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.

The Major Histocompatibility Complex (MHC), is a genomic region that expresses proteins involved in immune system functions and that are important for organ transplantation. In humans, this type of gene is referred to as the Human Leukocyte Antigen (HLA). The HLA region is haplotypic, with all of the region inherited from one parent. HLA is highly polymorphic within the human population, both in terms of protein structure as well as genomic variability.This high genomic diversity makes accurate genotyping difficult using methods such as short-read sequencing. That said, current long-read sequencing methods and analysis can yield incomplete and inaccurate results. 

Clustered regularly interspaced short palindromic repeats (CRISPR) screening is a cornerstone of functional genomics, enabling genome-wide knockout studies to identify genes involved in specific cellular processes or disease pathways. The success of CRISPR screens depends critically on the design of effective guide RNA (gRNA) libraries that maximize on-target activity while minimizing off-target effects. Current CRISPR screening lacks tools that can natively integrate next-generation sequencing (NGS) data for context-specific gRNA design, despite the wealth of genomic and transcriptomic information available from modern sequencing approaches. Traditional gRNA design tools have relied on static libraries with limited genome annotations and outdated scoring methods, lacking the flexibility to incorporate context-specific genomic information. Off-target effects are also a concern, with CRISPR-Cas9 systems tolerating up to three mismatches between single guide RNA (sgRNA) and genomic DNA, potentially leading to unintended mutations that could disrupt essential genes and compromise genomic integrity. Additionally, standard CRISPR library preparation methods can introduce bias through PCR amplification and cloning steps, resulting in non-uniform gRNA representation.

Professor Linlin Zhao and their team from the University of California, Riverside have developed mTAP, a new chemical probe engineered to selectively bind to abasic sites within mitochondrial DNA without affecting nuclear DNA. Unlike non-specific agents, mTAP is equipped with a mitochondria-targeting group, ensuring its precise localization. This invention is advantageous over current technology because its mechanism of action involves forming a stable chemical bond with damaged DNA sites, thereby protecting mtDNA from enzymatic cleavage and maintaining its replication and transcriptional activities.    Fig 1: The UCR mitochondria-targeting water-soluble probe mTAP exclusively reacts with mitochondrial abasic sites, and retains mitochondrial DNA levels under genotoxic stress which are responsible for certain mitochondrial diseases. 

Nucleic acid therapies hold vast therapeutic potential. FDA approved therapies include mRNA vaccines against SARS-COV2 and CRISPR/CAS9 treatment to treat sickle cell.  Both therapies use non-viral methods to deliver designer nucleic acid therapies to cells. However, a limitation of these approaches is the lack of organ and cell-specific delivery. Controlling gene delivery and expression in various cell subsets is challenging. UC Berkeley researchers have shown that the nanoscale topology of CpG oligodeoxynucleotide (CpG-ODN) motifs can be used to stimulate various immune cell subsets and alter gene expression from exogenously delivered mRNA in distinct immune cell subsets. CpG-ODNs of different classes are known to induce different inflammatory profiles in immune cells based on the structure and nanoscale topology of the short DNA strand. The researchers have found novel nanostructures which can be used to present or deliver CpGs to various cell subsets and regulate gene expression in these subsets.

A cornerstone of bacterial molecular biology is the ability to genetically manipulate the microbe under study. Manipulating the genomes of bacteria is critical to many fields. Such manipulations are made by genetic engineering, which often requires new pieces of DNA to be added to the genome. It is often difficult to move genes into a recalcitrant destination organism due to surveillance systems (CRISPR, Restriction Modification) of the destination/host which degrade invading DNA . It may be commercially desirable to evade these systems in the destination organism. However, evading these systems may require significant experimental effort to design and implement.

A groundbreaking method for the efficient isolation and preservation of high-purity small extracellular vesicles (sEVs - exosomes) from biofluids using a novel EXO-PEG-TR reagent.

Most tumors are extremely complex, having many oncogene drivers and are, therefore, not as amenable to a CRISPR-mediated therapies. Pediatric low-grade glioma (pLGG) is a type of brain cancer that arises during childhood. Some interventions exist, including surgery and inhibitor drugs, but there is no cure for pLGG. In contrast to most types of cancer (which feature a host of driver oncogenes), pLGG tumors tend to arise due to a single driver oncogene mutation. This aspect makes pLGG a potential target for a genome editing intervention. Because CRISPR enzymes can precisely discriminate between wild-type and mutant sequences in a single cell, enzymes such as Cas9 can target a mutant oncogene site without impacting the corresponding wild-type locus in a non-cancer cell. UC Berkeley researchers have developed a CRISPR-based strategies for anti-cancer genome editing.  The invention consists of a suite of genome editing strategies with the capacity to selectively inactivate the oncogene underlying tumor pathology, for example, mutations in pLGG. Deployed via a delivery strategy with the capacity for broad genome editing of brain cells, our strategy will have the capacity to halt – and potentially reverse – tumor growth.

