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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.

Endoribonucleases For Rna Detection And Analysis

96 Normal 0 false false false EN-US X-NONE X-NONE /* 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-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;} Bacteria and archaea possess adaptive immune systems that rely on small RNAs for defense against invasive genetic elements. CRISPR (clustered regularly interspaced short palindromic repeats) genomic loci are transcribed as long precursor RNAs, which must be enzymatically cleaved to generate mature CRISPR-derived RNAs (crRNAs) that serve as guides for foreign nucleic acid targeting and degradation. This processing occurs within the repetitive sequence and is catalyzed by a dedicated CRISPR-associated (Cas) family member in many CRISPR systems.  Endoribonucleases that process CRISPR transcripts are bacterial or archaeal enzymes capable of catalyzing sequence- and structure- specific cleavage of a single- stranded RNA. These enzymes cleave a specific phosphodiester bond within a specific RNA sequence.  UC Berkeley researchers discovered variant Cas endoribonucleases, nucleic acids encoding the variant Cas endoribonucleases, and host cells genetically modified with the nucleic acids that can be used, potentially in conjunction with Cas9, to detect a specific sequence in a target polyribonucleotide and of regulating production of a target RNA in a eukaryotic cell.  For example, it was found that the variant Cas endoribonuclease has an amino acid substitution at a histidine residue such that is is enzymatically inactive in the absence of imidazole and is activatable in the presence of imidazole.  

dCas9 Epigenome Editing Toolkit

Researchers at the University of California, Davis have developed a dCas9 toolkit for human epigenome editing.

Generation of Novel Genomic Tools for Use in the Normalization of Endogeneous RNA Expression Between Different Samples

Genome searching tools are a growing field within the medical and biological research communities. There are now a large number of companies offering services relating to understanding genetic information, and typical laboratory functional genomic assays produce a range of data, including sequencing of transcription factors and regulatory regions. Researchers routinely search over 1,417 functional genomic datasets that are publically available, and users have a range of tools to search the data, including many online. Genetic information requires further processing to become biologically meaningful and a pressing challenge is to effectively search functional genomic data and new tools and processes are needed for searching genomic information.

High-Throughput Microfluidic Gene-Editing via Cell Deformability within Microchannels

UCLA researchers in the Departments of Pediatrics and Chemistry & Biochemistry have developed a microfluidic device for delivery of biomolecules into living cells using mechanical deformation, without the fouling issues in current systems.

Global Training Of Neural Networks For Phenomic Classification

UCLA researchers in the Department of Electrical Engineering have developed a high-throughput, label-free cell classification method based on time-stretch quantitative phase imaging.

Type V CRISPR/CAS Effector Proteins for Cleaving ssDNA and Detecting Target DNA

Normal 0 false false false EN-US X-NONE X-NONE /* 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-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Class 2 CRISPR–Cas systems (e.g., type V CRISPR/Cas systems such as Cas12 family systems) are characterized by effector modules that include a single effector protein. For example, in a type V CRISPR/Cas system, the effector protein - a CRISPR/Cas endonuclease (e.g., a Cas12a protein) - interacts with (binds to) a corresponding guide RNA (e.g., a Cas12a guide RNA) to form a ribonucleoprotein (RNP) complex that is targeted to a particular site in a target nucleic acid via base pairing between the guide RNA and a target sequence within the target nucleic acid molecule.  Thus, like CRISPR-Cas9, Cas12 has been harnessed for genome editing based on its ability to generate targeted, double-stranded DNA (dsDNA) breaks.   UC Berkeley researchers have discovered that RNA-guided DNA binding unleashes indiscriminate single-stranded DNA (ssDNA) cleavage activity by Cas12a that completely degrades ssDNA molecules. The researchers found that target-activated, non-specific ssDNase cleavage is also a property of other type V CRISPR-Cas12 enzymes. By combining Cas12a ssDNase activation with isothermal amplification, the researchers were able to achieve attomolar sensitivity for DNA detection.  For example, rapid and specific detection of human papillomavirus in patient samples was achieved using these methods and compositions.   

Lipoplex-Mediated Efficient Single-Cell Transfection Via Droplet Microfluidics

The invention is an on-chip, droplet based single-cell transfection platform providing higher efficiency and consistency compared to conventional methods. Novel techniques following cell encapsulation yields uniform lipoplex formation, which increases the transfection accuracy. The invention solves the dilemma of the trade-off between efficiency and cell viability, and offers a safe, cell friendly and high transfection solution that is crucial for applications like gene therapy, cancer treatment and regenerative medicine.

