation and post-initiation phases.

Molecular dynamics is a computational method used to study signaling mechanisms of LOV domains through simulation-based analysis. In the cited literature, it functions as an in silico approach for mechanistic investigation rather than as a biological reagent or genetically encoded tool.

Monte Carlo Tree Search (MCTS) is a computational search method used to identify an optimal program within a discrete program space. In the cited approach, it operates over a domain-specific language and associated transformation rules to construct candidate programs.

Lipid nanoparticles (LNPs)-validated for potency and safety in COVID-19 mRNA vaccines-offer a versatile, scalable, and immunogenic platform.

Key developments include multi-antigen and logic-gated CAR designs to mitigate tumor immune evasion.

Nanofiber scaffold has built a bionic microenvironment for bone marrow mesenchymal stem cells by highly simulating the topological structure of natural extracellular matrix.

Antibody-based interventions primarily involve inducing broadly neutralizing antibodies (bNAbs) through native-like envelope (Env) trimer vaccines

A non-linear disturbance observer (NDO) is an engineering control method used within a feedback linearisation framework to estimate lumped uncertainty. In the cited in-wheel motor drive study, it was implemented as part of a DSP-based intelligent control system for a six-phase permanent magnet synchronous motor.

PACE (Phage Assisted Continuous Evolution) is an engineering method used in this study to evolve cryptochrome properties. In the cited work, it was applied to increase the dynamic range of the blue-light-dependent interaction between Arabidopsis thaliana CRY2 and BIC1.

First, we developed a constitutive excitatory synapse ablator, PFE3, analogous to the inhibitory synapse ablator GFE3. PFE3 targets the RING domain of the E3 ligase Mdm2 and the proteasome-interacting region of Protocadherin 10 to the scaffolding protein PSD-95, leading to efficient ablation of excitatory synapses.

Poly-transfection is a transfection-based engineering method for rapid, one-pot characterization and optimization of genetic systems within a single readily prepared transfection sample. It was reported as a high-throughput alternative for comprehensive evaluation of genetic systems and was applied to CRISPRa and synthetic miRNA systems.

This computation method is a predictive design framework for transcriptional programs reported in Performance Prediction of Fundamental Transcriptional Programs. It uses experimentally characterized single-input logical operations and associated metrology to model and predict the performance of more complex compressed transcriptional logic programs, including two-input AND, NOR, and mixed-phenotype NIMPLY operations.

Recently, several novel resistance strategies, including... protease-triggered resistance design... have enabled the customized development of disease resistance traits.

It enables a 20-fold increase in sensitivity, reducing the EC50 of PsiR-allulose biosensors (PABs) from 16 mM to 0.8 mM, and delivers a PAB box possessing the detection range from 10 bcM to 100 mM.

Pulsatile-signal filters and decoders are synthetic gene-network constructs generated by combining a demultiplexer with dCas9-based regulatory networks. They are designed to decode complex dynamic input patterns, including pulsatile signals, into differential gene-expression outputs.

The quantitative mathematical model is a computational design method used to guide the combination of synthetic biology-derived functional modules within a polymer framework. In the cited biohybrid materials system, this model-supported design enabled light pulse-counting behavior linked to distinct molecular outputs.

This quantitative model is a computational analysis component used in a 2013 study of multi-chromatic optogenetic control of mammalian gene expression and signaling. It was applied to determine critical system parameters for the reported light-responsive expression platform.

Rationally designed PopZ mutants are engineered variants of the bacterial condensate-forming protein PopZ in which sequence changes in a disordered domain are used to alter condensate behavior. Reported evidence indicates that these variants tune condensate function and that PopZ can be repurposed as a modular platform for synthetic condensates in human cells.

We engineered BLU-VIPR around... ribozyme-flanked gRNA. The BLU-VIPR design is genetically encoded and ensures precise excision of multiple gRNAs from a single messenger RNA transcript.

Self-assembling peptidic hydrogels are uniquely suited for this setting because their molecular programmability, supramolecular order, and tissue-conforming mechanics enable both precision drug delivery and immune modulation.

Innovations in AAV engineering, such as capsid modification (chemical conjugation, rational design, directed evolution), self-complementary genomes, and tissue-specific promoters (e.g., MHCK7), enhance muscle tropism while mitigating immunogenicity and off-target effects.

Recently, several novel resistance strategies, including... the sentinel approach, have enabled the customized development of disease resistance traits.

The simple self-assembly model is a computational method for active mixtures of microtubules and molecular motors. It captures the extensile-to-contractile transition by representing competition between nematic and polar aligning interactions that drive formation of bundles or asters.

Single cell-based analysis is a quantitative cellular assay framework developed to compare the activities of overexpressed full-length guanine nucleotide exchange factors in primary human endothelial cells. It was applied with single-cell FRET Rho GTPase biosensors to measure GEF-driven activation of Cdc42 and Rac1.

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

Single-headed kinesin molecular motors with optically enhanced clustering are engineered motors for microtubule-based active fluids that allow light-dependent control of extensile active stress. In the reported system, they support precise and repeatable spatiotemporal patterning of activity and rapid, reversible switching between flowing and quiescent states.

By designing MMs' split rings with luxuriant gaps, the biosensor achieves a theoretical sensitivity of ~328 GHz/RIU, enabling sensitive responses to suspended cells.

we reconstructed artificial TA pairs termed SRTS-OPRTS. A platform for generating orthogonal SRTS-OPRTS pairs with cross-species application ... was developed

SwiftLib is a computational method for optimizing degenerate codon libraries using dynamic programming. It is designed to rapidly generate degenerate-codon-library designs and was reported to improve on an existing integer-linear programming formulation for this task.

Switched differential equations were developed as a computational framework to model oscillatory behavior of circadian clock cells in the Madeira cockroach. The model was used to interpret RNAi perturbation phenotypes and to support a hypothesis of coupled morning and evening oscillators linked by mutual inhibition.

The theoretical probability of neighbor density (PND) is a computational method introduced to discern protein oligomeric states in cellular environments. It is described as robust, precise, and adaptable for analyzing oligomerization scenarios spanning monomers to hexamers.

The three-stranded DNAzyme probe (TSDP) is a CRISPR/Cas9-inducible DNA construct engineered with a 20-bp Cas9 recognition site that suppresses DNAzyme activity until cleavage. It was developed for in situ imaging of nuclear Zn2+ in living cells and was further combined with photoactivation and Boolean logic control for spatiotemporal imaging.

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.

Translational AND gates are artificial mammalian gene circuit elements created by interconnecting Cas-mediated translational switches. They implement combinatorial logic at the level of mRNA translation using Cas proteins that repress or activate transcripts bearing Cas-binding RNA motifs in the 5'-UTR, and a set of 60 such AND gates was reported.

This study introduces a novel tubular mechanical metamaterial featuring a sign-switchable Poisson's ratio and tunable mechanical properties, achieved by integrating hexagonal unit cells with positive Poisson's ratio and re-entrant unit cells with negative Poisson's ratio.

Here we use rational protein design and directed evolution to develop two new ARGs that can be distinguished from each other based on their acoustic pressure-response profiles, enabling 'two-tone' ultrasound imaging of gene expression.

UNIVERSAL CARs, engineered to recognise multiple tumour antigens simultaneously, ... are some of the most advanced instances.

The yeast gene deletion library is a genome-scale collection of yeast deletion strains used to perform systems-level analysis of branched-chain alcohol toxicity. In the cited study context, it enabled identification of principles underlying sensitivity and tolerance in yeast.

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.

utilizing bacterial cellulose scaffolds to enhance the texture of both cultured meat and plant-based products; In parallel, bacterial cellulose provides highly biocompatible nanoscaffolds

Additionally, cells are engineered to express a designed calcium-responsive transcription factor controlling the expression of a selected therapeutic gene, constituting a therapeutic cellular device.

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

This study aims to explore the design and preparation of a dual-functional porous titanium alloy scaffold with antibacterial and bone repair capabilities, and to validate its application efficacy in infectious bone defects.

we introduce a dual-single-guide RNA design that places two cuts flanking the insertion site to create a geometry-matched strand-invasion window

sophisticated logic-gated circuits

Here, we consider the potential of macrocyclic peptides to overcome this limitation.

These regulatory mechanisms, such as transcription and translation control, could be integrated into hybrid circuits termed "multi-level circuits".

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

Recent advances, including in silico optimization, in vivo SELEX, BBB chip-based MPS-SELEX, and nanoparticle-aptamer hybrids, have identified brain-penetrating aptamers and enhanced the brain delivery efficiency.

Our method identified a new PKN substrate peptide that we optimized for use in a fluorescent biosensor design.

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

stapled peptide methodologies have evolved to a point where they can be used with confidence to generate therapeutic leads

The CRY2-CIB1 optogenetic PIP3 production system is a blue-light-responsive multi-component switch built from Arabidopsis CRY2 and CIB1. It recruits a CRY2-fused constitutively active PI3-kinase from the cytosol to the plasma membrane through light-induced CRY2-CIB1 interaction, enabling sub-second spatiotemporal control of PIP3 production.

