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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.

Methods and Applications for Controlling Cellular Viability Using Fluoride-Sensitivity

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

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.

Temporal Control over DNA-Patterned Signaling Ligands In Vitro Using Sequence-Targeting Nucleases

UC Berkeley researchers have created a new technique that can rapidly “print” two-dimensional arrays of cells and proteins that mimic a wide variety of cellular environments in the body, be it the brain tissue surrounding a neural stem cell, the lining of the intestine or liver or the cellular configuration inside a tumor.  In the new technique, each cell or protein is tethered to a substrate with a short string of DNA. While similar methods have been developed that attach tethered cells or proteins one by one.  By repeating the process, up to 10 different kinds of cells or proteins can be tethered to the surface in an arbitrary pattern. This technique could help scientists develop a better understanding of the complex cell-to-cell messaging that dictates a cell’s final fate, from neural stem cell differentiating into a brain cell to a tumor cell with the potential to metastasize to an embryonic stem cell becoming an organ cell.

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.

Discovery Of A Novel Protease With High Specificity Toward Serine Side Chains

Pyrroloquinoline quinone (PQQ), a prominent redox cofactor in a variety of prokaryotes, is produced from a ribosomally synthesized and post-translationally modified peptide PqqA via a pathway comprised of four conserved proteins PqqB-PqqE. These four proteins are now fairly well characterized and span Radical SAM activity (PqqE), aided by a peptide chaperone (PqqD), a dual hydroxylase (PqqB), and an eight electron, eight proton oxidase (PqqC). A full description of this pathway has been hampered by a lack of information regarding a protease/peptidase required for the excision of an early, cross-linked di-amino acid precursor to PQQ.    UC Berkeley researchers have isolated and characterized a two component, heterodimer protein that is able to rapidly catalyze cleavage of PqqA into smaller peptides.  The UC researchers have developed: novel proteases that can cut peptide bonds both N- and C- terminal to the amino acid serine; compositions comprising such proteases; and methods of use, including to assay the extent, position, and time course of protein phosphorylation at serine side chains. 

Phenotypic Profiling Of Hepatocellular Carcinoma Circulating Tumor Cells For Treatment Selection

Researchers in the UCLA Departments of Surgery and Molecular and Medical Pharmacology have developed a novel blood-based assay that can capture and characterize circulating tumor cells indicative of both early- and late-staged hepatocellular carcinoma (HCC).

Lipid Bilayer Formation Using Sessile Droplets

UCLA researchers in the Department of Bioengineering have developed a method to form a biologically functional lipid bilayer in a high-throughput and automated fashion.

Surfaceome Profiling Of Advanced Prostate Cancer To Identify Target Antigens For Immune-Based Therapy

Dr. Witte and colleagues at UCLA have developed a novel approach to identify surface biomarkers and targetable antigens in prostate cancer by combining multiple omics analyses across different cell lines.

Development Of A Method For Endocrine Network Discovery Uncovers Peptide Therapeutic Targets

UCLA researchers in the Division of Cardiology at the Geffen School of Medicine have developed a bioinformatics methodology to identify and functionally annotate novel endocrine pathways.

Tissue Projection Electrophoretic Separation Of Protein

A range of related immunoblotting methods have enabled the identification and semi-quantitative characterization of e.g., DNA (Southern blot), RNA (northern blot), proteins (Western blot), and protein-protein interactions (far-western blot); by coupling biomolecule separations and assays.  However, there are a wide number of alternative splicing events, post-translational modifications, and co-translational modifications (e.g., phosphorylation, glycosylation, and protein cleavage) that give rise to proteoforms and protein complexes with distinct function and subsequent cell behavior that cannot be analyzed with conventional methods such as immunohistochemistry (IHC). Analytical variability (lack of isoform- or complex-specific antibody probes), biological variability (small cell subpopulations diluted in bulk analysis), and lack of multiplexing (measurement of multiple proteins from the same tissues) can all render proteoforms and protein complexes undetectable by current technologies.     UC Berkeley researchers have created electrophoretic separation platform that is capable of measuring proteoforms and protein complexes lacking specific antibodies alongside spatial information, at the cellular level.  This platform maintains the architecture of 2D tissue slices while projecting a protein separation in the 3rd dimension. The platform mitigates artifacts induced by tissue dissociation processes, as the intact tissue is lysed and subject to a protein separation. The platform is also compatible with differential detergent fractionation methods for further separation of proteins (e.g. separation by localization within the cell, by cell type, by protein complex formation, or by cellular vs. matrix proteins), opening the door for a novel, refined classification taxonomy using enhanced biomarker signatures for diagnostics and treatment selection in oncology among a wide range of additional future applications.  

