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Pyrite Shrink-Wrap Laminate As A Hydroxyl Radical Generator

The invention is a diagnostic technology, as well as a research and development tool. It is a simple, easy to operate, and effective platform for the analysis of pharmaceuticals and biological species. Specifically, this platform generates hydroxyl radicals for oxidative footprinting – a technique commonly employed in protein mapping and analysis. The platform itself is inexpenisve to fabricate, scalable, and requires nothing more than an ordinary pipet to use. In addition, it is highly amenable to scale-up, multiplexing, and automation, and so it holds promise as a high-throughput method for mapping protein structure in support of product development, validation, and regulatory approval in the protein-based therapeutics industry.

Two And Three Dimensional DNA Antenna And Photonic Transfer Nanostructures

Fluorescence Resonance Energy Transfer (FRET) is a mechanism which describes the photonic energy transfer between two light-sensitive molecules (chromophores). A donor chromophore, initially in its electronic excited state, may transfer energy in the form of undetectable virtual photons to an acceptor chromophore. FRET has been widely used to study the structure and dynamic of biomolecules. Specifically, by using dyes conjugated on a DNA strand, FRET can be applied to molecular sensors in which fluorescence signals change as a result of altered distance between donor and acceptor chromophores due to hybridization or enzymatic reactions. In addition, the DNA strand can act as a photonic wire along which the photonic energy is transferred. However, because fluorescence is highly influenced by environmental conditions and surrounding molecules, the energy transfer from a donor dye conjugated on a DNA strand is easily quenched by the dye-DNA and dye-dye interaction, often lowering FRET efficiency to the acceptor dye. Furthermore, when multiple chromophore/fluorescent donors and acceptor groups/entities are arranged on 2D and 3D DNA structures, contact and other quenching mechanisms can occur which greatly reduce the long range FRET efficiency. This rapid loss of long distance FRET efficiency greatly reduces the viability of DNA based photonic wires and antennas and negates any useful or practical applications. Therefore quenching should be resolved in order to apply the molecular FRET system to the device fabrication with efficient energy transfer.

Enzymatic Site Specific Labeling of RNA with Unnatural Nucleobases

The detection and manipulation of RNA is greatly aided by chemical modification. Therefore, there is tremendous interest in novel methods to site-specifically associate RNA with small molecules such as imaging probes and affinity labels.  Conventional methodologies for detecting RNA include the use of antisense probes, aptamers, and fusion proteins that recognize specific RNA secondary structures. Relatively less explored are the use of enzymatic reactions for site-specific RNA labeling. Notably, these past approaches have not demonstrated the ability to append large functional molecules directly onto the RNA of interest. Instead they typically rely upon small bio-orthogonal handles, which after undergoing a second chemical reaction, can be modified by functional probes such as fluorophores or affinity ligands. An ideal enzymatic reaction for labeling RNA would involve recognition of a minimal RNA structural motif, result in irreversible covalent modification, and would be capable of directly incorporating a diverse array of functional molecules such as fluorophores, affinity ligands, etc. in a single step.

Sequence Independent and Ordered Nucleic Acid Assembly

Currently DNA fragments are assembled from smaller oligonucleotides that contain overlapping DNA sequences.After overlapping sequences are annealed, each oligo will act as primer for polymerization, eventually fusing the two fragments together. This method relies on unique overlapping sequences that are favorable to anneal at a specific temperature.This strategy becomes problematic when you try to assemble more than two fragments, when the uniqueness of annealing sequences, the correct order of fragments annealing and optimal temperature for all the annealing reactions are major concerns.On the other hand, annealing only two fragments at a time is time consuming and low in scalability.There is a great need for a cost-effective and accurate approach.

High Throughput, Sequence Independent and Ordered Nucleic Acid Assembly

Currently DNA fragments are assembled from smaller oligonucleotides that contain overlapping DNA sequences.  After overlapping sequences are annealed, each oligo will act as primer for polymerization, eventually fusing the two fragments together.  This method relies on unique overlapping sequences that are favorable to anneal at a specific temperature.  This strategy becomes problematic when you try to assemble more than two fragments, when the uniqueness of annealing sequences, the correct order of fragments annealing and optimal temperature for all the annealing reactions are major concerns.  On the other hand, annealing only two fragments at a time is time consuming and low in scalability.  There is a great need for a cost-effective and accurate approach.

SEQUENCING OF NUCLEIC ACIDS VIA BARCODING IN DISCRETE ENTITIES

This invention identifies a method to prepare nucleic acid barcodes using microfluidic methods; allowing for high throughput analysis of many individual samples.