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.

OptoBAX is an optimized light-activated Cry2-BAX multi-component optogenetic system developed for one-click initiation of the BAX-mediated apoptotic cascade. It is used to trigger outer mitochondrial membrane permeabilization and induce early apoptotic events with light.

Optogenetic networks are multi-component light-controlled genetic devices built from genetically encoded photosensitive proteins to regulate cellular behaviors and biological processes. They are developed to provide user-defined, minimally invasive, and spatiotemporally precise control for biomedical applications, including human disease therapy.

The synthetic optogenetic transcription device is a multi-component light-responsive signaling cascade that links melanopsin signal transduction to the nuclear factor of activated T cells (NFAT) control circuit to drive light-inducible transgene expression. It was reported to enable remote regulation of implanted transgenic cells in mice and to enhance blood-glucose homeostasis.

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.

Key advances discussed include the use of dominant-negative receptors (e.g., TGFβRII) to combat immunosuppression

Advances in genetic engineering, hybrid vesicle design, and nanotechnology have extended exosome applications to the delivery of CRISPR/Cas systems, chemotherapeutic agents, immunoregulatory RNAs, and vaccines, with liposome or nanoparticle integration enhancing targeting and efficacy.

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.

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.

This "evasion-to-solution" framework highlights how innovations such as dual-antigen CARs... directly mitigate known mechanisms that lead to therapeutic failure.

This "evasion-to-solution" framework highlights how innovations such as dual-antigen CARs, low-affinity designs, NK-specific signaling, iPSC-derived NK platforms, and multiplex gene editing directly mitigate known mechanisms that lead to therapeutic failure.

Next-generation approaches, including universal CAR-T cells and microenvironment-responsive designs, show promise in improving efficacy and safety.

This "evasion-to-solution" framework highlights how innovations such as dual-antigen CARs, low-affinity designs, NK-specific signaling, iPSC-derived NK platforms, and multiplex gene editing directly mitigate known mechanisms that lead to therapeutic failure.

Next-generation approaches, including universal CAR-T cells and microenvironment-responsive designs, show promise in improving efficacy and safety.

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.

we introduce norbornene-functionalized gelatin (GelNB) hydrogels crosslinked with a laminin-based peptide as a bioactive scaffold for NSC culture

We propose the concept of the virophore: a genetically or chemically encoded functional unit integrated into the structure of a virus particle that acts as a programmable structural switch, enabling reversible, triggerable reconfiguration in response to defined stimuli.

This question was answered by turning to radical chemistry and employing the known stabilization behavior of a bipyridinium radical cation and the bisradical dication, generated on reduction of the CBPQT(4+) ring, to pluck rings out of solution and thread them over the charged end of the pump portion of a semidumbbell. On subsequent oxidation, the pump is primed and the rings pass through a one-way door, given a little thermal energy, onto a collecting-chain where they find themselves accumulating where they would rather not be present.

Forging a path from molecular switches to motors involved designing a molecular pump prototype. An asymmetric dumbbell with a 2-isopropylphenyl (neutral) end and a 3,5-dimethylpyridinium (charged) end with a DNP recognition site to entice CBPQT(4+) rings out of solution exhibits relative unidirectional movement of the rings with respect to the dumbbell.

The supplied review scaffold highlights the emergence of the first human TB mRNA vaccine program, BioNTech's BNT164, and lists BNT164 as an explicitly supported related item candidate.

Explicitly supported related components/tools include HIV-protective engineering features (CCR5-locus knock-in, C34-CXCR4). Relevant for extraction of cell-intrinsic protection modules co-expressed with antiviral CARs.

Explicitly supported related components/tools include HIV-protective engineering features (CCR5-locus knock-in, C34-CXCR4). Supported as a genome-editing integration site for HIV-protective CAR-T designs.

The development of constrained peptides represents an emerging strategy to generate peptide-based PPI inhibitors, typically mediated by α-helices.

CRISPR is a widely used engineering method for targeted RNA and DNA manipulation across multiple organisms. The cited review highlights its use for viral genome manipulation, including gene knock-in and gene knock-out, and for precise diagnosis of viral infections.

Domain fusion is a protein engineering method in which protein domains are fused or split to improve existing protein functions or create novel functions. In the supplied evidence, it is described as a general strategy for expanding CRISPR-Cas9 applications.

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

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.

Gene knock-in is described in this review as a CRISPR-based genome engineering approach used for virus-targeted genetic manipulation. It is presented alongside sgRNA design and gene knock-out as an effective design strategy for making accurate changes in viral genetic material.

Gene knock-out is described in the cited review as a CRISPR-based engineering method for targeted genome manipulation, including virus-targeted manipulation through sgRNA design and knock-out strategies. The review places this method within broader RNA and DNA manipulation applications across multiple organisms.

Genome engineering is described in the cited review as a complementary engineering method that, together with progress in mammalian gene circuit design, may support the creation of tailored engineered mammalian cells for cell-based applications. The supplied evidence does not identify a specific genome engineering platform, molecular effector, or implementation.

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).

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).

Mathematical and statistical modelling is a computational design approach used in synthetic biology to improve the predictability of engineered biological systems. In the cited plant synthetic biology literature, it supports model-informed rational design for engineering plant gene regulation and metabolism.

Model-informed rational design is an engineering method in synthetic biology that uses models to guide the design of biological systems. In the cited plant context, it has been successfully applied to engineering plant gene regulation and metabolism.

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

This review provides a comprehensive overview of recent advances in the supramolecular organisation and hierarchical self-assembly of organo-functionalised hybrid polyoxometalates (hereafter referred to as hybrid POMs), and their emerging role as multi-functional building blocks in the construction of new nanomaterials.

Programmable genetic circuits are engineered genetic constructs used to create designer cells with controllable behaviors in mammalian synthetic biology. The cited literature describes circuits that can incorporate targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices to regulate complex cellular functions with high spatial and temporal resolution.

Protein splitting is a protein engineering method in which proteins are modified through domain fusion or splitting to improve existing functions or develop novel functions. In the provided evidence, it is discussed as a strategy relevant to expanding CRISPR-Cas9 applications.

Protein structure prediction is a computational method for inferring protein three-dimensional structure. In the supplied evidence, it is identified only as a topic covered in a 2019 review on advances in protein structure prediction and protein design.

Here, we review the recent literature dealing with the design and application of QD-bioconjugates for advanced in vitro and in vivo imaging.

Rational design is a protein engineering method used to improve or create novel protein functions. In the supplied evidence, it is discussed as one of the strategies used to expand CRISPR-Cas9 applications.

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.

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.

Hydrogels have become one of the most important scaffolds for tissue engineering due to their biocompatibility, biodegradability and water solubility. Especially, the stiffness of hydrogels is a key factor... Herein, this review focus on the design of hydrogels with different stiffness and their effects on the behavior of MSCs.

utilizing therapeutic or imaging agents-loaded stimuli-responsive block copolymer assemblies that are responsive to tumor internal microenvironments (pH, redox, enzyme, and temperature, etc.) or external stimuli (light and electromagnetic field, etc.) have emerged to be an important solution to improve therapeutic efficacy and imaging sensitivity through rationally designing as well as self-assembling approaches

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

This computation method is a bioinformatic analysis applied to protein components of the Saccharomyces cerevisiae ribosome assembly pathway. In the cited study, it compared ribosome biogenesis factors with ribosomal proteins and found that biogenesis factors contain significantly more predicted trans interacting regions.

This computation method is a mathematical model that integrates tissue mechanics into morphogen dynamics to quantitatively explain tissue-scale responses to BMP4 signaling in human gastrula models. In the cited study context, it was linked to BMP4-driven SMAD1-5 phosphorylation and amnion differentiation.

ML Int&in is a machine learning–guided computational design method for identifying unnatural split sites in the fast split inteins gp41-1 and NrdJ-1. In the cited preprint, these designs yielded functional split intein variants with reduced fragment affinity and supported blue-light-activatable protein splicing systems that controlled Cre recombinase in mammalian cells.

Rosetta is a molecular modeling program used for computational design of new protein structures and protein complexes. The cited evidence specifically attributes its design capability to rotamer-based sequence optimization protocols that support accurate design of protein tertiary and quaternary structure.

Countermeasures now integrate ... Domain III chimerization (e.g., Cry1A.105)

the anti-CD19 Fast-CAR, designed to shorten production time ... [is] regarded as very efficacious

The light-switchable condensate system is a genetically encoded, multi-component platform for blue light-controlled organization of functional cargoes in Escherichia coli. It couples a condensation-enabling scaffold to cargo proteins through the iLID/SspB light-responsive interaction pair to dynamically regulate cargo localization.

Accelerated MD simulation is an in silico computational method reported for elucidating the photoactivation mechanism of the AsLOV2 light-responsive domain. The available evidence supports its use as a mechanistic analysis approach for a protein photosensor rather than as a deployable biological reagent.

