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(SD2024-149) Strategy for pooled nuclear expressed antisense RNAs to identify consequential RNA processing events

Researchers from UC San Diego developed a new technology that facilitates pooling of nuclear expressed antisense RNAs (NEARs) to identify consequential RNA processing events such as alternative or constitutive RNA splicing or polyadenylation.This technology will identify a phenotype of interest and/or a group of RNA processing events (for example RNA splicing sites of interest or alternatively spliced exons), and transduce cells with a library of NEARs targeting these events. Applications include: Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman",serif;} Research tool. As screens to identify exons of phenotypic relevance in a high throughput manner.Therapeutic target identification. To identify therapeutic targets of cancer cell suppression, such as poison exons in cancer specific transcripts.Therapeutic discovery. As a therapeutic agent to identify therapeutic NEARs for splicing related disorders.  

(SD2022-279) Mutant ZRANB2 zinc finger proteins with GGG RNA sequence targeting specificity

Existing RNA-targeting tools for sequence-specific manipulation include anti-sense oligos (ASOs), designer PUF proteins and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas systems. However, there are significant limitations to each of the current tools. ASOs are usually not available for most RNA manipulations other than gene silencing. Designer proteins, such as PUF (Pumilio and FBF homology protein), possess low RNA recognition efficiency and it remains challenging to target RNA sequences >8-nucleotides (nt) in length. The bulky Cas protein (Cas13d: average 930 amino acids) leads to complication for transgene delivery and concerns of its immunogenicity due to its bacterial origin. Mutants of zinc finger(ZnF) proteins in ZRANB2 recognize a single-strand RNA containing a novel GGG motif with micromolar affinity, compared to the original motif GGU. These mutants serve as a foundation for RNA-binding ZnF designer protein engineering for in vivo RNA sequence-specific targeting.ZnFs are generally compact domains (~3kDa each) that have been successfully engineered for DNA recognition as modular arrays. A ZnF-based system has unique advantages, especially in a therapeutic context: (1) Broad application with the possibility to fuse with other effector domains; (2) High efficiency of RNA recognition (3 RNA bases recognized per 30-amino-acid ZnF) with a small size of protein. Only 4 ZnFs (~100 aa) is required for specific targeting in the transcriptome. (3) Humanized components without immunogenic concern.By engineering new sequence specificity of the ZRANB2 ZnF1, researchers from UC San Diego identified 13 mutants that altered their preferred RNA binding motif from GGU to GGG. They are N24R, N24H, N14D/N24R, N14D/N24H, N14R/N24R, N14R/N24H, N14H/N24R, N14H/N24H, N14Q/N24R, N14Q/N24H, N14E/N24R, N14S/N24R, N14E/N24H.

(SD2022-255) A robust approach to camera radar fusion

Researchers from UC San Diego have developed RadSenNet, a new approach of sequential fusing of information from radars and cameras. The key idea of sequential fusion is to fundamentally shift the center of focus in radar-camera fusion systems from cameras to radars. This shift enables their invention (RadSegNet) to achieve all-weather perception benefits of radar sensing. Keeping radars as the primary modality ensures reliability in all situations including occlusions, longrange and bad weather.

(SD2024-269) Bento: An open-sourced toolkit for subcellular analysis of spatial transcriptomics data

Bento is an open-source software toolkit that uses single-molecule information to enable spatial analysis at the subcellular scale. Bento ingests molecular coordinates and segmentation boundaries to perform three analyses: defining subcellular domains, annotating localization patterns, and quantifying gene-gene colocalization. The toolkit is compatible with datasets produced by commercial and academic platforms. Bento is integrated with the open-source single-cell analysis software ecosystem.

(SD2025-068) Low-Cost, Scalable Passive Sensors: a battery-free wireless general sensor interface platform

Researchers from UC San Diego present a fully-passive, miniaturized, flexible form factor sensor interface titled ZenseTag that uses minimal electronics to read and communicate analog sensor data, directly at radio frequencies (RF). The technology exploits the fundamental principle of resonance, where a sensor's terminal impedance becomes most sensitive to the measured stimulus at its resonant frequency. This enables ZenseTag to read out the sensor variation using only energy harvested from wireless signals. UCSD inventors further demonstrate its implementation with a 15x10mm flexible PCB that connects sensors to a printed antenna and passive RFID ICs, enabling near real-time readout through a performant GUI-enabled software. They showcase ZenseTag's versatility by interfacing commercial force, soil moisture and photodiode sensors. 

(SD2024-084) Spatio-Temporal Sensing Strategies for Synthesizing Structured Virtual Array Manifolds with Applications to MmWave Systems

Researchers from UC San Diego developed a patent-pending novel Synthesis of Virtual Array Manifold (SVAM) sensing approach for the mmWave single RF chain systems. More specifically, this new technology for sensing leads to faster and more robust beam alignment. UCSD believes this contribution will have significant impact on the traditional paradigm for sensing in mmWave systems.

(SD2022-151) Engineered Protein Fusions that Bind G4C2 Human Repeats

Researchers from UC San Diego have engineered human zinc finger-containing fusion proteins that target and can destroy or modify human RNA transcripts that contain expanded G4C2 hexanucleotide repeats. This approach, which they have termed zinc fingerdirected RNA targeting, provides a means to, depending on the fusion protein, 1) target and degrade disease-causing RNA transcripts containing G4C2 expansions and to 2) target, label, and track the same transcripts in living cells.

(SD2022-222) Optimized CAG repeat‐targeting CRISPR/cas13d designs

Reseachers from UC San Diego demonstrated a proof of principle for a CAGEX RNA-targeting CRISPR–Cas13d system as a potential allele-sensitive therapeutic approach for HD, a strategy with broad implications for the treatment of other neurodegenerative disorders.