Researchers at the University of California, Davis have developed a modular CRISPR activation platform that enables precise upregulation of the haploinsufficient gene FOXG1 to address neurodevelopmental disorders without DNA cleavage.

Researchers at the University of California, Davis have developed a targeted gene editing system that reactivates the silenced CDKL5 gene by precise epigenetic modulation to treat CDKL5 deficiency disorder (CDD).

Researchers at the University of California, Davis have developed advanced epigenetic methods and systems that detect and assess developmental risks in embryos caused by maternal stress prior to conception.

RNA-guided systems mediate diverse functions ranging from mobile genetic element propagation to adaptive immunity. These systems comprise proteins that use guide RNAs bearing sequence complementarity to nucleic acid substrates, facilitating programmable recognition of different substrates by the same protein or enzyme. In RNA-guided systems known to date, one or two continuous segments in the guideRNA determines target specificity and can be altered to direct the system to a new target, including genomic DNA in eukaryotic cells. However, there are constraints to such systems, e.g., protein size and the need for a protospacer adjacent motif (PAM) in target DNA. However, there is a need for nucleic acid guided systems that overcome constraints of known systems, such as protein size or protospacer adjacent motif.UC Berkeley researchers have developed a programmable RNA-guided nucleic acid targeting platform termed the Viral Interference Programmable Repeat (VIPR) system. The system employs a repeat-based guide RNA architecture and an associated targeting protein to direct sequence-specific recognition of nucleic acid substrates. Target specificity is programmable through modification of selected guide regions, enabling adaptable targeting of DNA or RNA substrates across different biological contexts, including cellular and viral genetic material.

Monitoring of viral infections such as with the SARS-CoV-2 virus was vital to detection and characterization of new variants before they became widespread and allowed public health agencies to deploy resources and develop policies in advance of new waves of the virus. I The ARTIC Network developed a panel of primers and a workflow for whole genome sequencing of SARS-CoV-2 using multiplex PCR. This became a popular strategy for sequencing. The ARTIC protocol generates overlapping PCR amplicons that span the SARS-CoV-2 genome using a defined multiplex PCR primer set. These were sequenced and mapped to the SARS-CoV-2 genome to generate a high quality consensus sequence of the variant in the sample. While ARTIC was developed for SARS-CoV-2, the protocol is readily adaptable to a wide array of viruses. Despite its clear utility, challenges arose for ARTIC: new variants would arise that the consensus primers would not recognize and all testing for those new variants would be compromised. Normalization of samples with high variation of starting template proved difficult and sequencing library preparation was not optimized for convenience, speed, or cost.  

A highly precise and efficient gene-editing tool designed to correct single-nucleotide DNA mutations responsible for genetic diseases.

RNA-guided DNA targeting systems have fundamentally changed the landscape of genomic research and therapeutic development, yet the large size of traditional CRISPR tools creates a "delivery bottleneck" for therapeutic vectors. While the TIGR-Tas protein family offers a compact alternative for streamlined delivery, naturally occurring TasR proteins often lack the cleavage efficiency required for complex biological environments. UC Berkeley researchers have overcome this by engineering high-performance variants of ParTasR. This system is approximately one-quarter the size of Cas9. The engineered proteins demonstrate significantly higher on-target cleavage activity than wild-type sequences, offering a potent and hyper-compact alternative for the next generation of in vivo genome editing. 

Researchers at the University of California, Davis have enabled the creation of hybrid crops with enhanced fertility and yield by overcoming genetic distance barriers.

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RNA editing enables safe, reversible, and dose-tunable genetic correction without the permanent genomic risks or cargo limits of traditional DNA editing. However, conventional RNA editing tools often lack the ability to perform precise, large-scale modifications or site specific cut and paste operations on transcripts, which limits their therapeutic and research utility. UC Berkeley researchers have developed a programmable RNA editing platform that utilizes Type III CRISPR-Cas complexes integrated with a ligase to generate chimeric RNA molecules. This method enables robust RNA trans splicing, allowing for the replacement of defective exons, the insertion of large genetic sequences into transcripts, and the creation of novel fusion proteins. This approach provides a transient and potentially safer method for correcting genetic errors at the transcript level while offering greater flexibility for large scale RNA engineering. 

Researchers at the University of California, Davis have developed a scalable, plant-based method using somatic embryogenesis to produce high yields of water-soluble melanin externally from walnut tissues.

Together with Researchers at the University of Texas at Austin, researchers at the University of California, Davis have developed a method for synthesizing long polynucleotides using scaffolded cooperative binding and enzymatic ligation to improve yield, modification compatibility, and assembly accuracy.

Agrobacterium mediated plant transformation is a slow process that integrates foreign DNA into the genome, necessitating years of backcrossing to meet regulatory requirements. Current DNA free delivery methods often suffer from low editing efficiency and struggle to target multiple genes simultaneously. UC Berkeley researchers have developed a high efficiency genome editing platform that utilizes anionic polymers to enhance the delivery of CRISPR ribonucleoproteins into plant cells. This method can increase editing efficiency by up to 2400% and enable the simultaneous modification of four or more target sites in a single cell. 

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Researchers at the University of California, Davis have developed alacto-oligosaccharide (GOS) formulations selectively promote growth of beneficial Bifidobacteria species by tailoring oligosaccharide chain lengths.

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UC Berkeley researchers have developed a sophisticated computer-implemented framework that leverages transformer architectures to model the evolution of biological sequences over time. Unlike traditional phylogenetic models that often assume sites evolve independently, this framework utilizes a coupled encoder-decoder transformer to parameterize the conditional probability of a target sequence given multiple unaligned sequences. By capturing complex interactions and dependencies across different sites within a protein or genomic sequence, the model estimates the transition likelihood for each position. This estimation allows for a high-fidelity simulation of evolutionary trajectories. This approach enables a deeper understanding of how proteins change across different timescales and environmental pressures.

Researchers at the University of California, Davis have developed a diagnostic screen using DNA methylation and genetic variant analysis from newborn blood spots that enables early prediction of autism spectrum disorder (ASD) risk.

Researchers at the University of California, Davis have developed a technology that introduces an approach to creating semi-living, non-replicating cellular systems for advanced therapeutic applications.

Researchers at the University of California, Davis have developed novel antisense oligonucleotide (ASO) therapies that enhance ADNP protein expression to address haploinsufficiency in ADNP syndrome.

Researchers at the University of California, Davis have developed a computer-implemented method to identify viral mutations that enhance transmission and predict their prevalence in populations over time.