Activatable photosensitizers (aPSs) have emerged as a promising solution to this challenge. These smart agents are designed to remain inactive under normal physiological conditions and become activated only by disease-specific stimuli.

Here we report vibrational photochromism by engineering alkyne tagged diarylethene to realize photo-switchable SRS imaging.

The alkynyl-functionalized photocleavable linker is a construct pattern used in caged antisense morpholino reagents, in which an ethynyl-bearing photocleavable linker is coupled to an oligonucleotide. In the caged state it inhibits DNA binding, and brief 405-nm illumination restores antisense activity through linker photocleavage.

The Bayesian optimization framework is a computational method built from high-throughput Lustro measurements to guide control of blue light-sensitive optogenetic systems. It uses data-driven learning, uncertainty quantification, and experimental design to identify light induction conditions for multiplexed regulation in Saccharomyces cerevisiae.

Booster is a red-shifted genetically encoded FRET biosensor backbone generated by optimizing the order of fluorescent proteins and modulatory domains within a biosensor architecture. In the reported implementation, a Booster-PKA sensor enabled kinase activity readout in a spectral window compatible with CFP/YFP-based FRET biosensors and blue light-responsive optogenetic tools.

Caged guide RNAs are synthetic CRISPR guide RNAs containing photolabile nucleobase substitutions in the 5′ protospacer that enable light-activated control of Cas9 function. They were developed to conditionally regulate genome editing in mammalian cells and zebrafish embryos by suppressing guide RNA binding to target DNA until optical activation.

The CIB1-TALE fusion targeting the Ascl1 promoter is a locus-anchoring component of a blue-light-responsive epigenetic editing system. In combination with CRY2 fused to the catalytic domain of DNMT3A or TET1, it enables light-induced recruitment at the Ascl1 promoter and modulation of promoter methylation state and gene activity.

Closed loop optogenetic compensation (CLOC) is an engineering methodology that monitors pathway output in real time and computes an optogenetically driven transcriptional input to compensate for deletion of a feedback regulator. It was applied to the Saccharomyces cerevisiae pheromone response pathway to define the dynamic requirements of feedback control.

Component I is a 13,000-dalton phosphoprotein identified in frog rod outer segments that undergoes light-induced dephosphorylation. In the cited 1979 study, it was characterized as an abundant outer-segment-associated protein whose phosphorylation state changes as a function of illumination intensity.

Component II is a 12,000-dalton protein identified in frog rod outer segments that undergoes illumination-dependent dephosphorylation. Its phosphorylation state changes as a function of light intensity, with half-maximal and maximal responses reported over defined rhodopsin-bleaching rates.

CoTV is a multi-agent deep reinforcement learning system that cooperatively controls traffic light signals and connected autonomous vehicles in mixed-autonomy urban traffic scenarios. It was reported as a computational control method and evaluated in SUMO simulation.

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.

CRY2-DNMT3A-CD fusion is an optogenetic epigenetic editing component in which the photoreceptor CRY2 is fused to the catalytic domain of DNMT3A and used with a CIB1-TALE targeting partner. In the reported system, blue-light stimulation induced recruitment of DNMT3A-CD to the Ascl1 promoter, enabling locus-specific methylation changes and regulation of gene activity.

CRY2-TET1-CD fusion is an optogenetic epigenome-editing component in which the Arabidopsis CRY2 photoreceptor is fused to the TET1 catalytic domain and used with a CIB1-TALE targeting partner. In the reported system, blue-light illumination induced co-localization at the Ascl1 promoter and selectively altered local methylation state with associated regulation of gene activity.

Diya is a universal light illumination platform for multiwell plate cultures that is compatible with a wide range of cell culture plates and dishes. It provides programmable optical induction and has been used to drive light-controlled operation of an in vivo biomolecular feedback circuit.

The enzymatically crosslinked marine collagen-alginate hydrogel blend is an orthogonally crosslinked composite for visible-light-triggered, on-demand BMP-2 release. It combines microbial transglutaminase-crosslinked marine collagen with leachable alginate to generate microporosity, increase oxygen diffusion, and enhance osteogenic responses in dental pulp stem cells.

This tool is an experimental pipeline, together with new optogenetic reagents, for creating designer Nodal signaling patterns in live zebrafish embryos. It uses patterned light to impose synthetic Nodal activation states in vivo and control developmental signaling outputs.

CARs influenced or activated by external stimuli like light, heat, oxygen, or nanomaterials

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.

Here we report the design and development of two far-red fluorescent GECIs, FR-GECO1a and FR-GECO1c, based on the monomeric far-red fluorescent proteins mKelly1 and mKelly2.

Here we report the design and development of two far-red fluorescent GECIs, FR-GECO1a and FR-GECO1c, based on the monomeric far-red fluorescent proteins mKelly1 and mKelly2.

This tool is a generalised computational modeling technique for simulating optogenetic mechanisms in the NEURON environment. It was presented using channelrhodopsin-2 and halorhodopsin to model optical activation and optical silencing in neurons.

The I-BAR domain is used as a component of CRY-BARs, a family of light-gated I-BAR-domain-containing tools designed for remodeling membrane architecture. In this context, the domain contributes to optogenetic control of membrane-associated cellular dynamics and membrane protrusion-related processes.

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

The input reconstruction algorithm is a computational method used to infer prior light pulse inputs from cellular signaling outputs. In the cited MAPK/ERK communication study, it detected light pulses with 1-minute accuracy 5 minutes after their occurrence.

Intracellular spatially segregated reporters of optoPAK1 activity are genetically designed reporter constructs intended to report optoPAK1-dependent phosphorylation at defined intracellular locations. The available evidence indicates that they were created alongside the light-responsive PAK1 analog optoPAK1 to monitor its activity after light-triggered relocalization.

Among tested variants, the KCR1-C29D mutant shows a relatively high and the most stable K+ to Na+ permeability ratio during illumination. While other KCR variants often evoke excitatory responses, KCR1-C29D consistently provides robust in vivo inhibition across cell types, illumination conditions, and species.

LAVA is a set of engineered illumination devices for optogenetic photostimulation and light activation at variable amplitudes. It delivers user-defined light intensity, temporal sequences, and spatial patterns to control signaling responses, including optogenetic Wnt/beta-catenin pathway activation.

Light-Oxygen-Voltage (LOV) domains are small, light-responsive protein modules found in algae, plants, bacteria, and fungi that function as blue-light sensors controlling cellular responses to light. They are presented as a platform for constructing optogenetic tools that confer photoregulated control of cellular signaling.

Lustro is a high-throughput optogenetics platform for studying and controlling blue light-sensitive optogenetic systems. In the cited 2023 work, it was combined with machine learning to achieve multiplexed control of split transcription factor responses in Saccharomyces cerevisiae.

Markov State Modeling (MSM) is a computational method applied with molecular dynamics simulations to resolve conformational dynamics in the AsLOV2 photosensory domain. In the cited 2023 study, MSM was used to explain blue-light-induced stepwise unfolding of the C-terminal Jα-helix and to identify seven structurally distinguishable unfolding states spanning initiation and post-initiation phases.

This mathematical model is a computational method used to quantitatively analyze the kinetics of blue light-inducible and blue light-repressible gene expression in an EL222-based bidirectional promoter system in Escherichia coli. It describes expression dynamics under optical input in the context of a rapidly reversible bacterial optogenetic transcription system.

This tool is a mathematical modeling method used together with an optogenetically engineered cell line and custom hardware to optically re-create calcium oscillation patterns. It enables independent variation of a single calcium waveform component within reconstructed oscillatory inputs.

This tool is a mathematical model used to quantitatively analyze light-induced gene expression kinetics in a red/far-red light-responsive mammalian gene switch. It supports interpretation of how illumination drives expression dynamics in that optogenetic expression system.

MerMAIDs are a metagenomically identified, phylogenetically distinct family of anion-conducting channelrhodopsins. Their intense rapid desensitization during continuous illumination enables transient optogenetic silencing, including suppression of individual action potentials without preventing subsequent spiking.

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.

miRFP720 is a monomeric near-infrared fluorescent protein reported in the cited study as the most red-shifted monomeric NIR fluorescent protein. It functions as a fluorescent component for reporter construction that can be imaged with reduced spectral interference from visible-range probes and blue-green optogenetic tools.

MORp constructs designed from promoter regions upstream of the mouse Oprm1 gene (mMORp) were validated for transduction efficiency and selectivity in endogenous MOR+ neurons

Model bioinformatics analysis in this context is a computation-based analysis of Arabidopsis thaliana transcript expression responses to UV-B light, drought, and cold stress using the AtGenExpress global stress dataset. It interprets stress-responsive gene expression patterns across multiple abiotic conditions measured with the Affymetrix ATH1 microarray under standardized parallel protocols.