Small RNAs From Fungal Pathogents Act As Effector Molecules To Suppress Host Immunity

Background: Plant-pathogen relationships have been studied meticulously for many years because fungi are notorious for causing detrimental yield losses. Many have taken a biotechnological approach to combatting fungal infections by genetically engineering fungal-resistant genes into plants. The market segment of genomic-enabled products is projected to grow 10% annually and reach $38.6B by 2019.    Brief Description: UCR Researchers have discovered the underlying mechanism of action of Botrytis cinerea, a fungal pathogen that causes grey mold disease in various plants and crops. They’ve identified novel non-protein effectors, small RNAs, that silence specific genes in the host. These fungal sRNAs are transferred into the host cells to suppress its immunity and achieve full infection. With this insight, we can genetically engineer plants to successfully combat harmful pathogenic attacks by inhibiting small RNA effectors.  

A Transposon Vector From Aedes Aegypti For Use In Vertebrate And Invertebrate Gene Transfer

Background: Therapeutic delivery of genes is a rapidly evolving technique used to treat or prevent a disease at the root of the problem. Another widely used variation of this technique is to insert a transgene into animals and crops for production of desirable proteins. The global transgenic market is currently $24B with annual growth projections of 10%.  Brief Description: UCR Researchers have identified a novel transposon from Aedes aegypti mosquitoes. This mobile DNA sequence can insert itself into various functional genes to either cause or reverse mutations. They have successfully developed a transposon vector system that can be used in both unicellular & multicellular organisms, which can offer notable insight to enhance current transgenic technologies as well as methods of gene therapy.

Multiplex Digital PCR

Researchers at the University of California, Irvine have developed methods to enable greater multiplexing abilities for digital polymerase chain reaction (PCR) so that up to 100 genetic targets may be analyzed. In the past multiplexing of digital PCR samples has been limited to only one probe per color. However multiple probes may be labeled by using combinatorial encoding of color, exploiting reaction rates of PCR cycles and modulating the intensity of Taqman and/or intercalating dyes therefore allowing a greater number of probes to be labeled.

Real-Time, Label-Free Detection of Nucleic Acid Amplification in Droplets Using Impedance Spectroscopy and using Solid-Phase Substrates

Researchers at UC Irvine have developed a technology to detect the presence of nucleic acid amplification in a droplet. This technology yields real time detection of DNA or RNA amplication in a high throughput integrated microfluidic platform.

Dielectrophoresis-Based Cell Destruction to Eliminate/Remove Unwanted Subpopulations of Cells

This invention allows for label free cell separations and cell enrichment.

Inhibitory Antibodies From Synthetic Long CDR Libraries

Background: About 2M new cancer cases are diagnosed annually with a projected national economic burden of $160B by 2020. A means for better diagnostics and tailored therapies is needed to prevent cancer and detect it early. Even with early detection, effective therapies are limited and very expensive. Targeted therapies have been shifting towards monoclonal antibodies as an alternative to small molecule drugs due to their propensity for highly selective inhibition of enzymes involved in tumorigenesis. Brief Description: UCR Researchers have created synthetic antibodies by customizing a specific encoding region where antigen binding occurs. Antibody-antigen binding allows for activation and inhibition. Through their novel antibody design, they successfully inhibited protease enzymatic activity – with a very high hit rate of 65% for matrix metalloproteinase (MMP) – with high specificity and potency over traditional methods. Tumor-promoting MMP inhibition has never been accomplished due to difficulties in distinguishing them from tumor-suppressing MMP.

BrAD Seq: A simple, rapid and inexpensive method for constructing strand specific cDNA libraries for RNA-seq

Breath Adapter Directional sequencing (BrAD Seq) is a novel method for the production of strand specific RNA-seq libraries. The process reduces sample handling and requires far fewer enzymatic steps than current approaches while still producing high quality reads. The resulting technology is a quicker and cheaper way to generate RNA-seq libraries. Available for licensing are methods and compositions of matter for performing BrAD Seq.

Alignment-Free Rapid Sequence Census Quantification (Kallisto)

Sequence census experiments utilize next-generation sequence data to estimate the relative abundance of target sequences.  Since the samples are often short DNA fragments, they must first be assigned to the correct transcripts and genes that produced them, and this alignment or mapping step currently takes up the majority of computing power and time in most expression analyses. To avoid this costly process, UC Berkeley researchers have developed a software program (kallisto) for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads based on pseudo-alignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Pseudo-alignment of reads preserves the key information needed for quantification. 

Low-Cost Chromatin Assembly Kit

Brief description not available

Bubble-Free Rapid Microfluidic PCR

Microfluidic-based polymerase chain reaction (PCR) methods have been widely used in research and diagnostics. Compared to standard PCR, microfluidic PCR reactions use less reagents, shorten analysis time, and can be integrated with other equipment.   Current methods, however, have major problems, including water evaporation, loss of reagents, and inconsistent heat distribution due to bubble generation. Moreover, the microfluidic devices used are challenging to fabricate.   To overcome the problems with conventional PCR and microfluidic PCR devices, UC Berkeley researchers have developed an efficient bubble-free microfluidic PCR device with a thin polymer membrane, inhibiting mass transport.  The device provides rapid cycling and a simple and reliable integrated fabrication system that is capable of being easily integrated with other standard equipment. 