Protein-Coated Microparticles For Protein Standardization In Single-Cell Assays

Single-cell analysis offers powerful capabilities of identification of rare sub-populations of cells, understanding heterogeneity of cancerous tumors, and tracking cell differentiation and reprogramming. Despite great potentials for uncovering new biological systems and targeting diseases with precision medicine, single-cell approaches are composed of complex device processes that can cause bias in measurement.  In deep sequencing, technical variation in single cell expression data occurs during capture and pre-amplification steps. Similarly, in single-cell protein assays, technical variability can obscure functionally relevant variance.    To better control protein measurement quality in single-cell assays, researchers at the University of California, Berkeley developed a novel method to loading and release protein standard. This method utilizes the surface of modified and functionalized microparticles as vehicles to capture target proteins with desired concentrations. Chelation-assisted click chemistry is applied to demonstrate that protein standards with different molecular masses can be loaded and bounded in a single-cell protein assay. Microparticles are introduced into single-cell devices by either passive gravity, magnetic attraction, or other physicochemical forces. These protein standards from microparticles provide a reference to measure protein mass sizes from individual cells and a quality control for any biases in device fabrication, cell lysis, protein solubility, protein capture, and protein readouts (i.e. antibody probing).   

Living Bioreactor for Stoichiometric Protein Production

Living bioreactors are powerful systems for producing a variety of valuable compounds. The versatility of such bioreactors is one of the more useful aspects of the system. Large quantities of compounds or cellular components can be produced efficiently, with minimal cost. Alternately, these systems can be used to produce pathway components that are necessary in the production of secondary products. A common problem with such systems is that they are limited by non-uniform production of pathway components, or require an isolation process to ensure the components are in the appropriate quantity and sequence in the process. Inventors at Texas A&M and UC San Francisco have developed a novel technique to address these issues. The technology effectively results in a stoichiometric production of protein components that are produced in an array, ready for secondary production.

Rapid Screening and Identification of Antigenic Components in Tissues and Organs

Researchers at the University of California, Davis have developed an approach to rapidly screen and identify antigenic components in tissues and organs.

Versatile Labeling of Protein N-Termini for Site-specific Bioconjugation

Improved subtiligase variants allow broad and versatile site-specific chemical modification or conjugation of proteins on their N-termini.

Aptamer functionalized shrink-induced high surface area electrochemical sensors

A low-cost method of manufacturing a, rough high surface area electrodes with a dissolvable polymer coating to improve surface wettability and electrochemical sensing.

Process For Sorting Dispersed Colloidal Structures

Researchers from the Chemistry and Biochemistry department at UCLA have developed method of separating and/or sorting specific target structures from other non-target structures in a complex mixture using custom-made target-specific colloidal particles.

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.

Metal-free affinity media/agents for the selective capture of histidine-rich peptide sequences

The present invention utilizes metal-free synthetic polymer-based materials for the purification of peptides and proteins containing or being fused with histidine-rich sequences, which does not damage the function of the target protein and is less costly.

Improved Cell-Free Protein Synthesis For Protein Microarray

Researchers at UC Irvine have developed a cell-free (CF) protein synthesis system to solubilize and synthesize highly hydrophobic membrane proteins that would typically aggregate using current CF synthesis systems. With such high amounts of synthesized proteins, researchers intend to build protein microarrays for diagnostic purposes.

Enhanced Cell/Bead Encapsulation Via Acoustic Focusing

The invention consists of a multi-channel, droplet-generating microfluidic device with a strategically placed feature.The feature vibrates in order to counteract particle-trapping micro-vortices formed within the device.Counteracting these vortices allows for single particle encapsulation in the droplets formed by the device and thereby makes this technology a good candidate for use in single cell diagnostics and drug delivery systems.

Mesenchymal Stem Cell Derived Exosomes for Treating Peripheral Artery Disease

Researchers at the University of California, Davis have developed a method to isolate exosomes from mesenchymal stem cells that contain signaling molecules that induce angiogenesis. The isolated exosomes can be used for treating peripheral arterial disease.

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