The multi-chromatic multi-gene control system is a combined optogenetic platform for mammalian cells that integrates UVB-, blue-, and red-light-inducible gene control modules. It enables differential induction of up to three genes within a single cell culture using distinct wavelengths and was applied to gene expression and signaling control.

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.

The optogenetic MAPK inhibitor is a reported construct design that uses light to inhibit MAPK signaling. In a 2017 Nature Communications report, this design was used to reveal resonance between transcription-regulating circuitry and temporally encoded inputs.

We present ORFannotate, a lightweight, GTF-native Python command-line tool that predicts ORFs from transcript annotations and reinserts precise, exon-aware CDS and UTR features into the original GTF/GFF file.

In addition, we developed a light-inducible version of GFE3, paGFE3, using a novel photoactivatable complex based on the photocleavable protein PhoCl2c. paGFE3 degrades Gephyrin and ablates inhibitory synapses in response to 400 nm light.

pcVP16 is a highly compact optogenetic regulator built by photo-controlling the VP16 transactivation peptide. It is described as a light-responsive construct for regulating transcriptional activation.

Photo-controlled VP16 transactivation peptide exposure regulators are highly compact optogenetic constructs that control exposure of the VP16 transactivation peptide with blue light. In the reported system, they were used as part of complementary platforms for blue-light-triggered termination of transcriptional activation and were incorporated into the LOOMINA toolbox.

Photoactivatable cyclic caged morpholino oligomers (ccMOs) are light-responsive antisense morpholino reagents engineered in a cyclic, caged format to suppress target binding until photoactivation. In the reported design, brief 405-nm illumination photocleaves the cage and restores antisense activity, enabling spatiotemporal regulation of gene expression.

QM calculations are a quantum-chemical computational method used to predict conformer energetics, rotational barriers, and infrared spectra of transient glutamine isomers in LOV photoreceptors. In EL222, AsLOV2, and RsLOV, these calculations were used to infer favored glutamine orientations along an assumed light-driven reaction path and to interpret transient infrared behavior.

Quantum chemistry is used here as a computational method to analyze the primary light-driven reactions of the LOV2 domain of phototropin. In the cited 2009 Biophysical Journal study, it is paired with ultrafast mid-infrared spectroscopy to investigate LOV2 photochemistry.

The radiative transfer equation is a computational method used to model light propagation in cylindrical mammalian cell culture bioreactors for optogenetic applications. In the cited 2023 study, it was applied to estimate whether incident light can penetrate dense cultures at production-relevant scales.

This tool is a reinforcement learning-based computational method for multi-intersection traffic signal scheduling that incorporates visible light communication (VLC) queuing, request, and response behaviors. It is described as part of a traffic management system integrating VLC localization services with learning-driven signal control.

The RhVI1 promoter is an 895 bp promoter fragment from Rosa hybrida Vacuolar Invertase 1 that mediates transcriptional responses to light, sugars, and gibberellins. A 468 bp subfragment is sufficient for reporter activation by these inputs, and a 127 bp region from -595 to -468 bp is critical for combinatorial regulation by light with sugar or gibberellin signals.

SOS-CIS(D) is a quantum-chemical excited-state calculation method used to compute vertical excitation energies. In the cited 2010 BLUF photoreceptor study, it was applied to model flavin-associated structural and spectral changes and to evaluate light-induced states.

SPI1085g3 is a red/green cyanobacteriochrome GAF domain from Spirulina subsalsa. It photoconverts from a red-absorbing dark Pr state to an orange-absorbing Po state, and the Pr state exhibits intense red fluorescence that is lost upon photoconversion and recovers through moderate dark reversion.

The tet-controlled riboregulatory module is a synthetic RNA regulatory element incorporated into a blue-light split T7 RNA polymerase-Magnets optogenetic system. In the supplied evidence, it functions as an added regulatory layer intended to improve circuit behavior in light-controlled gene expression.

Transition path sampling is a computational method applied to explicit-solvent molecular dynamics trajectories to extract atomistic features of conformational reaction networks. In the cited study, it was used to analyze the millisecond partial unfolding transition in the light-driven photocycle of photoactive yellow protein and to predict reaction coordinate models and tentative transition states.

The triangular DNA nano sucker (TDS) is a rationally designed UV light-responsive DNA nanostructure reported as a component of the composite nanoprobe UCNPs@TDS. In the cited study, it is paired with upconversion nanoparticles for light-controlled imaging.

As for the light-repressive translation system, the "triple brake" design successfully eliminated leakage and achieved light repression on protein synthesis without any impact on mRNA expression.

We highlight the following technologies: ... ultrasound-responsive nanoparticles...

An upconversion nanoparticle is used as a light-transducing component in an immunodevice that converts near-infrared input into activation of a UV light-activatable immunostimulatory agent. In the reported 2019 Nature Communications system, this enabled remote and spatially selective control of antitumor immunity in vitro and in vivo.

The UV light-activatable immunostimulatory agent is a rationally designed component of an upconversion nanoparticle-based immunodevice for optical control of antitumor immunity. In the reported system, the agent is activated by UV light, and coupling to an upconversion nanoparticle shifts effective triggering into the near-infrared window for remote activation in vitro and in vivo.

Complementary methods – mainly UV/visible single-crystal spectroscopy – have proven essential to design, interpret and validate kinetic crystallography experiments.

The wireless-powered optogenetic designer cell implant is a delivery harness reported in Nature Communications (2014) to enable mind-controlled transgene expression. The available evidence identifies a wireless-powered optogenetic implant concept coupled to transgene regulation, but does not provide construct-level or device-level detail here.

Here, we synthesize recent advances in cell design, dual/split CARs, switchable control systems, armored payloads and synthetic-biology circuits.

Here we report the validation and further development of the channelrhodopsin pore model via crystal structure-guided engineering of next-generation light-activated chloride channels (iC++)

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.

Here, we synthesize recent advances in cell design, dual/split CARs, switchable control systems, armored payloads and synthetic-biology circuits.

The benzoate-/vanillate-responsive mammalian gene switch is a dual-input transgene control system engineered for mammalian cells that is induced and repressed by the food additives benzoate and vanillate. It was also reported to function as a modular component in higher-order gene control networks and to regulate a SEAP reporter in implanted designer cells in mice.

The pharmaceutically controlled designer circuit is a synthetic multi-component signaling cascade activated by the clinically licensed antihypertensive drug guanabenz. In the reported system, guanabenz drives dose-dependent expression and secretion of a GLP-1-Fc(mIgG)-Leptin output relevant to metabolic syndrome treatment.

PmeR-OPmeR paraben-responsive mammalian transcription-control devices are engineered multi-component gene switches built from the bacterial repressor PmeR and its cognate operator OPmeR. They provide inducible or repressible control of transgene expression in mammalian cells and mice in response to paraben derivatives, including dose-dependent tuning.

The liquid-crystal-on-silicon spatial light modulator is an LCOS-based device engineered for phase-only optical modulation. It modulates incident light wavefronts with a phase range exceeding one wavelength and was developed for wavefront control applications including adaptive optics, optical manipulation, and laser processing.

CRISPR-DNAzyme is a three-stranded DNAzyme probe engineered for in situ imaging of nuclear Zn2+ in living cells. Its catalytic activity is initially blocked by a 20-bp CRISPR/Cas9 recognition site and is activated in the nucleus after Cas9/sgRNA cleavage forms the active DNAzyme structure.

The LOV2 domain from Avena sativa phot1 phototropin is a blue-light-responsive protein domain analyzed as an all-optical switching medium. In the cited theoretical study, a 442 nm pulsed pump modulates transmission of a 660 nm continuous-wave probe through LOV2 via nonlinear intensity-induced excited-state absorption.

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.

However, the design of hemisynthetic analogues and the use of micellar drug delivery systems should facilitate a broader utilization of the compound in human and veterinary medicines.

Milk proteins and peptides can also act as adjuvants for the design of more potent novel antiviral drugs.

Finally, we focus on the promise of redox proteomics and systems biology to help us fully understand the relationship between ROS and hypertension and their potential for designing and evaluating novel antihypertensive therapies.

PubMed abstract explicitly states the system is a β-hairpin tryptophan zipper equipped with non-canonical amino acids for femtosecond pump-probe VET measurements plus non-equilibrium MD and master-equation analysis.

In this review, we examine the principles behind the design and engineering of light-sensitive calcium actuators and modulators (designated LiCAMs) and the applications of representative LiCAMs in remote and noninvasive control of Ca2+-modulated physiological processes both in vitro and in vivo.

Through mechanistic decipherment of the photophysical processes, structural design strategies for generating new AIE luminogens are developed.

Bioreactor designs for optogenetic stimulation are light-delivery and culture-platform configurations used to stimulate optogenetic systems across experimental formats ranging from simple illumination set-ups to microscopy, microtiter plate, and bioreactor designs. These platforms support applications spanning single-cell stimulation to whole-culture illumination and can be integrated with automated measurement and stimulation for computer-controlled experiments.