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.  

Hybridization capture approaches allow targeted high-throughput sequencing analysis at reduced costs compared to shotgun sequencing. Hybridization capture is particularly useful in analyses of genomic data from ancient, environmental, and forensic samples, where target content is low, DNA is fragmented and multiplex PCR or other targeted approaches often fail. Hybridization capture involves the use of "bait" nucleotides that capture genomic sequences that are of particular interest for the researcher. Current bait synthesis methods require large-scale oligonucleotide chemical synthesis and/or in vitro transcription. Both RNA and DNA bait generation requires synthesizing template oligonucleotides using phosphoramidite chemistry. Microarray-based synthesis generates oligonucleotides in femtomole scales with high chemical coupling error rates. Templates synthesized at small-scale require enzymatic amplification before use in hybridization capture.The solution proposed here involves a simple and highly efficient method to generate target probes using isothermal amplification. Target sequences are circularized and then amplified by rolling circle amplification. This method generates concatemers comprising thousands of copies of the target seqeuence. Restriction digestion of the amplified product then produces probes to use in target enrichment applications. 

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.

Lipid Nanoparticles (LNPs) are a leading platform for nucleic acid delivery, widely used in therapeutics and vaccine development. However, the process of optimizing new LNP formulations has been significantly hindered by labor-intensive and costly screening methods, which require individual injections into animal models. Given the vast array of potential lipid compositions and formulation variables, these constraints severely impede the efficiency of research and development.To overcome these challenges, UC Berkeley researchers have developed a novel approach for identifying and characterizing functional nucleic acid delivery vehicles. This innovative method leverages circular RNA barcoding technology, enabling a more efficient screening process. Instead of relying on conventional cell sorting techniques, which restrict screening to specific organs and host species, this breakthrough allows direct detection of barcoded nucleic acids within circular RNAs in treated cells. By analyzing the barcodes detected, researchers can accurately determine which lipid compositions and formulations successfully delivered RNA molecules.  This technology represents a significant advancement in LNP research, offering a scalable, cost-effective solution that enhances the precision and scope of nucleic acid delivery screening.

Researchers at the University of California, Davis have developed a technology enabling hybrid crops to reproduce cloned seeds, boosting yield and stability.

Researchers at the University of California, Davis have developed advancements in understanding exodermal differentiation in plant roots highlighting the role of two transcription factors in plant adaptation and survival.

Professor Giulia Palermo and colleagues from the University of California, Riverside and the University of Rochester have developed high-fidelity Cas13a variants with increased sensitivity for base pair mismatches.The activation of these Cas13a variants can be inhibited with a single mismatch between guide-RNA and target-RNA, a property that can be used for the detection of SNPs associated with diseases or specific genotypic sequences.  

Researchers at the University of California, Davis have developed a novel cell segmentation technology for accurate analysis of non-spherical cells and that offers a comprehensive, high-throughput approach for analyzing the transcriptomic and metabolomic data to study complex biological processes at the single-cell level.

This technology offers a groundbreaking approach to map biomolecules in 3D space with subcellular resolution, revolutionizing our understanding of tissue organization and disease propagation.

The invention is a self-selection DNA editing system for modifying microbial communities. It consists of a gene editing tool and a donor DNA with a bacteriocin unit. This unit is integrated into the target cell's genome, providing a survival advantage and ensuring that only the successfully modified cells proliferate. This allows for precise, targeted editing of microbial populations in various settings, including in vitro and in vivo environments.

This invention provides a novel method for delivering epigenetic editor components into cells using virus-like particles (VLPs). The VLPs are designed to encapsulate the necessary genetic and protein components for targeted epigenetic editing without integrating into the host cell's genome. This non-integrating approach reduces the risk of off-target effects and potential for unintended genetic modifications, making it a safer and more precise delivery system for therapeutic and research applications. The VLPs can be engineered to target specific cell types, ensuring that the epigenetic editing components are delivered only where they are needed.