Highly Sensitive Detection Of Biomolecules Using Proximity Induced Bioorthogonal Reactions

There is tremendous interest in the use of fluorogenic reactions for detecting and imaging nucleic acids, especially specific DNA and RNA sequences. Applications include time-resolved imaging of transcription, detection of disease-related single nucleotide polymorphisms, and tracking RNA fragments such as microRNAs. Despite advances in the use of molecular beacons, aptamers and antisense agents, the rapid detection and imaging of oligonucleotides in live cells and physiologically relevant media remains challenging. Current methods, although powerful, suffer from numerous drawbacks. For example, previous ligation reactions have been hampered by slow kinetics and autohydrolysis, often relying on nucleophilic/electrophilic reactions, which allow cellular or solvent nucleophiles to compete for reactivity. Fluorogenic bioorthogonal ligations offer a promising route towards the fast and robust fluorescent detection of specific DNA or RNA sequences. Tetrazine bioorthogonal cycloadditions benefit from rapid tunable reaction rates and high stability against hydrolysis in buffer and serum. Furthermore, tetrazines act as both a fluorescent quencher and a reactive group, minimizing the complexity of fluorogenic ligation probe design.

Novel Multivalent Bioassay Reagents

The guiding principle for the creation of biomolecular recognition agents has been that affinity is essential for both strength and specificity.  Monoclonal antibodies, the dominant workhorse of affinity reagents, have mono-valent affinities in the uM-nM range with apparent affinities that can be sub nM with the bi-valency intrinsic in intact immunoglobulin structure.  The avidin-biotin interaction used ubiquitously for biomolecular assembly is femto-molar and both highly specific and essentially irreversible.  High affinity has been proclaimed the essential goal for the selection of useful specific aptamers, though there has been disagreement about a tight coupling of affinity and specificity.  

Ferrofluid Droplets to Locally Measure the Mechanics of Soft Materials

A technique and apparatus that can measure the mechanical properties of any kind of soft material, including complex fluids, living embryonic and adult tissues (such as skin), as well as tumors. 

Synthetic Enhancer Library

Enhancers are discrete genomic DNA segments that control tissue-specific patterns of gene expression and are essential to the development and homeostasis of multicellular organisms. Changes in gene activity have been linked to diseases such as autoimmune disorders. Despite the importance of enhancers, the relationship between the primary DNA sequence and enhancer function is poorly defined. In part, this is due to the need to systematically test hundreds of thousands of enhancer mutants in whole animals in order to fully understand enhancer activity.   To address this issue, UC Berkeley researchers have developed a Synthetic Enhancer Library-Seq (SEL-Seq).  The technology couples the synthesis of enhancer variants to a barcoding method, and provides millions of unique sequences for functionally testing enhancers. 

A Method For Autocatalytic Genome Editing

The CRISPR/CAS9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) system has been found to be adaptable to nearly every organism studied including mammalian cells, fruit flies, and plants.  The broad adaptability of this system has lead in the past year to significant strides in refining the methodology and in the generation of many additional applications.  The innovation we propose is based solidly on existing technologies and should work in flies, mosquitos, human cells, and plants. 

Novel Method of Packaging Peptides to Ensure Bioactivity, Proteolytic Resistance, and Cellular Uptake

As of 2012, the pharmaceutical market share of peptide/protein therapeutics was >$40 billion annually. However, due to their instability in vivo, most peptide therapeutics must be directly injected at the site of action. This has a negative impact on patient compliance and, as such, many peptide therapies are only used clinically as salvage treatments.Several existing approaches for producing peptides protected from proteolysis involve chemical modification of the amino acid sequence. This generally necessitates multiple rounds of structure-function studies to verify that the activity of the peptide is not altered. Other approaches not using chemical modification of the amino acid sequence may involve conjugation of the peptide to a pre-formed higher molecular weight structure, such as a polymer or nanomaterial. The downside of these approaches is that they require multiple conjugation and purification steps and the generation of the high molecular weight carrier. Inefficiencies in cellular uptake and rapid digestion by proteases are two key problems that have limited the clinical efficacy of peptide-based therapeutics.

PCR-Activated Sorting (PAS)

This invention identifies a novel method for nucleic acid sorting, whether free-floating or contained in structures (eg. cells and viruses) using droplet microfluidics and PCR.

Nucleic Acid Extraction and Preparation From Whole Blood

One of the keys to effective treatment of blood borne diseases is rapid detection and diagnosis. One of the bottlenecks in rapid diagnosis is the lack of a whole blood pre-treatment method that can provide purified nucleic acids on site and is not time consuming, costly, labor intensive and does not pose a risk of infection to operators and cross-contamination. UC Berkeley researchers have developed an integrated, universal, whole blood lysis and nucleic acid extraction device which is efficient, easily automatable, portable and requires low power.  A proof of concept design showed pathogen DNA samples were eliminated of blood protein contaminations, which can inhibit PCR, and had a purity comparable with a spin column based DNA extraction kit.  

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