The demand for more application-specific Channelrhodopsin variants started a race between protein engineers to design improved variants. Here, we review new variants whose efficacy has already been proven in neurophysiological experiments, or variants which are likely to extend the optogenetic toolbox.

Computational methods for LOV-based optogenetic tool development are design-enabling approaches used in the ongoing development of Light-Oxygen-Voltage domain-based optogenetic systems. The cited evidence supports a role for computational methods as one of several factors advancing LOV-based tools for light-controlled biological regulation.

This Review addresses the types and classifications of windows used in optical neuroimaging while describing how to perform in vivo studies using rodent models in combination with other experimental modalities during behavioral tests.

We focus primarily on designer GPCRs (receptors activated solely by synthetic ligands, designer receptors exclusively activated by designer drugs)

Genetically encoded fluorescent biosensors are biosensor constructs described as particularly well suited for studying signaling. In the cited review, many such biosensors have been designed to spatially and temporally resolve cAMP dynamics in cells.

Remaining challenges include brightness/photostability limits and the need for broader translational validation, yet progress in structure-guided mutagenesis, computational/AI-assisted protein design, and hybrid imaging strategies promises to close these gaps.

Biomaterial based surface ligands are designed and developed based on theoretical simulations. The hybrid nanobiomaterials satisfy anisotropic facet-selective coating, enabling effective compartmentalization beyond non-specific staining.

Hybrid protein optogenetics is an engineering method for introducing light regulation into proteins by fusing a protein of interest to photoreactive biological modules. It is presented in a 2022 review as one of three major strategies for targeted photocontrol of protein function.

Hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) is an assay method used to complement structural characterization of light-activated photoreceptors. It reports on protein conformational dynamics in solution and can probe multiple functionally relevant states.

In silico feedback control strategies are computationally implemented control schemes coupled to optogenetic measurement and light stimulation platforms. They are used to create computer-controlled living systems through automated measurement and stimulation workflows.

Light-activated GPCR control is an engineering approach that uses designer G-protein-coupled receptors activated by the physical stimulus of light. It is described as a way to control intracellular signalling cascades in cell- and receptor-type-specific manners.

Light-controllable designer cells are optogenetically engineered mammalian cells whose behavior is regulated by light. The available evidence supports their use as a precise and noninvasive control modality in therapeutic synthetic biology.

Light-dependent protein (un)folding reactions are an optogenetic engineering strategy for constructing novel photoreceptors by coupling light input to changes in protein folding state. The cited review presents light-dependent protein association and protein folding or unfolding reactions as reusable design principles for photoreceptor engineering.

Light-dependent protein association is an optogenetic engineering strategy in which light input is coupled to inducible protein-protein interactions to create novel photoreceptors. A 2018 Chemical Reviews article identifies it as one of the most important reusable design strategies for photoreceptor engineering.

Light-induction hardware-software platforms are optogenetic delivery systems that provide controlled illumination using formats ranging from simple illumination set-ups to microscopy, microtiter plate, and bioreactor designs. They are used to stimulate biological systems with light, and automated implementations can support computer-controlled experiments with in silico feedback control.

Light-regulated association reactions are an engineering design principle in photoreceptor-based systems in which illumination changes protein oligomeric state as part of light-regulated allostery. A survey of engineered photoreceptors identifies this principle as particularly powerful and versatile for constructing light-responsive tools.

Linker-mediated LOV fusion to enzyme target sites is a protein engineering strategy in which a LOV photoreceptor domain is fused to functional sites within an enzyme effector using an appropriate linker. The reported goal is to retain effector functionality while enabling light-dependent modulation of enzyme activity, thereby creating light-controllable biocatalysts.

LOV-based optogenetic devices are engineered tools built from small, light-responsive LOV modules to confer photoregulated control of cellular signaling. The supplied evidence supports their role as a general platform for optogenetic tool construction but does not specify individual device architectures or target proteins.

This computational method compares and meta-analyzes transcriptomic datasets generated after manipulation of ethylene levels or signaling under varying light conditions. It is used to identify ethylene-responsive transcriptional programs that are light-dependent versus light-independent.

Microscopy designs for optogenetic stimulation are light-delivery platform configurations that range from simple illumination set-ups to sophisticated microscopy, microtiter plate, and bioreactor designs. These platforms support optogenetic stimulation across experimental scales from single-cell stimulation to whole-culture illumination, and some incorporate automated measurement and stimulation for computer-controlled operation.

Microtiter plate designs for optogenetic stimulation are light-delivery platform formats used to apply regulated optical inputs in biological experiments. The cited review places these designs within a broader range of optogenetic hardware spanning simple illumination setups to microtiter plate and bioreactor implementations, with use cases from single-cell stimulation to whole-culture illumination.

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.

OptoGels are hydrogels whose material properties are programmed by light through incorporation of naturally occurring photoswitchable proteins. They are described as extracellular optogenetic materials that enable dynamic optical control of hydrogel behavior.

Optogenetic instruments and devices are light-delivery platforms used to test optogenetic strains across multiple culture scales in bioproduction settings. The cited literature frames these systems as evaluation and scale-up hardware relevant to adapting industrial bioprocesses for optogenetic control.

An optrode, also called an optode, is a neural probe that integrates conventional electrophysiological recording with one or more optical channels for optogenetic activation in live animals. It is used to deliver light to neural tissue while measuring electrical activity from the same preparation.

Order-disorder transitions are a light-regulated design principle identified in a 2015 survey of engineered photoreceptors. In this framework, light-driven structural transitions are used as a versatile basis for building optogenetic tools within photoreceptor engineering.

Photobioreactor designs are light-delivery and cultivation hardware concepts used to test optogenetic strains for bioproduction at multiple culture scales. The cited literature indicates that existing photobioreactor designs and industrial-scale bioproduction processes could be adapted to support optogenetic control.

Photopharmacology is an engineering method that uses chemically engineered small-molecule photosensitive effectors to impose light control over biological targets. In the cited literature, it is identified as one of the major strategies for targeted photocontrol in proteins and as an optical approach for modulating adrenergic receptor signaling with temporal and spatial precision.

Photoreceptors are naturally occurring or engineered photosensitive protein domains that respond to light at varying wavelengths and function as light-regulated actuators in optogenetics. They have been used to confer genetically encoded, light-dependent control of cellular functions, including regulation of gene expression in bacteria.

Additionally the applications that have emerged in recent years are discussed, including gene regulation, drug delivery and materials design.

Additionally the applications that have emerged in recent years are discussed, including gene regulation, drug delivery and materials design.

Photoxenoprotein engineering is a protein engineering method for targeted light regulation of protein function through incorporation of photoactive non-canonical amino acids by genetic code expansion. It is described as one of three major approaches developed for designing photocontrol in proteins.

Protein design is a computational engineering method discussed in reviews on protein structure prediction and on optogenetic tool development. It is presented as enabling the creation of protein-based tools, including light-responsive optogenetic systems, that can manipulate and monitor cellular activities.

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.

Either thinning down or removing portions of the skull or spine is necessary for unobstructed long-term in vivo observations, for which types of the cranial and spinal window and applied materials vary depending on the study objectives.

Remaining challenges include brightness/photostability limits and the need for broader translational validation, yet progress in structure-guided mutagenesis, computational/AI-assisted protein design, and hybrid imaging strategies promises to close these gaps.

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.

Two-photon-based functional nucleic acid probes are functional nucleic acid biosensing and imaging probes that operate through two-photon excitation or two-photon activation. Reported examples are positioned for biosensing and biomedical imaging, with claimed performance advantages over conventional one-photon functional nucleic acid probes.

A wireless implantable system is described as a configuration class within platforms for combined optogenetics and electrophysiology in live animals. In the supplied evidence, it functions as an implantable format for in vivo light delivery together with electrophysiological work, but no specific device architecture or operating characteristics are provided.

AlphaFold3 is a computational structure-prediction method used in the cited study to model the MagMboI–DNA complex. In that work, it was applied to infer interactions with the 5'-GATC-3' recognition sequence and to guide optimization of the photoactivatable endonuclease variant MagMboI-plus for top-down genome engineering.

The artificial intelligence-guided designed LOV domain is a computationally designed light-oxygen-voltage protein domain that remains photoreactive despite being sequence-divergent from its maternal template. It preserves core LOV photocycle behavior while displaying distinct biophysical properties, indicating access to a new region of LOV-domain functional space.

macrophages ... establishing CAR-engineered macrophages (CAR-M) as a highly promising next-generation therapeutic platform

Finally, we developed a chemically inducible version of GFE3, chGFE3, which degrades inhibitory synapses when combined with the bio-orthogonal dimerizer HaloTag ligand-trimethoprim.

Compact PE is a truncated prime editor in which the reverse transcriptase RNase H domain is completely deleted. In the cited 2021 study, this compact PE showed editing activity comparable to full-length PE2 and enabled flexible split prime editor designs for in vivo delivery.

