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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 high-throughput sequencing to estimate abundance or copy count or copy number of each of one or more target sequences by comparing the DNA of a sequenced sample to its reference sequence. This aligning or mapping step consumes a considerable amount of computing power however.   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

Mobile Molecular Diagnostics System

There is a growing interest in point-of-care testing (POCT) where testing is done at or near the site of patient care, since POCT has a short therapeutic turnaround time, decreased process steps where errors can occur and only a small sample volume is required to perform a test.    UC Berkeley researchers have developed a mobile molecular diagnostics system that leverages efficient and dependable blood sampling, automated sample preparation, rapid optical detection of multi-analyte nucleic acids and proteins, and user-friendly systems integration with wireless communication.  The system includes a hand-held automated device with an adaptive sample control module, an optical signal transduction module, and an interface to a smartphone making this a reliable and field-applicable system for point-of-care and on-demand diagnostics. 

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 optical pathlengths 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.  The device provides rapid cycling and a simple and reliable integrated fabrication system that is capable of being easily integrated with other standard equipment. 

Optical Cavity PCR

Outbreaks of infectious diseases especially require diagnostic tools that can be used at the point-of-care (POC). Polymerase chain reaction (PCR) is sensitive and allows accurate diagnoses, but developing simple and robust PCR methods that can be used at POC remains a challenge. In particular, slow thermal cycling capability and high power consumption continue to be barriers.  Researchers at UC Berkeley have developed optical cavity PCR to address these challenges. This technology allows ultrafast cycling with low power consumption, high amplification efficiency and a simple fabrication process, enabling its use as a POC device. 

High-Throughput Profiling of Point Mutations across the HIV-1 Genome

The Sun Group at UCLA has developed a quantitative, high-throughput assessment of the mutational susceptibility of genomic regions of HIV-1 to aid drug design.

System and Method for Fast Sequence Census Analysis

Massively Parallel Sequencing (MPS) approaches are attractive tools for sequencing. Typically, MPS methods can only obtain short read lengths (e.g., 50 to 250 base pairs), but generate many millions to billions of such short reads on the order of hours. Sequence census experiments utilize high-throughput sequencing to estimate abundance or copy count or copy number of each of one or more target sequences by comparing the DNA of a sequenced sample to its reference sequence. This step is called aligning or mapping the reads against the reference sequence. Aligning the read to the reference consumes a considerable amount of computing power. Thus, a major bottleneck in current methods for analysis of sequence census data is the requirement to align reads to reference.   UC Berkeley researchers have developed techniques for fast sequence census analysis that avoids the bottleneck of aligning a read with a reference sequence by inferring a non-alignment measure of compatibility; thus, improving accuracy or speed, or both, in comparison to previous methods. 

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 isoforms of a regulator of the Hippo Pathway

This invention identifies two novel genetic spliced forms of a gene frequently involved in human cancer tissues, which could be developed as a biomarker for cancer and as a potential therapeutic target in the Hippo pathway.

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.  

A method for autocatalytic genome editing II

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 proposed is based solidly on existing technologies and should work in flies, mosquitos, human cells, and plants.

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 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.  

Novel Chitosan Derivative as a Systemic Drug Delivery Agent and an Antibiotic Treatment

Researchers at the University of California, Irvine have developed a novel chitosan derivative that may be used simultaneously as a systemic drug delivery agent and a systemic antibiotic treatment.

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