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A Point Of Care Method To Detect Covid19 Infected And Immune Patients For Pennies

The emergence of a novel coronavirus disease (COVID-19) in late 2019 has caused a worldwide health and economic crisis. Determining which members of the population are infected is key to re-opening of schools, universities, and non-essential businesses. To address this, researchers at UCI and UIC have developed an inexpensive point of care test using RNA aptamer technology for detecting COVID19 infected and immune patients that can be taken at home like a pregnancy test.

XNA enzymes to Validate and Treat Genetic Diseases

Allelic proteins are often considered undruggable targets, because therapeutics that interfere with these proteins while leaving the wild-type protein unharmed are difficult to come by. Researchers at UCI have developed a xeno-nucleic enzyme (XNAzyme) that offers a solution to this problem by selectively cleaving the mRNA of mutant alleles while leaving the wild-type mRNA unharmed. This novel gene silencing technology offers an efficient, safe, and effective approach to treating genetic diseases.

COMPOSITIONS AND METHODS FOR INCREASING HOMOLOGY-DIRECTED REPAIR

Molecular self-assembly with scaffolded DNA origami offers a route for folding nucleic acid molecules in user-defined ways, to generate DNA nanostructures. DNA nanostructures have a single-stranded DNA that is folded into distinct shapes via oligonucleotides termed “staples.” Engineered nuclease systems can be used to cleave a target DNA at a specified location. Examples of engineered nuclease systems include TALENs, zinc finger nucleases, mega-nucleases, and CRISPR-Cas systems. Introduction of a break in a nucleic acid (e.g. genome) can facilitate the introduction of a donor nucleic acid.    UC Berkeley researchers have discovered compositions comprising a gene-editing polypeptide, a single-stranded donor DNA, and one or more staple oligonucleotides which can be used for gene editing. 

Low Molecular Weight Xanthene-Based Fluorophore For Near- And Shortwave Infrared

Fluorophores are considered as optical “paints” to allow direct visualization of biological structures and processes with high spatial-temporal resolution. Small molecule fluorophores have been extensively studied and the color palette of these paints has expanded to the whole visible region of electromagnetic spectrum. Although powerful, the use of these imaging reagents is restricted to inherently transparent organisms and shallow imaging depths.   UC Berkeley researchers have discovered a low molecular weight xanthene-based fluorophore that exhibits excitation and emission profiles in the short wave near infrared region of the electromagnetic spectrum (SWIR). The fluorophore, KeTMR, was found to have an excitation and emission maxima at 853 nm and 1014 nm, respectively, Additional studies found the fluorophore had a Stokes shift of 161 nm, which is much larger than most rhodamine dyes.   

COMPOSITIONS AND METHODS FOR IDENTIFYING HOST CELL TARGET PROTEINS FOR TREATING RNA VIRUS INFECTIONS

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.

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.

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.

In Vitro Reconstituted Plant Virus Capsids For Delivering Rna Genes To Mammalian Cells

UCLA researchers in the Department of Chemistry & Biochemistry have developed a method for using in vitro reconstituted plant virus-derived vectors to package and deliver RNA genes for targeted delivery of vaccines, MRI contrast agents, and therapeutic proteins in RNA form.

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

CRISPR-CAS EFFECTOR POLYPEPTIDES AND METHODS OF USE THEREOF

The CRISPR-Cas system is now understood to confer bacteria and archaea with acquired immunity against phage and viruses. CRISPR-Cas systems consist of Cas proteins, which are involved in acquisition, targeting and cleavage of foreign DNA or RNA, and a CRISPR array, which includes direct repeats flanking short spacer sequences that guide Cas proteins to their targets.  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. The programmable nature of these minimal systems has facilitated their use as a versatile technology that is revolutionizing the field of genome manipulation.  Current CRISPR Cas technologies are based on systems from cultured bacteria, leaving untapped the vast majority of organisms that have not been isolated.  There is a need in the art for additional Class 2 CRISPR/Cas systems (e.g., Cas protein plus guide RNA combinations).     UC Berkeley researchers discovered a new type of Cas 12 protein.  Site-specific binding and/or cleavage of a target nucleic acid (e.g., genomic DNA, ds DNA, RNA, etc.) can occur at locations (e.g., target sequence of a target locus) determined by base-pairing complementarity between the Cas12 guide RNA (the guide sequence of the Cas12 guide RNA) and the target nucleic acid.  Similar to CRISPR Cas9, Cas12 enzymes are expected to have a wide variety of applications in genome editing and nucleic acid manipulation.    