Precision genome editing can be achieved by using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) along with long-acting slow-effective release antiretroviral therapy.

latent-type SNACIPs including cRTC are designed that are functionally assembled inside living cells. cRTC contains a nanobody against an intrinsically disordered protein TPX2

This tool is an engineered protein-based Ca2+ sensor that switches through mutually exclusive folding of two alternate frames. Computational design and biophysical experiments were used to improve its conformational switching kinetics, producing Ca2+-responsive behavior on the timescale of fast physiological Ca2+ fluctuations.

The H1/TO promoter is a tetracycline-operator-modified H1 RNA polymerase III promoter used in a multi-component CRISPR/Cas9 switch to drive doxycycline-dependent guide RNA expression. In the reported system, it functioned with TetR-mediated regulation and supported in vitro DNA editing with efficiency similar to a U6/TO promoter.

Key developments include multi-antigen and logic-gated CAR designs to mitigate tumor immune evasion.

LUNAS is a bioluminescent nucleic acid sensor in which a target double-stranded DNA sequence is recognized by two dCas9-based probes that mediate split NanoLuc luciferase complementation. Reported implementations couple this sensor to recombinase polymerase amplification, including RT-RPA-LUNAS for SARS-CoV-2 RNA detection.

This review would like to focus on the unique photocyclic animal opsin ... and also discuss the possibility of designing "artificial photocyclic opsins" from natural opsins for potential application in optogenetic gene therapy.

This tool is a de novo designed reversible phosphorylation-dependent switch for membrane targeting. The supplied evidence indicates that it links phosphorylation state to reversible membrane localization, but does not provide additional molecular or performance details.

Our strategy permanently inactivates VWF variants by selectively disrupting the pathogenic allele's open reading frame via the introduction of indels by Cas9. To circumvent the challenge of designing variant-specific strategies, we targeted the common single nucleotide polymorphism (SNP) rs1800378 in VWF.

Split prime editor is a multi-component prime editing system in which prime editor is divided into two fragments to support flexible split configurations and dual-adeno-associated virus delivery. The reported design was enabled by a compact PE2 variant with complete deletion of the reverse transcriptase RNase H domain while retaining editing activity comparable to full-length prime editor.

The split-Cas9D10A nickase version is an intein-mediated split form of Cas9 carrying the D10A nickase mutation, designed to reconstitute an active nickase from separate polypeptide components. In the cited 2015 study, the analogously designed split-Cas9D10A showed similar activity to full-length Cas9D10A.

Synthetic condensates are an engineered modular system for building synthetic membraneless organelles that separates condensate assembly from client recruitment. The framework uses constitutive oligomerization of intrinsically disordered regions to form clusters and fused interaction domains to define condensate composition.

The two-input protein logic OR gate is an engineered single-protein focal adhesion kinase (FAK) system designed to integrate chemical and optical inputs within the native FAK domain architecture. It functions as an allosterically regulated OR gate by combining a rapamycin-inducible uniRapR module in the kinase domain with a light-inducible LOV2 module in the FERM domain.

The design of photoactive complex coacervate protocells in laboratory settings by utilizing photochromic molecules such as azobenzene and diarylethene is further discussed.

MagMboI is a photoactivatable split version of the type II restriction endonuclease MboI configured as a multi-component switch for light-controlled nuclease function. The supplied evidence indicates that an optimized variant, MagMboI-plus, produced stronger genome rearrangement activity than the original MagMboI in Saccharomyces cerevisiae.

MagMboI-plus is a redesigned photoactivatable endonuclease variant used as a light-controlled multi-component switch in Saccharomyces cerevisiae. In vivo, blue-light activation yields slightly increased DNA-cleavage activity relative to the original MagMboI construct, but also more pronounced genomic rearrangements.

The set includes plasmids with four different, most commonly used bacterial expression cassettes - RhaS/RhaBAD, LacI/Trc, AraC/AraBAD, and XylS/Pm

The set includes plasmids with four different, most commonly used bacterial expression cassettes - RhaS/RhaBAD, LacI/Trc, AraC/AraBAD, and XylS/Pm

The QM(B3LYP/cc-pVDZ)/MM(AMBER) approach is a hybrid quantum mechanics/molecular mechanics computational method used for geometry optimization and vibrational frequency calculations in flavin-binding photoreceptor proteins. In the cited BLUF photoreceptor study, it was used to model light-induced structural changes and associated spectral shifts.

The set includes plasmids with four different, most commonly used bacterial expression cassettes - RhaS/RhaBAD, LacI/Trc, AraC/AraBAD, and XylS/Pm

The set includes plasmids with four different, most commonly used bacterial expression cassettes - RhaS/RhaBAD, LacI/Trc, AraC/AraBAD, and XylS/Pm

Secondly, strategies intended to optimize the acclimation of photosynthesis to changes in the environment are presented, including redesigning mechanisms to dissipate excess excitation energy (e.g., non-photochemical quenching) or reduction power (e.g., flavodiiron proteins).

Secondly, strategies intended to optimize the acclimation of photosynthesis to changes in the environment are presented, including redesigning mechanisms to dissipate excess excitation energy (e.g., non-photochemical quenching)...

AsLOV2-Jα-Rac1 is an artificial fusion protein that connects the Avena sativa AsLOV2-Jα photosensor to the Rac1 GTPase to create a light-responsive signaling switch. Light-triggered structural changes in the LOV2 module disrupt steric inhibition of Rac1 and permit binding of the effector protein PAK1.

Synthetic Notch (synNotch) receptors are modular engineered receptors expressed in mammalian cells that detect signals presented by neighboring cells or ligand-bearing materials and activate prescribed transcriptional programs. In the cited work, synNotch was used as a programmable material-to-cell signaling interface for spatial control of cell phenotypes in multicellular constructs.

The Light Oxygen Voltage 2 (LOV2) domain is a light-responsive protein domain from Avena sativa phototropin 1 that serves as a well-characterized foundation for the design of engineered photoswitches. The supplied evidence supports its role as a cornerstone component for optogenetic and protein-engineering applications.

Boolean logic gates are synthetic genetic circuits that integrate multiple biological inputs into a defined output state. The supplied evidence indicates that such circuits have been developed with up to six inputs and are discussed as components within synthetic circuits of varying complexity.

Complex gene circuits are synthetic multi-component regulatory systems in mammalian cells assembled from gene switches as basic building blocks. They are described as enabling cellular memory, oscillatory protein production, and complex information-processing behaviors.

Gene circuits are higher-order engineered synthetic biomolecular systems discussed as components of therapeutic gene-circuit therapy. The cited 2021 review describes proof-of-principle and clinical applications of gene circuits in engineered therapeutics, but does not provide a specific circuit architecture in the supplied evidence.

A protein conformational switch is an engineered protein system in which a signaling event induces a conformational change. Reported uses include reagent-free biosensing and regulation of biological function.

Explicitly supported component names recovered from the sources include EPYC1, carboxysome, pyrenoid, e-Photosynthesis, and specific synthetic glycolate bypass designs such as GCBG/API.

Explicitly supported component names recovered from the sources include EPYC1, carboxysome, pyrenoid, e-Photosynthesis, and specific synthetic glycolate bypass designs such as GCBG/API.

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.

Countermeasures now integrate synergistic Cry/Vip pyramiding

PubMed figure captions for the anchor paper indicate a specific construct designation, ECN-pE(C/A)2, in a study on programmable probiotics for IBD after oral delivery.

Animal opsin-based pigments are light-responsive receptor systems composed of an opsin protein bound to the chromophore 11-cis retinal. Most are typical G protein-coupled receptors, and their diversity, particularly among nonconventional visual pigments, has been proposed as a basis for optogenetic modulation of GPCR signaling.

BphP-based biosensors are proposed near-infrared optical sensor designs derived from bacterial phytochrome photoreceptors. They are suggested on the basis of bacterial phytochrome photochemistry and structure as a possible class of genetically encoded biosensors spectrally complementary to other probes.

Remaining challenges include brightness/photostability limits and the need for broader translational validation, yet progress in structure-guided mutagenesis, computational/AI-assisted protein design, and hybrid imaging strategies promises to close these gaps.

Human opsins are protein domains used as optogenetic tools in visual restoration strategies. The supplied evidence indicates that applying human opsins can improve light sensitivity and wavelength sensitivity in optogenetic systems, and places these tools within ongoing clinical translation for retinal therapy.

Nonconventional visual pigments are opsin-based light-sensitive pigments proposed as a source of optogenetic actuators for controlling G protein-coupled receptor signaling. A 2013 review highlights their diverse molecular characteristics as potentially useful for designing light-regulated GPCR tools.

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.

BACCS is a genetically engineered blue light-activated Ca2+ channel switch developed as an optogenetic tool for generating intracellular Ca2+ signals. It acts by opening Ca2+-selective ORAI ion channels in response to blue light and has been used to drive downstream cellular and physiological responses.