Class 2 CRISPR-Cas are streamlined versions in which a single Cas protein bound to RNA is responsible for binding to and cleavage of a targeted sequence. Theprogrammable nature of these minimal systems has facilitated their use as a versatile technology for genome editing.  CRISPR-Cas enzymes with reduced requirements for a protospacer-adjacent motif (PAM) sequence adjacent to the target site could improve the breadth of target sites available for genome editing.  UC Berkeley researchers have developed a novel PAM-loose 12a variants, nucleic acids encoding the variant Cas12a proteins and systems using these variants that make the Cas12a-based CRISPR technology much easier to design a DNA target for carrying out genome editing in human cells. 

Deoxyribonucleic acid- (DNA-) based identification in forensics is typically accomplished via genotyping allele length at a defined set of short tandem repeat (STR) loci via polymerase chain reaction (PCR). These PCR assays are robust, reliable, and inexpensive. Given the multiallelic nature of each of these loci, a small panel of STR markers can provide suitable discriminatory power for personal identification. Massively parallel sequencing (MPS) technologies and genotype array technologies invite new approaches for DNA-based identification. Application of these technologies has provided catalogs of global human genetic variation at single-nucleotide polymorphic (SNP) sites and short insertion-deletion (INDEL) sites. For example, from the 1000 Genomes Project, there is now a catalog of nearly all human SNP and INDEL variation down to 1% worldwide frequency. Genotype files, generated via MPS or genotype array, can be compared between individuals to find regions that are co-inherited or identical-by-descent (IBD). These comparisons are the basis of the relative finder functions in many direct-to-consumer genetic testing products. A special case of relative-finding is self-identification. This is a trivial comparison of genotype files as self-comparisons will be identical across all sites, minus the error rate of the assay. For many forensic samples, however, the available DNA may not be suitable for PCR-based STR amplification, genotype array analysis, or MPS to the depth required for comprehensive, accurate genotype calling. In the case of PCR, one of the most common failure modes occurs when DNA is too fragmented for amplification. For these samples, it may be possible to directly observe the degree of DNA fragmentation from the decreased amplification efficiency of larger STR amplicons from a multiplex STR amplification. In the case of severely fragmented samples, where all DNA fragments are shorter than the shortest STR amplicon length, PCR simply fails with no product.

Aberrant splicing contributes to the etiology of many inherited diseases. Pathogenic variants impact pre-mRNA splicing through a variety of mechanisms. Most notably, variants remodel the cis-regulatory landscape of pre-mRNAs by ablation or creation of splice sites, and auxiliary splicing regulatory sequences such as exonic or intronic splicing enhancers (ESE and ISE, respectively) and splicing silencers (ESS and ISS, respectively). Splicing-sensitive variants cripple the integrity of the gene, resulting in the production of a faulty message that is either unstable or encodes an internally deleted protein. Antisense oligonucleotides (ASOs) are a promising therapeutic modality for rescuing pathogenic aberrant splicing patterns as their direct base pairing abilities make them highly customizable and specific to targets. Although challenges such as toxicity, delivery and stability represent barriers to the clinical translation of ASOs, solutions to these challenges exist, as exemplified by the recent FDA approval of multiple ASO drugs.Generally, ASO's that target splicing mutations are limited to mutations in and around splicing enhancers and exonic mutations are commonly not targeted because of the idea that the mutation causes a significant change in protein function. 

The strategy employed by the invention is inspired by splicing factors, a category of RNA-binding protein that influence alternative splicing outcomes. These splicing factors are trans-acting, and act to enhance or silence exon inclusion by binding near or on the target exon and promoting or repressing the activity of splicing machinery. Scientifically, a highly programmable, minimally disruptive system to increase exon inclusion could allow for higher-throughput identification of functional roles of specific exons than have been previously shown.

A patent-pending platform technology designed to work in any gravity, which includes in microgravity environments, able to execute advanced molecular biology workflows; representing a paradigm shift in automation for molecular biology.

Researchers from UC San Diego developed an invention that enables protein expression to be upregulated using specific proteins and/or peptide sequences derived from SARS-CoV-2 proteins that are engineered to recognize specific mRNA transcripts by fusion to RNA-targeting modules such as CRISPR/Cas systems. They anticipate that these proteins can be fused or tethered to any engineered RNA-targeting moiety/module such as PUF/Pum, and pentatricopeptide proteins.