Sustained Intracellular RNA Delivery and Expression

UCLA researchers in the Department of Chemistry and Biochemistry have developed a novel method for high protein expression levels, in situ, involving RNA-based therapeutics.

Catalytic MicroRNA Antagonists

UCLA researchers in the Department of Biological Chemistry have developed a novel approach for miRNA inhibition.

Simultaneous Detection Of Protein Isoforms And Nucleic Acids From Low Starting Cell Numbers

Embryo-specific nucleic acid modifications, including retrotransposon activity-derived genomic modifications and alternative splicing of mRNA, is crucial for the development of mammalian embryos. However, determining if all genomic modifications and mRNA isoforms translate to protein variations remain intriguing questions due to difficulty in measuring protein isoforms and nucleic acids from small starting cell numbers.    UC Researchers have developed a system for performing dual nucleic acid and protein isoform measurements on low starting cell numbers equivalent to the number of blastomeres composing early embryonic development stages (morula and blastocysts).  The system integrates fractionation polyacrylamide gel electrophoresis (fPAGE) with off-chip analysis of nucleic acids in the nuclei. An additional method can be used to remove nuclei for off-chip analysis. The system can measure expression of protein isoforms from the cytoplasmic fraction of 1-100 cells while achieving analysis of either DNA or mRNA retained in the nuclei. The researchers have demonstrated signal from immunoprobed protein correlates strongly with protein expression prior to lysis in TurboGFP-expressing cells and that mRNA levels correlate with protein abundance in TurboGFP-expressing cells.

Rapid, Sensitive Detection of Nucleic Acid Sequences in Environmental Samples

UCLA Researchers at the California NanoSystems Institute have developed a methodology that permits PCR-based detection of nucleic acid sequences in soil that does not require the isolation of DNA.

Lipid-Modified Oligonucleotides For Sample Barcoding in Droplet Microfluidics-Based Single-Cell RNA Sequencing

A new strategy for barcoding single living cells using lipid-modified oligonucleotides that can vastly enhance sample multiplexing in droplet microfluidics-based RNA sequencing

A Protein Inhibitor Of Cas9

  Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9 nucleases, when complexed with a guide RNA, effect genome editing in a sequence-specific manner. RNA-guided Cas9 has proven to be a versatile tool for genome engineering in multiple cell types and organisms.  There is a need in the art for additional compositions and methods for controlling genome editing activity of CRISPR/Cas9.   UC Berkeley researchers have discovered a new protein that is able to inhibit the Cas9 protein from Staphyloccocus aureus (SauCas9). SauCas9 is smaller than the frequently used Cas9 from Streptococcus pyogenes, which has a number of benefits for delivery. The inhibitor is a small protein from a phage and is capable of strongly inhibiting gene editing in human cells.

Gene Editing: An Improved Methodology For Homology Directed Repair In Cells

Gene editing in cells involves the use of sequence-specific nucleases that generate double-strand DNA breaks (DSBs) at specifically targeted sites in the genome. The DSBs are then repaired by non-homologous end joining (NHEJ) or, much less efficiently, by homology directed repair (HDR). In NHEJ, the two free DNA ends are joined together. This commonly results in small DNA deletions or insertions that inactivate the target gene. In HDR, the DSB is repaired by a mechanism that converts the DNA into the specific sequence that is provided by a DNA donor template. Thus, HDR enables genes to be modified or inserted at specifically desired sites.  The main drawback to HDR is the low efficiency of the process.

NANOPORE MEMBRANE DEVICE AND METHODS OF USE THEREOF

Several chemical, physical, and biological techniques have been used for delivering macromolecules into living cells. Delivery of biomolecules into living cells is essential for biomedical research and drug development as well as genome editing. However, conventional methods of delivery of biomolecules such as viral vectors, cell penetrating peptides, cationic lipids, positive charged polymers, bulk electroporation, and microinjection pose several challenges. Such challenges include safety concerns, toxicity, damage to the cells, limited loading capacity, low delivery efficiencies, low cell viabilities, low cell throughput, high cellular perturbation, and high costs.  Thus, there is a need for delivery devices and methods that allow for permeabilization of the cell membrane to facilitate delivery of biomolecules into cells.   UC Berkeley researchers have developed a universal delivery electroporation system that makes cell transfection very simple for all of types of cells. The technology can be used to replace conventional cellular delivery methods such as cationic lipid, positive charged polymer and bulk electroporation as well as microinjection.  The system can deliver biomolecules (e.g., DNA, RNA, proteins, nucleic acid-protein complexes (e.g., RNPs)) or other reagents into all cell types, including T-cells, which cannot be efficiently transfected with conventional approaches.  

