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Profiling Translation Rate With Ribo-Eclip

The eukaryotic ribosome is composed of 79 ribosomal protein – large (RPL) and ribosomal protein – small (RPS) subunit proteins that interweave with 4 highly structured RNAs (5S, 5.8S, 18S, and 28S rRNAs) to form the final translation-capable ribonucleoprotein. Thus, quantification of ribosome-associated RNA is highly similar to profiling of RNAs associated with other RNA binding proteins. We recently described the development of enhanced crosslinking and immunoprecipitation (eCLIP), a method to profile RNAs bound by an RNA binding protein of interest that showed thousand-fold improved recovery of protein-bound RNA [Van Nostrand et al 2016]. Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang MY, Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, et al: Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 2016, 13:508-514. https://pubmed.ncbi.nlm.nih.gov/27018577/


Viral infection is a multistep process involving complex interplay between viral life cycle and host immunity. One defense mechanism that hosts use to protect cells against the virus are nucleic-acid-mediated surveillance systems, such as RNA interference-driven gene silencing and CRISPR-Cas mediated gene editing. Another important stage for host cells to combat virus replication is translational regulation, which is particular important for the life cycle of RNA viruses, such as Hepatitis C virus and Coronavirus.  While efforts to characterize structural features of viral RNA have led to a better understanding of translational regulation, no systematical approaches to identify important host genes for controlling viral translation have been developed and little is known about how to regulate host-virus translational interaction to prevent and treat infections caused by RNA viruses.   UC Berkeley researchers have developed a high-throughput platform using CRISPR-based target interrogation to identify new therapeutics targets or repurposed drug targets for blocking viral RNA translation.  The new kits can also be used to identify important domains within target proteins that are required for regulating (viral RNA translation) and can inform drug design and development for treating RNA viruses.

Compositions And Methods For Allelic Gene Drive Systems And Lethal Mosaicism

Efficient super-Mendelian inheritance of transgenic insertional elements has been demonstrated in flies, mosquitoes, yeast, and mice. While numerous potentially impactful applications of such so-called gene-drive systems have been proposed they are currently limited to copying relatively large DNA cargo sequences (~1-10 Kb). Many desired genetic traits (e.g., drought tolerance in plants, crop yield, pest-resistance, or insecticide sensitivity), however, result from allelic variants altering only one or a few base pairs. An efficient system for super-Mendelian inheritance of such subtle genetic variants would accelerate a wide array of efforts to disseminate favorable traits throughout populations, or to assemble complex genotypes consisting of point-mutant alleles in combination with insertional transgenes for a multitude of research and applied purposes.

Methods and Applications for Controlling Cellular Viability Using Fluoride-Sensitivity

This technology employs fluoride-sensitivity to overcome the limitations of existing selection methods.

In plantae production of heterologous proteins using viral amplicons

Researchers at the University of California, Davis have developed a viral amplicon-based vector system for heterologous protein expression and production in plants.

Decorating Chromatin for Precise Genome Editing Using CRISPR

A novel fusion construct that fuses Cas9 to a truncated version of human PRDM9 with the purpose of improving precise genome editing via homologous direceted repair (HDR). PRDM9 is a protein that deposits histone marks H3K4me3 and H3K36me3 simultaneously during meiosis to mark recombination hot spots where crossover occurs and is resolved by homologous recombination. H3K36me3 has also been demonstrated to be required upstream of homologous recombination repair after double stranded breaks (DSBs) and during V(D)J recombination for adaptive immunity. Recent evidence suggests PRDM9 acts as a pioneer factor opening closed chromatin. The newly engineered PRDM9C-Cas9 fusion construct shows increased HDR and decreased non-homologous end joining mediated insertions and deletions (indels).

Small Cas9 Protein Inhibitor

A new protein that is able to inhibit the Cas9 protein from Streptococcus iniae (SinCas9). SinCas9 is capable of robust DNA cleavage and offers an immune orthogonal Cas9 for use in gene editing in human cells. The inhibitor is a small protein from a phage and is capable of inhibiting SinCas9 activity in vitro and in human cell genome editing experiments.

Novel Phage CRISPR-Cas Effectors and Uses Thereof

UC Berkeley researchers have discovered a novel family of proteins denoted Cas12L within the Type V CRISPR Cas superfamily distantly related to CasX, CasY and other published type V sequences.  These Cas12L proteins utilize a guide RNA to perform RNA-directed cleavage of DNA.

Single Conjugative Vector for Genome Editing by RNA-guided Transposition

The inventors have constructed conjugative plasmids for intra- and inter-species delivery and expression of RNA-guided CRISPR-Cas transposases for organism- and site-specific genome editing by targeted transposon insertion. This invention enables integration of large, customizable DNA segments (encoded within a transposon) into prokaryotic genomes at specific locations and with low rates of off-target integration.