BLISS is a blue-light-inducible SpyTag system generated by inserting SpyTag into different positions of the AsLOV2 Jα-helix. In this design, blue light exposure enables conditional SpyTag reactivity with SpyCatcher, allowing light-gated coupling.

BphP1-QPAS1 is a near-infrared light-inducible protein interaction system in which the bacterial phytochrome BphP1 binds an engineered partner, QPAS1, for optical protein regulation in mammalian cells. It has been incorporated into multi-component optogenetic tools for transcriptional control and protein targeting, including use in neurons and non-neuronal cells.

Cph8 is a photo-reversible phytochrome-based optogenetic switch used to control gene expression in Escherichia coli. The cited work applies stimulated depletion quenching to improve control over its photoswitching behavior.

CRY-BARs are a family of light-gated optogenetic tools that contain an I-BAR domain and are designed to remodel membrane architecture. They are intended to provide spatial and temporal control over cellular processes involving membrane protrusion formation.

CRY2clust is an engineered CRY2-based optogenetic module that drives blue light-dependent homo-oligomerization and clustering of fused target proteins. It was reported as a new CRY2 variant that enables rapid and efficient protein clustering with spatiotemporal optical control.

The DNMT3A-CRY2/CIB1-TRF1 system is a blue-light-responsive multi-component optogenetic construct that recruits human DNMT3A to telomeric regions through CRY2-CIB1 interaction and TRF1-mediated telomere binding. In the reported HeLa cell configuration, light activation selectively increased subtelomeric CpG methylation at six examined chromosome ends and was associated with progressive telomere lengthening over three cell generations.

The engineered focal adhesion kinase (FAK) is a single-protein, two-input logic OR gate that integrates chemogenetic and optogenetic control within the native FAK domain architecture. It places a rapamycin-inducible uniRapR module in the kinase domain and a light-inducible LOV2 module in the FERM domain to allosterically regulate FAK activity.

Hybrid phototropin LOV2 domains were engineered to incorporate the BID Bcl homology region 3 (BH3), creating a light-dependent optogenetic switch. Illumination induces LOV2 conformational changes that expose the BH3 element and modulate binding to the anti-apoptotic Bcl-2 family protein Bcl-xL.

The light pulse-counting materials system is a biohybrid polymer framework assembled from synthetic biology-derived modules that detects the number of input light pulses. It releases distinct output molecules as a function of pulse count.

The light-controlled CRISPR/dCas9 transactivation system is a multi-component optogenetic transcriptional activator that couples CRISPR/dCas9-mediated gene activation to a light-responsive PAL–RNA aptamer interaction. It enables reversible optical control of transactivation and was described as a variation of the CRISPR/dCas9 system for light-controlled activation of gene expression.

Light-inducible TrkA activation strategies comprise four engineered optical designs for activating TrkA signaling without nerve growth factor. The reported approaches use light to drive plasma membrane recruitment and homo-interaction of the intracellular domain of TrkA, recapitulating native NGF/TrkA-associated functions.

The miRFP670-miRFP720 FRET pair is a fully near-infrared genetically encoded Förster resonance energy transfer pair used to construct biosensors. It enables multiplexed biosensor imaging that is compatible with CFP-YFP imaging channels and blue-green optogenetic tools.

MLCP-BcLOV4 is an optogenetic fusion of myosin light chain phosphatase with the Botrytis cinerea light-oxygen-voltage flavoprotein BcLOV4. It was developed to control actomyosin contractility in the Ciona larval epidermis through light-dependent membrane localization and suppression of phosphorylated myosin activity.

The optimized Enhanced Magnet transcription factor is a light-responsive split transcription factor developed in Saccharomyces cerevisiae using Enhanced Magnet dimerization modules. It was rationally designed and tested to improve light-sensitive gene expression.

OptoBinders (OptoBNDRs) are a class of light-sensitive protein binders exemplified by OptoMB, a light-controlled monobody. Reported OptoBinders enable reversible light-dependent modulation of protein binding affinity, including an SH2-binding OptoMB with an approximately 300-fold light-dependent affinity shift.

The optogenetic epigenetic editing toolbox for Ascl1 promoter targeting is a multi-component light-responsive system that combines CRY2/CIB1 fusions, a TALE DNA-targeting module, and either the DNMT3A catalytic domain or TET1 catalytic domain. Under optimized blue-light illumination, it co-localizes these effectors at the Ascl1 promoter to alter local DNA methylation state and regulate Ascl1 gene activity.

optoPAK1 is a genetically encoded, light-responsive optogenetic analog of p21-activated kinase 1 (PAK1) engineered for photoinduced recruitment to specified intracellular sites. It was designed as a constitutively active PAK1 variant that functions independently of endogenous biochemical regulation while maintaining minimal dark-state activity.

OptoPB is an optogenetic multi-component switch generated by installing photosensitivity into engineered minimal phosphoinositide-binding domains. It enables rapid and reversible light-controlled protein translocation, plasma membrane targeting, and inter-membrane tethering at membrane contact sites in living cells.

OptoProfilin is an optically activated profilin-based, single-component biosensor reported in 2023. It was described as an optically triggered sensor of applied cellular stress in select immortalized cell lines and presented as the first profilin-based optogenetic biosensor for stress-induced cytoskeletal changes.

OXTR-iTango2 is a genetically encoded optogenetic gene-expression system designed to label neuronal populations activated by oxytocin under blue-light illumination. It supported quantitative reporter induction in HEK cells and neurons and was used to identify oxytocin-responsive neurons in vivo.

The photoactivatable CRISPR/Cas9 system is a light-gated genome-editing configuration comprising Cas9, either a synthetic 102-nt sgRNA or a crRNA/tracrRNA pair, and blocking photocleavable oligodeoxyribonucleotides. UV irradiation in the presence of the photomodified blocking oligodeoxyribonucleotides enables photoactivatable gene editing in vitro.

PiL[D24] is an engineered mammalian pyruvate kinase M2 (PKM2) photoswitch containing an internal insertion of the Avena sativa LOV2 light-sensing domain at position D24. Illumination preserves the LOV2 photoreaction and allosterically modulates PKM2 behavior, increasing pyruvate kinase activity and cellular labeling of pyruvate from glucose.

The TA system is a BphP1-QPAS1-based near-infrared light-sensing optogenetic system for transcription activation. It was tested in several mammalian cell types, including cortical neurons, and is described within a study of near-infrared-controlled gene expression and protein targeting.

The upconversion nanoparticle-based immunodevice is a multi-component, light-activatable immunodevice for remote optical control of antitumor immunity in vitro and in vivo. It combines a rationally designed UV light-activatable immunostimulatory agent with an upconversion nanoparticle that transduces near-infrared light sensitivity into device activation.

The UVB-inducible expression system is a UVB-responsive split transcription factor engineered from the Arabidopsis thaliana UVB receptor UVR8 and the COP1 WD40 domain. In mammalian cells, UVB illumination triggers transcriptional activation and provides one wavelength-specific channel for multichromatic gene control.

Microbial opsins are genetically encoded seven-transmembrane proteins from diverse microorganisms that render cells light responsive by transporting ions across cellular lipid membranes. In optogenetics, they are used as molecular sensitizers to activate or silence neural activity with brief pulses of light.

synPCB is a genetically encoded phycocyanobilin synthesis system that supplies the chromophore required for PhyB-PIF phytochrome-based optogenetics. The improved synPCB version increased PCB production by approximately 4-fold and was incorporated with PhyB-PIF into doxycycline-inducible lentiviral and transposon vectors to support light-inducible dimerization system expression or function.

Designer receptors exclusively activated by designer drug (DREADDs) are engineered G protein-coupled receptors used as a chemogenetic or pharmacogenetic system. They enable selective remote control of neuronal activity through activation by otherwise inert drug-like small molecules.

Engineered G protein-coupled receptors are bioengineered pharmacogenetic tools for selective, remote control of neuronal activity. The supplied evidence describes receptors that are activated by otherwise inert drug-like small molecules rather than native ligands.

Genetically encoded photoswitches are opsin-free optogenetic components that can be modularly engineered into protein scaffolds or host cells to control biological processes with light. The cited review places these systems within optophysiology, where they are used to interrogate cellular physiology.

Optical dimerizers are genetically encoded actuators that use light to control protein-protein interactions. The cited examples are the CRY2/CIB and UVR8/UVR8 systems, which have been applied to light-regulated transcription, protein localization, and protein secretion.

DEL-VPR is a blue-light-responsive multi-component transcriptional switch for mammalian cells that drives strong inducible gene expression. It was reported to produce up to 570-fold induction and to reach expression levels comparable to strong constitutive promoters.

LightOnC.glu is a programmable light-responsive genetic circuit for Corynebacterium glutamicum that regulates gene expression in response to light signaling. It uses light-controlled RNA-binding proteins to build light-controlled transcription factors for dynamic transcriptional control.

Opto-mGluR6 is a chimeric optogenetic receptor designed for retinal ON-bipolar cells. It combines light-sensing domains from melanopsin with intracellular domains from mGluR6 to couple light activation to mGluR6-like GPCR signaling.