A Dual-RNA Guided CasZ Gene Editing Technology

Normal 0 false false false EN-US X-NONE X-NONE /* 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-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} 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 systems 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, so 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 protein, CasZ.  (CasZ) is short compared to previously identified CRISPR-Cas endonucleases, and thus use of this protein as an alternative provides the advantage that the nucleotide sequence encoding the protein is relatively short.  The researchers have shown that the CRISPR CasZ protein and its variants can be used in a complex for specific binding and cleavage of DNA. The CRISPR CasZ complex utilizes a novel RNA and a guide RNA to perform double stranded cleavage of DNA and the complex is expected to have a wide variety of applications in genome editing and nucleic acid manipulation. 

Cas12c/C2C3 Compositions and Methods of Use

96 Normal 0 false false false EN-US X-NONE X-NONE /* 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-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;} 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 systems 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, so there is a need in the art for additional Class 2 CRISPR/Cas systems (e.g., Cas protein plus guide RNA combinations).   Researchers have shown that a Cas12c protein (also referred to as a Cas12c polypeptide or a C2c3 polypeptide) complex as well as Cas12c variants can be used for specific binding and cleavage of DNA. The Cas12c complex utilizes a novel RNA and a guide RNA to perform double stranded cleavage of DNA. Similar to CRISPR Cas9, Cas12c enzymes are expected to have a wide variety of applications in genome editing and nucleic acid manipulation.   

Predictive Optimization Of Pharmeceutical Efficacy

UCLA researchers in the Department of Mechanical and Aerospace Engineering have developed a machine learning platform to virtually screen combinatorial drug therapies.

EpiSort: A Novel Method Using Deep Bisulfite Sequencing to Determine Immune Cell Types in Solid Tissue Samples

EpiSort is a novel method of using DNA methylation patterns to determine the proportion of immune cell populations in solid tissue samples.

Computational Sensing Using Low-Cost and Mobile Plasmonic Readers Designed by Machine Learning

UCLA researchers have developed a novel method for computational sensing using low-cost and mobile plasmonic readers designed by machine learning.

An Efficient Gene Editing Approach to Create Transgene-free Mutant Plants

Effective isolation of targeted mutations generated by CRISPR/Cas9 requires not only reasonable editing efficiency, but also an easy method to screen for the mutations. Editing events generated by CRISPR/Cas9 are normally identified by restriction enzyme digestion of PCR fragments or by in vitro digestion using purified Cas9 protein. Both methods are time-consuming and laborious. Simplified screening methods are urgently needed.

Integrated Electrowetting Nanoinjector and Aspirator

Gene therapy applications necessitate cell transfection techniques for delivering biomaterial into multiple or a single cell(s). The global market for transfection technologies can be worth more than half a billion by 2017. Current viral and chemical transfection techniques have limited ease of fabrication, transfection efficiency, dosage control, and cell viability. The invention discloses a simple yet efficient technique for nanoinjection of material into a single cell with high transfection efficiency, controlled dosage delivery, and full cell viability.

THERMOSTABLE RNA-GUIDED ENDONUCLEASES AND METHODS OF USE THEREOF (GeoCas9)

96 Normal 0 false false false EN-US X-NONE X-NONE /* 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-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;} 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. The programmable nature of these systems has facilitated their use as a versatile technology that is revolutionizing the field of genome manipulation. There is a need in the art for additional CRISPR-Cas systems with improved cleavage and manipulation under a variety of conditions and ones that are particularly thermostable under those conditions.     UC researchers discovered a new type of RNA-guided endonuclease (GeoCas9) and variants of GeoCas9.  GeoCas9 was found to be stable and enzymatically active in a temperature range of from 15°C to 75°C and has extended lifetime in human plasma.  With evidence that GeoCas9 maintains cleavage activity at mesophilic temperatures, the ability of GeoCas9 to edit mammalian genomes was then assessed.  The researchers found that when comparing the editing efficiency for both GeoCas9 and SpyCas9, similar editing efficiencies by both proteins were observed, demonstrating that GeoCas9 is an effective alternative to SpyCas9 for genome editing in mammalian cells.  Similar to CRISPR-Cas9, GeoCas9 enzymes are expected to have a wide variety of applications in genome editing and nucleic acid manipulation.   

Novel Inhibitors of Mitochondrial Electron Transport

Researchers at the University of California, Davis have discovered a class of compounds that both bind to a unique newly-discovered binding site in respiratory complex III and act as inhibitors of electron transport for use as mitochondrial anti-cancer drugs.