Modulation Of Engineered Immune Cell Receptor Translation Using Noncoding Sequence Elements

It would be beneficial to control the expression of engineered immune cell receptors for use in cell-based cancer immunotherapy, known as adoptive cell therapy (ACT), or in other cell-based therapies using engineered regulatory T cells (engineered Tregs) to treat immune dysfunction such as autoimmunity or organ transplant rejection. In these therapies, immune cells such as T cells or natural killer (NK) cells are genetically modified to express an engineered cell surface receptor that directs these immune cells to tumor cells or specific tissues expressing a target ligand recognized by the receptor, thereby leading to tumor cell destruction (ACT) or moderated immune reaction (engineered Tregs). However, it has been found that ACT can suffer from severe toxic side effects due to overactivation of engineered immune cells used in ACT such as CAR T-cells, due to signaling by the engineered cell surface receptor. Conversely, overactive immune cells can become exhausted and lose efficacy over time. Present attempts to regulate CAR expression do not account for control exerted at the level of protein synthesis. It would therefore be useful to be able to tune the activity of immune cells engineered for ACT or for treatment of immune dysfunction, by either increasing or decreasing the protein synthesis of the engineered immune cell surface receptor, i.e. the engineered TCR or CAR. This research describes compositions and methods for selectively increasing or decreasing the protein synthesis of engineered immune cell surface receptors using noncoding sequences in the 3’-untranslated region (3’-UTR) of messenger RNAs (mRNAs) encoding the engineered TCRs or CARs. These 3’-UTR sequences are sensitive to regulation by translation initiation factor eIF3 and can be used to modulate the strength and time duration of TCR or CAR protein synthesis.  

Improved Plant Regeneration Method Using GRFs, GIFs or Chimeric GRF-GIF Proteins

Researchers at the University of California, Davis and the Institute of Molecular and Cellular Biology of Rosario in Argentina have collaborated to develop methods for improving plant regeneration efficiency using transformations via a GRF, a GIF, or a GRF-GIF chimera. 

Reacting Molecules and Colloids Electrophoretically

Researchers in UCLA's Department of Chemistry and Biochemistry have harnessed gel electrophoresis in order to direct and program controlled collisional reactions between pulse-like bands of molecules and/or colloidal reagent species.

Automated Drosophila Maintenance System

Drosophila spp., also known as fruit flies, are widely used in genetic research. Drosophila lines (e.g. flies with a particular mutation) can only be stored as live animals – they cannot be frozen and remain viable. So to maintain the stocks, the live flies are manually transferred from an old vial to a new vial on a regular basis (every 1-2 weeks). Some Drosophila labs maintain hundreds or even thousands of individual lines and so maintenance of these lines can be very time consuming. A UC Santa Cruz Drosophila researcher has developed a simpler and more efficient method of transferring the flies that requires significantly less hands-on work.

Identification Of Pan-Cancer Small Cell Neuroendocrine Phenotypes And Vulnerabilities

UCLA researchers in the Department of Molecular and Medical Pharmacology have developed a classifier for the identification and treatment of small cell neuroendocrine cancers and small-round-blue cell tumors not previously identified.

Enzymatic Modification Of Amino Acids And Their Products

The inventors report the structural characterization of BesD, a recently discovered radical halogenase from the FeII/-ketogluturate family that chlorinates the free amino acid lysine. They also identify and characterize additional halogenases that produce mono- and di-chlorinated as well as brominated and azidated amino acids. The substrate selectivity of this new family of radical halogenases takes advantage of the central role of amino acids in metabolism and enables engineering biosynthetic pathways to afford a wide variety of compound classes, such as heterocycles, diamines, -keto acids, and peptides. 

DNA Methylation Measurement For Mammals Based On Conserved Loci

UCLA researchers in the Departments of Human Genetics and Biological Chemistry have developed a new approach for measuring DNA methylation levels in mammals based on short and highly conserved nucleotide sequences.  This method facilitates the development of chip for measuring DNA methylation that can be used for cross-species comparisons and used for building universal epigenetic aging clocks (age estimators) that apply to all mammals.

Augmentations to Lentiviral Vectors to Increase Expression

UCLA researchers in the Department of Microbiology, Immunology and Molecular Genetics have developed a novel method to produce short lentiviral vectors with tissue-specific expression, with a primary focus on lentiviral vectors for treating sickle cell disease and other disorders of hemoglobin.

Optimized Lentiviral Vector for Stem Cell Gene Therapy of Hemoglobinopathies

UCLA researchers in the Department of Microbiology, Immunology and Molecular Genetics have developed a novel method to produce short lentiviral vectors with tissue-specific expression, with a primary focus on lentiviral vectors for treating sickle cell disease and other disorders of hemoglobin.