Assay for Oligonucleotides in Serum Without Extraction or RT-PCR

Prof. Ameae Walker’s laboratory at the University of California, Riverside (UCR) has developed an assay to quantify oligos in sub-picomole amounts without the need for sample purification and amplification. This new competitive assay is called an ELOHA (Enzyme-Linked Oligonucleotide Hybridization Assay). The method is illustrated in Fig. 1, below.  Capture Oligos that are to hybridize with an oligo to be measured are covalently linked to a plate (1), a Detection Oligo, with the same sequence as the oligo to be measured, has a conjugated label, such as horseradish peroxidase or biotin.  The Detection Oligo then competes with the oligo of interest for binding to the Capture Oligo (2).  Once the hybridization is complete, the unbound oligos are washed away (3).  A colorimetric readout is produced (4) to inversely quantify the oligo of interest.  Fig. 1 Schematic of the ELOHA assay Fig. 2 shows the use of an ELOHA for amounts of Antimaia in mouse serum. Antimaia is a splice modulating oligomer therapy for breast cancer developed in the UCR lab of Prof. Walker.  

Inhibition Of Stress Granule Formation Through Manipulation Of UBAP2L

Stress granule (SG) formation has been suggested as a two-step process, with initial formation of a dense stable SG ‘‘core’’ followed by accumulation of proteins containing intrinsically disordered regions (IDRs) and low-complexity domains (LCDs) into a peripheral ‘‘shell’’ through a process involving liquid-liquid phase separation (LLPS). Recently, SGs have been associated with human neurodegenerative disorders characterized by the presence of toxic insoluble protein aggregates. This link is most compelling in the case of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), where numerous disease-causing mutations are purported to interfere with LLPS-dependent growth and dynamics of SGs.

Scalable Lipid Bilayer Microfluidics for High-Throughput Gene Editing

Researchers led by Paul Weiss from the Department of Chemistry and Pediatrics at UCLA have created a new microfluidic device for high-throughput gene editing of cells.

Cas12-mediated DNA Detection Reporter Molecules

Class 2 CRISPR-Cas systems are streamlined versions in which a single Cas protein (an effector protein, e.g., a type V Cas effector protein such as Cpf1) bound to RNA is responsible for binding to and cleavage of a targeted sequence. The programmable nature of these minimal systems has facilitated their use as a versatile technology that continues to revolutionize the field of genome manipulation.    Cas12 is an RNA-guided protein that binds and cuts any matching DNA sequence. Binding of the Cas12-CRISPR RNA (crRNA) complex to a matching single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) molecule activates the protein to non-specifically degrade any ssDNA in trans. Cas12a-dependent target binding can be coupled to a reporter molecule to provide a direct readout for DNA detection within a sample.  UC Berkeley researchers have developed compositions, systems, and kits having labeled single stranded reporter DNA molecules that provide a sensitive readout for detection of a target DNA. 

System and Methods for Efficient Collection of Single Cells and Colonies of Cells and Fast Generation of Stable Transfectants

A plate manufactured to enable samples of cells, microorganisms, proteins, DNA, biomolecules, transfectants, and other biological media to be positioned at specific sites. Some or all of the sites are built from removable material so that samples may be isolated.

CRISPR-based Graphene Biosensor for Digital Detection of DNA Mutations

UC Berkeley and Keck Institute researchers have reported the development and testing of a graphene-based field-effect transistor that uses CRISPR technology to enable the digital detection of a target sequence within intact genomic material. Termed CRISPR–Chip, the biosensor uses the gene-targeting capacity of catalytically deactivated Cas9 complexed with a specific single-guide RNA and immobilized on the transistor to yield a label-free nucleic-acid-testing device whose output signal can be measured with a simple handheld reader.  

Single Molecule DNA Profiling

UCLA researchers from the Department of Chemistry and Biochemistry have developed a cutting-edge technique that enables “fingerprinting” of a large number of molecules from a single cell. This technique could revolutionize current molecular diagnostics and prognostics, and therefore lead to personalized medicine in the future.

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