Gene Delivery Into Mature Plants Using Carbon Nanotubes

96 Normal 0 false false false EN-US X-NONE X-NONE /* 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-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;} Current methods of biomolecule delivery to mature plants are limited due to the presence of plant cell wall, and are additionally hampered by low transfection efficiency, high toxicity of the transfection material, and host range limitation. For this reason, transfection is often limited to protoplast cultures where the cell wall is removed, and not to the mature whole plant.  Unfortunately, protoplasts are not able to regenerate into fertile plants, causing these methods to have low practical applicability. Researchers at the University of California have developed a method for delivery of genetic materials into mature plant cells within a fully-developed mature plant leaf, that is species-independent. This method utilizes a nano-sized delivery vehicle for targeted and passive transport of biomolecules into mature plants of any plant species. The delivery method is inexpensive, easy, and robust, and can transfer biomolecules into all phenotypes of any plant species with high efficiency and low toxicity.

Methods for Global RNA-Chromatin Interactome Discovery

Recent decades of genomic research reveal that mammalian genomes are more prevalently transcribed than previously anticipated. It is now quite clear that mammalian genomes express not only protein-coding RNAs but also a large repertoire of non-coding RNAs that have regulatory functions in different layers of gene expression. Many of those regulatory RNAs appear to directly act on chromatin, as exemplified by various long noncoding RNAs (IncRNAs). Some of those regulatory RNAs mediate genomic interactions only in cis, while others, such MALAT1 and NEAT1, are capable of acting in trans. These findings suggest an emerging paradigm in regulated gene expression via specific RNA-chromatin interactions. Various techniques have been developed to localize specific RNAs on chromatin. These methods, such as chromatin Isolation by RNA purification or comprehensive identification of RNA binding proteins (ChIRP), capture hybridization analysis of RNA targets (CHART), and RNA affinity purification (RAP), all rely on using complementary sequences to capture a specific RNA followed by deep sequencing to identify targets on chromatin. Importantly, all of these methods only allow analysis of one known RNA at a time, and up to date, a global view is lacking on all RNA-chromatin interactions, which is critical to address a wide range of functional genomics questions.

Diagnostic Gene Signature For Cancer Vascular Mimicry in Solid Tumors

One of the characteristic trademarks of tumorigenesis is the need for an extensive vascular system to supply blood for the tumor to grow and disseminate from the original node to distant sites via the process of metastasis. This involves the growth of new vessels from existing vessels, as well as the migration of tumor cells through the extracellular matrix (ECM) and into the lymphatic or vascular systems. However, some very aggressive solid tumors can form vascular channels by themselves, which is termed vascular mimicry (VM). Moreover, only certain cells in these tumors have the ability to produce blood-transporting channels, contributing to metastasis. There is growing evidence that supports the idea that VM can be a prognostic factor for poor clinical outcomes in various types of cancer. Currently, VM is identified by a pathologist’s evaluation of histological slides, wherein vascular-like structures that do not stain positive for endothelial cells are identified as VM. Thus far, conserved molecular biomarkers that define this phenotype have remained unknown.

Assay for Inhibitors of Nonsense-Mediated RNA Decay

Prof. Sika Zheng at UCR has developed a new endogenous NMD assay that is both sensitive and quantitative. The assay can be used on its own to assess changes in cellular NMD activity with high specificity and sensitivity. It can facilitate analysis of NMD controls by cellular pathways in response to stimuli or during development and is particularly suitable for unbiased screening of NMD modulators. The assay is designed to distinguish NMD regulation from transcriptional regulation and alternative splicing control.

Drop-Carrier Particles For Digital Assays

UCLA researchers in the Department of Bioengineering have developed a novel drop-carrier particle for single cell or single molecule assays.

Low Cost Wireless Spirometer Using Acoustic Modulation

The present invention relates to portable Spirometry system that uses sound to transmit pulmonary airflow information to a receiver.

Microfluidic Component Package

The present invention describes a component package that enables a microfluidic device to be fixed to a Printed Circuit Board (PCB) or other substrate, and embedded within a larger microfluidic system.

Method and System for Ultra High Dynamic Range Nucleic Acid Quantification

Researchers at UC Irvine developed a device and method that combines the high dynamic range and high accuracy of digital PCR (dPCR) with the real-time analysis of quantitative PCR (qPCR) to achieve a ultra-high dynamic range PCR over 10 to 12 orders of magnitude. The present method is accomplished by a highly integrated design that optimally packs, thermocycles, and images as many as 1 million reaction vessels.

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