Generation Of Minimal Enhancer Elements Using Massively Parallel Reporter Assays

UCLA researchers in the Department of Microbiology, Immunology and Molecular Genetics have developed a novel method to produce short lentiviral vectors with tissue-specific expression, with a primary focus on lentiviral vectors for treating sickle cell disease and other disorders of hemoglobin.

Improved Cas12a Proteins for Accurate and Efficient Genome Editing

Mutated versions of Cas12a that remove its non-specific ssDNA cleavage activity without affecting site-specific double-stranded DNA cutting activity. These mutant proteins, in which a short amino acid sequence is deleted or changed, provide improved genome editing tools that will avoid potential off-target editing due to random ssDNA nicking.

Method To Implement A Crispr-Cas9 Copycat Gene Drive In Rodents

Currently, alleles at multiple loci in the mouse genome must be combined by Mendelian genetics in crosses of animals to one another to produce a desired compound mutant genotype. For example, to combine homozygous mutations at two loci, animals that are heterozygous for each gene must be produced by breeding, and these are subsequently crossed to one another. Since the frequency of homozygosity for each allele is 1:4 the frequency of homozygosity for both genes is 1:16. Since the average litter of mice is approximately 10 pups, and the generation time from conception to reproductive age is about 3 months, this requires a substantial number of animals and time. With the addition of each new locus (three, four, etc), the cost measured in animals, time, and money increases exponentially. These factors increase substantially more if two or more loci are genetically linked, which requires rare recombination events to combine engineered alleles on the same chromosome. The CRISPR-Cas9 gene drive system stands to revolutionize rodent breeding. If each desired allele is encoded as a gene drive element that contains an sgRNA designed to target the same genomic location in the wild type homologous chromosome, each locus will be “driven” to homozygosity in the presence of Cas9. Therefore, in order to combine three alleles, for example, a mouse with one gene drive element (A) would be crossed to a mouse that encodes Cas9. Offspring of this cross would then be crossed to mice carrying gene drive element B, and these offspring would be crossed to mice carrying gene drive element C. In the presence of Cas9 at each generation, these gene drive elements at three distinct loci will be converted to homozygosity such that 50% of offspring, those that inherit Cas9, will be triple homozygous after three generations, even if they are genetically linked loci. A CRISPR-Cas9 mediated gene drive leverages the native cellular mechanism of homology directed repair to copy a desired allele from one chromosome to another. This process can convert a heterozygous genotype to homozygosity in a single generation. While CRISPR-Cas9 gene drives have been implemented in two species of insects, flies and mosquitos, it has not been reported in any non-insect animal species. 

Biotinylated Ligand-Directed Targeting Lentiviral Vectors

UCLA researchers in the Department of Medicine have developed a novel method to conjugate targeting ligands on lentiviral vectors.  The method allows for selective transduction of mammalian cells types avoiding non-target organs.

4D-seq: Single Cell RNA-sequencing with in situ Spatiotemporal Information

To develop a novel imaging-based single cell RNA-sequencing (scRNA-Seq) platform that allows capturing of spatiotemporal information and cellular behavior of the sequenced cells within tissue.

DARTS: Deep Learning Augmented RNA-seq Analysis of Transcript Splicing

Researchers led by Yi Xing have developed a novel deep learning algorithm to detect alternative splicing patterns in RNA-seq data

Illumination Device for Dynamic Spatiotemporal Control of Photostimulation

A programmable LED device that illuminates multiple spatial locations (termed wells) with user-defined light patterns whose intensity can be modulated as a function of space and time. The devices are used for optogenetic stimulation of tissue culture plates (24-well and 96-well) kept in a heated and humidified tissue culture incubator, as well as photopatterning of hydrogels. In brief, light from LEDs passes through optical elements that ensure uniform illumination of each well. Parameters of the optical system, such as LED configuration, optical diffuser elements, materials, and geometry, were modeled and optimized using the optical ray tracing software Zemax OpticStudio. An electronics subsystem allows programmed control of illumination intensity and temporal sequences, with independent control of each well. Spatial precision is conveyed through a photomask attached to the culture plate. The hardware design also includes a cooling system and vibration isolation to reduce heating and damage to the sample. Lastly, a graphical user interface (GUI) was used to wirelessly program the illumination intensity and temporal sequences for each well. The devices can thus illuminate 24 independent channels with visible, NIR, or UV light with intensity ranges of 0 to 20-100 microwatts per millimeter-squared with 16-bit intensity resolution, and a temporal resolution of 1 millisecond and spatial resolution of 100 microns. In summary, the device allows uniform illumination of multiple wells for multiplexed photoactivation or photopolymerization of various substrates (light-responsive bacterial or mammalian cells grown in tissue culture, hydrogels, dyes, etc) with user-defined patterns. The device can be combined with a robotic handler, microscope, spectrometer, etc, to enable high-throughput illumination and simultaneous recording of the sample.

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