Toolkit Items

Browse the toolkit beneath workflows. The mechanism branch runs mechanism -> architecture -> component, while the technique branch runs from high-level approaches down to concrete methods.

33 items matching 1 filter

Mechanism Branch

Layer 1

Mechanisms

Top-level concepts: biophysical action modes such as heterodimerization, photocleavage, or RNA binding.

Layer 2

Architectures

Arrangements that realize or deploy mechanisms, including switches, construct patterns, and delivery strategies.

Layer 3

Components

Low-level parts and sequence-defined elements used inside architectures, including protein domains and RNA elements.

Technique Branch

Layer 1

Approaches

High-level engineering practices such as computational design, directed evolution, sequence verification, and functional assay.

Layer 2

Methods

Concrete methods used to design, build, verify, or characterize engineered systems.

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viral gene delivery

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adeno-associated virus delivery

Delivery Strategy

Adeno-associated virus delivery is a viral gene delivery harness used to deploy the far-red light-induced split-Cre recombinase (FISC) system in vivo. In the cited study, AAV delivery enabled implementation of optogenetically controlled genome engineering in living systems.

CFBacMamMusHumTxRep
Ev 28Rep 9Pr 71

adenoviral infection

Delivery Strategy

Adenoviral infection is a viral delivery harness used in vitro to introduce the optogenetic actuators ChR2(H134R) and ArchT into primary cardiac fibroblasts. In the cited Methods in Molecular Biology protocol, it enables quick, robust, and consistent opsin expression and supports generation of light-responsive cardiac fibroblast preparations.

CFBacMamMusHumTxRep
Ev 28Rep 9Pr 59

recombinant AAV1/2 viral particles

Delivery Strategy

Recombinant AAV1/2 viral particles are a viral gene delivery harness used to express the LOV2-PAH1 optogenetic REST inhibitor in HEK293T cells, primary neurons, and mouse hippocampal neurons in vivo. In the cited study, these particles enabled efficient hippocampal neuronal transduction and subsequent functional testing of the delivered cargo.

CFBacMamMusHumTxRep
Ev 28Rep 9Pr 59

Adenovirus is described here as a viral delivery harness used in optogenetic experiments to introduce genes encoding photosensitive proteins into specific neural regions. This delivery enables subsequent light-gated control of ion passage for neuronal activation or inhibition.

CFBacMamMusHumTxRep
Ev 20Rep 9Pr 59

viral vectors for ocular gene delivery

Delivery Strategy

Viral vectors for ocular gene delivery are described as available tools that can support optogenetic strategies for vision restoration. The supplied evidence identifies their use context in the eye but does not specify vector type, cargo architecture, or cellular targets.

CFBacMamMusHumTxRep
Ev 20Rep 9Pr 59

recombinant adeno-associated virus (rAAV) vectors

Delivery Strategy

Recombinant adeno-associated virus (rAAV) vectors are viral gene delivery vehicles used for in vitro and in vivo transgene delivery, including in the retina. In the cited retinal ganglion cell study, rAAV supported motif-mediated subcellular targeting of optogenetic tools to shape expression patterns.

CFBacMamMusHumTxRep
Ev 14Rep 9Pr 59

AAV serotype (AAV2.2 versus engineered AAV2.NN)-were systematically optimized. Whole-retina-to-brain imaging was performed using fMOST on samples injected with the optimal condition (AAV2.2-double-1/1000).

CFBacMamMusHumTxRep

Anchor PMC text explicitly states sciatic nerve injection with AAV6 vectors carrying SwiChR-eYFP and analogous AAV6 constructs for hM4D(Gi), making AAV6 a key delivery component.

CFBacMamMusHumTxRep

Subsequent evaluation of a codon-optimised microdystrophin transgene under the control of the optimal CAG promoter and capsid (AAV9K51Q) ... Based on the improved performance of AAV9K51Q vectors during intramuscular gene transfer, we performed a systemic administration of these vectors alone

CFBacMamMusHumTxRep

AAV-based vectors

Delivery Strategy

AAV-based vectors-including AAV8 and synthetic AAVDJ-have demonstrated effective delivery of genes like Lhcgr into testicular interstitial tissues, restoring testosterone synthesis and fertility in mouse models.

CFBacMamMusHumTxRep

AAV-mediated gene augmentation

Delivery Strategy

Additionally, we describe the latest approaches for treatment, including AAV-mediated gene augmentation, genome editing, and late-stage therapies such as optogenetics, cell transplantation, and retinal prostheses.

CFBacMamMusHumTxRep

dual AAV vectors

Delivery Strategy

Innovations in viral and non-viral delivery systems, such as dual AAV vectors, lipid nanoparticles, and novel biomaterials, have enhanced the efficiency and specificity of gene delivery to the retina.

CFBacMamMusHumTxRep

HSV-1 amplicon vectors

Delivery Strategy

The web research summary states that the anchor paper describes an adult human neocortical acute-and-cultured slice platform optimized for rapid molecular-genetic manipulation, emphasizing short-latency HSV-1 neuronal transduction, and lists HSV-1 amplicon vectors as the core genetic-delivery component.

CFBacMamMusHumTxRep
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