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

We developed a computational pipeline and applied it to analyzing 3D point clouds of SMLM localizations (event lists) of the caveolar coat protein, caveolin-1 (Cav1).

Remarkably, 4D bioprinting, a newly emerged technology/concept, aims to rationally design 3D patterned biological matrices from synthesized hydrogel-based inks with the ability to change structure under stimuli.

Future directions focus on AI-driven vector design, hybrid systems (AAV-exosomes), and standardized manufacturing to achieve "single-dose, lifelong cure" paradigms for muscular disorders.

we generated AAV with mosaic capsid, AAV-PHP.(S + eB), by co-packaging the AAV with two engineered capsid variants: AAV-PHP.eB and AAV-PHP.S

Here we utilized rational design techniques to make five point mutations in the AAV9 capsid. In doing so, we developed a novel AAV9 variant, AAV9-DM, that is characterized by reduced liver tropism as compared to AAV9 and other liver de-targeted AAV9 mutants.

Acoustic microfluidic devices are powerful tools that use sound waves to manipulate micro- or nanoscale objects or fluids in analytical chemistry and biomedicine.

The paper explicitly describes adaptive additive superlets (ASLT) as a named adaptive superlet variant.

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

Artificial neural networks (ANN) and adaptive neuro-fuzzy inference systems (ANFIS) were proposed to model a voltammetric biosensor for plasma miR-155 detection.

An adaptive weighted fusion strategy was then employed to map these optical signals to the sound pressure field.

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.

AI-assisted sgRNA design, and machine-learning approaches for predicting off-target effects further enhance the safety, stratification, and monitoring of CRISPR therapeutics

Recent breakthroughs in cryo-electron microscopy (cryo-EM) and artificial intelligence (AI)-based structure prediction have revolutionized protein modeling by enabling highly accurate computational predictions from amino acid sequences.

The supplied web research summary states that the review spans enabling technologies such as "AI-driven phase-separation prediction".

Nanobodies have been used on bispecific and trispecific antibody platforms, as well as in CRISPR/Cas9 editing and AI-driven technologies, to expand their applications.

Future directions focus on AI-driven vector design, hybrid systems (AAV-exosomes), and standardized manufacturing to achieve "single-dose, lifelong cure" paradigms for muscular disorders.

artificial intelligence (AI) enhanced design is hastening optimization of RNA sequences, chemistries and vectors

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 web research summary states that the anchor study explicitly uses Allen CCFv3 for spatial registration.

Allosteric transcription factor (aTF)-based in vitro biosensors constitute a class of detection tools formed by the functional coupling of the ligand-binding domain of aTFs with a reporter system.

Based on the developed PABs, we ... demonstrate an allulose-triggered CRISPR interference circuit for dynamic metabolic regulation. It facilitates a 68% increase in allulose titer and achieves a high yield of 0.43 g/g glucose.

AlphaFold-a deep learning-based protein structure prediction system-has transformed structural biology by providing near-experimental accuracy models directly from amino acid sequences.

We discuss the complementary roles of cryo-EM and AI, including developments in direct electron detectors, advanced image processing, and deep learning algorithms exemplified by AlphaFold 2 and the emerging AlphaFold 3.

AlphaFold-Multimer improves multi-chain complex assembly prediction.

The paper explicitly names AlphaFold2 multimer modeling as part of the study workflow for AtaApore trimer prediction.

To achieve this, we engineered CD4+ T cells with chimeric antigen receptors (CARs) targeting fibrillar forms of aggregated amyloid-b2... we established the feasibility of amyloid plaque-specific CAR-T cells as a potential therapeutic avenue for AD.

the hypoglycemic ability (b1-amylase, b1-glucosidase and dipeptidyl peptidase 4), probiotic property and antioxidant activity of lactic acid bacteria were comprehensively evaluated by a principal component analysis (PCA) and analytic hierarchy process (AHP).

The supplied web research summary identifies antiSMASH as a core genome-mining platform aligned with the review's genome mining and biosynthetic gene cluster prediction/annotation themes.

Using approximate analytical approach, the mechanical properties of structures can be predicted quickly and efficiently.

novel aptamers generated using our proprietary transformer-based AI language model, AptaBLE

Here, we developed aptamer-functionalized lipid nanoparticles (LNPs) for targeted mRNA delivery to CD4+ T cells.

We designed and synthesized a novel LNP by integrating the pro-inflammatory fatty acid, arachidonic acid (ARA), as a functional structural component (ARA-LNP).

Recent technological innovations, including ... artificial intelligence (AI) ... have created new opportunities for investigating the cellular and molecular basis of VDs. AI enhances data integration, risk prediction, and clinical interpretability.

Integration of automation, artificial intelligence (AI), and three-dimensional (3D) bioprocessing technologies aims at further enhancement of standardization, quality control, and throughput.

Finally, we highlight how chemical modification, nanotechnology, and artificial intelligence-assisted design are enhancing the specificity, stability, and safety of RNA therapeutics.

Non-viral vectors, nanoparticle systems, and artificial intelligence-guided diagnostics are being explored to address these limitations and support personalized care.

Artificial neural networks (ANN) and adaptive neuro-fuzzy inference systems (ANFIS) were proposed to model a voltammetric biosensor for plasma miR-155 detection.

Here, we have studied the photoswitching mechanism of the reversibly switchable fluoroprotein asFP595 at the atomic level...

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

The Aureochrome1a LOV domain from Phaeodactylum tricornutum is a flavin-binding blue-light sensory protein domain used as the basis for designed LOV-domain flavoproteins. In the cited 2020 Scientific Reports study, tailored LOV-domain flavoproteins produced nuclear hyperpolarization upon illumination, functioning as light-driven spin machines.

His work also contributed to automated data analysis pipelines that uncover fine-scale astrocytic microdomain dynamics.

The Automatic Rhodopsin Modeling ( ARM ) protocol is focused on providing exactly the necessary computational tools to study rhodopsins, those being either natural or resulting from mutations.

The supplied web research summary identifies Azo-PROTAC as an explicitly supported related item candidate and as a major photoswitchable degrader design emphasized by the anchor review.

an "AND"-logic gated SynNotch CAR targeting B7-H3 and TROP2 was engineered to minimize off-tumor, on-target toxicity of TROP2 CAR-T cells... showed comparable antitumor efficacy without causing apparent adverse effects

Special emphasis is placed on BMCs for their spatial precision, selective permeability, and ability to encapsulate multi-enzyme pathways. Recent advances in synthetic biology, from orthogonal shell engineering to modular cargo recruitment, underscore their transformative potential for pathway design and metabolic control.

Bibliometric analyses performed using Bibliometrix, CiteSpace, and VOSviewer software to compensate for the differences in their respective algorithms.

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

Molecular docking and knowledge of bioinformatics are also being used to predict potential applications and manufacturing by industry.

The launching pad is a bistable [2]rotaxane whose dumbbell component contains two electron-donating recognition sites...

We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available.

We highlight the following technologies: ... blood-brain barrier opening...

Here, we present a new optogenetic CRISPR tool (Blue Light-inducible Universal VPR-Improved Production of RGRs, BLU-VIPR)...

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

plant virus-like particles (VLPs), derived from Brome Mosaic Virus (BMV), as a biodegradable and biocompatible nanocarrier for small interfering RNA (siRNA) delivery aimed at modulating immune checkpoints in melanoma

Capturing and manipulating activated neuron ensembles, is a recently-designed technique to permanently label activated neurons responsible for a physiological function and manipulate them.

CAR-NK cell therapy, as an emerging immunotherapeutic approach, has demonstrated significant potential. CAR-NK cells recognize and eliminate tumor cells through chimeric antigen receptors (CARs).

The CatBoost C1a model achieved an ROC-AUC of 0.71/0.86 (train/test) on average across ten random five-fold cross-validations, using EV features alone to distinguish S0 from S1-S3.

The CatBoost C2h-21 model achieved an ROC-AUC of 0.81/1.00 (train/test) on average across ten random three-fold cross-validations, using engineered features including EVs, clinical features like diabetes and advanced fibrosis, and anthropomorphic data like body mass index and weight for identifying severe steatosis (S3).

The paper develops a novel analytical method decomposing patterned activity into discrete network events; the web research summary explicitly identifies the named method as CBASS.

resulting in various coiled-coil heterodimers-mediated base editors (CC-BEs), including ... adenine base editor (CC-ABE)... Using CC-ABE, we validate in vivo editing efficiency and successfully achieve A-to-G conversion in the Pcsk9 and Dmd genes via dual-AAV vectors in mice.

resulting in various coiled-coil heterodimers-mediated base editors (CC-BEs), including cytidine base editor (CC-CBE)... achieving maximum enhancements of 9.6-fold in human immortalized cells and 12.4-fold in primary somatic cells for CC-CBE.

We then develop CellChat, a tool that is able to quantitatively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data.