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Simulated Annealing For Network Alignment

This is an algorithm that compares protein interactions which aids in identifying new therapeutic targets for treating many different types of diseases. This novel algorithm presents a new opportunity/tool which allows for “better results” that previously would have taken decades of computational time.

Salmonella-Based Gene Delivery Vectors and their Preparation

Nucleic acid-based gene interference technologies, including ribozymes and small interfering RNAs (siRNAs), represent promising gene-targeting strategies for specific inhibition of mRNA sequences of choice. A fundamental challenge to use nucleic acid-based gene interfering approaches for gene therapy is to deliver the gene interfering agents to appropriate cells in a way that is tissue/cell specific, efficient and safe. Many of the currently used vectors are based on attenuated or modified viruses, or synthetic vectors in which complexes of DNA, proteins, and/or lipids are formed in particles, and tissue-specific vectors have been only partially obtained by using carriers that specifically target certain cell types. As such, efficient and targeted delivery of M1GS sequences to specific cell types and tissues in vivo is central to developing this technology for gene targeting applications. Invasive bacteria, such as Salmonella, possess the ability to enter and transfer genetic material to human cells, leading to the efficient expression of transferred genes. Attenuated Salmonella strains have earlier been shown to function as a carrier system for delivery of nucleic acid-based vaccines and anti-tumor transgenes. Salmonella-based vectors are low cost and easy to prepare. Furthermore, they can be administrated orally in vivo, a non-invasive delivery route with significant advantage. Thus, Salmonella may represent a promising gene delivery agent for gene therapy. Scientists at UC Berkeley have developed a novel attenuated strain of Salmonella, SL101, which exhibited high gene transfer activity and low cytotoxicity/pathogenicity while efficiently delivering ribozymes, for expression in animals. Using MCMV infection of mice as the model, they demonstrated that oral inoculation of SL101 in animals efficiently delivered RNase P-based ribozyme sequence into specific organs, leading to substantial expression of ribozyme and effective inhibition of viral infection and pathogenesis. This strategy could easily be adopted deliver other gene targeting technologies.

Diagnostic and Screening Methods for Atopic Dermatitis

Atopic dermatitis (AD) is a chronic itch and inflammatory disorder of the skin that affects one in ten people. Patients suffering from severe AD eventually progress to develop asthma and allergic rhinitis, in a process known as the “atopic march.” Signaling between epithelial cells and innate immune cells via the cytokine Thymic Stromal Lymphopoietin (TSLP) is thought to drive AD and the atopic march. TSLP is up regulated in atopic dermatitis patients and is thought to act on immune cells to trigger atopic dermatitis. Scientists at UC Berkeley discovered that TSLP also activates a subset of sensory neurons to signal itch by acting on TSLPR, which signals to TRPA1. They demonstrated that sensory neurons that transmit itch signals in AD are the only instance of signaling between TSLPR and TRPA1 in the same cell type. Therefore, blocking the signaling between TSLPR and TRPA1 is a novel and specific target for therapeutics for itch in atopic dermatitis. They also discovered that the Orai I/Stim I pathway triggers expression and secretion of TSLP. This pathway has never been directly demonstrated in human primary keratinocytes and has never before been linked to TSLP. Decreasing expression of Orai I or stim I using siRNA, or the downstream transcription factor, NFATc I, significantly attenuates TSLP secretion, as proven in mice studies. Thus inhibition of Orai I/Stim I/NFATc I signaling pathway is a novel target for therapeutics for itch in atopic dermatitis.

Monoclonal Antibody Against Cer164 (Clone 11)

Mouse monoclonal antibody against the human centrosomal protein 164kDa (Cep164). This antibody binds to the phosphorylation site of Cep164 and has been tested for use in immunocytochemistry/immunofluorescence, immunoprecipitation, and western blot.

Monoclonal Antibody Against ATR-IP (Clone 5)

Mouse monoclonal antibody against the human ATR-interacting protein (ATR-IP). This antibody has been tested for use in immunocytochemistry/immunofluorescence, immunoprecipitation, and western blot.

Monoclonal Antibody Against Cer164 (Clone 26)

Mouse monoclonal antibody against the human centrosomal protein 164kDa (Cep164). This antibody binds to the phosphorylation site of Cep164 and has been tested for use in immunocytochemistry/immunofluorescence, immunoprecipitation, and western blot.

Monoclonal Antibody Against PNPase (Clone 4C11)

Mouse monoclonal antibody against the human mitochondrial polyribonucleotide nucleotidyltransferase 1 (PNPase). This antibody has been tested for use in immunocytochemistry/immunofluorescence, immunoprecipitation, and western blot.

Monoclonal Antibody Against Pnpase (Clone 2A2)

Mouse monoclonal antibody against the human mitochondrial polyribonucleotide nucleotidyltransferase 1 (PNPase). This antibody has been tested for use in immunocytochemistry/immunofluorescence, immunoprecipitation, and western blot.

Monoclonal Antibodies Against Spc24/25 (Clone 2A10)

Mouse hybridoma cell line secret antibody against the human Kinetochore protein Spc24 (SPC24) and Kinetochore protein Spc25 (SPC25). This antibody has been tested for use in immunocytochemistry/immunofluorescence, immunoprecipitation, and western blot.

Monoclonal Antibodies Against Spc24/25 (Clone 2C8)

Mouse hybridoma cell line secret antibody against the human Kinetochore protein Spc24 (SPC24) and Kinetochore protein Spc25 (SPC25). This antibody has been tested for use in immunocytochemistry/immunofluorescence, immunoprecipitation, and western blot.

Method For Detecting Protein-Specific Glycosylation

O-GlcNAc modification is a common form of post-translational modification that mediates cellular activity and stem cell programming by modifying transcription factors. Multiple human diseases, including cancer and diabetes, have been linked to aberrant O-GlcNAcylation of specific proteins.Despite the importance of this modification, current methods for detection require advanced instrumentation and expertise as well as arduously enriched or purified samples. The “Glyco-seq” method developed by UC Berkeley researchers is highly sensitive, easy to use, and enables O-GlcNAc detection on proteins of interest in cell lysate. 

Self-Inactivating Targeted DNA Nucleases For Gene Therapy

The clinical application of targeted nucleases - such as zinc-finger nucleases, TALENs, and CRISPR/Cas9 – are exciting genome editing platforms. Delivery of nucleases to cells and tissues using as viral methods, however, can leave the nucleases stably present in the target cells, even after editing has been accomplished. One major safety concern is off-target effects (i.e. cutting a non-intended site), which pose a safety risk.  Another safety concern for gene therapies is the long-term expression of a foreign protein potentially provoking inflammatory reactions, another safety risk.   To avoid these potential detrimental outcomes, researchers at UC Berkeley have modified the delivered nuclease DNA which will cleave the host genome target DNA site and also excise its own DNA from the stable delivered construct.  The researchers have shown that there is no trace of any active delivered DNA remaining, thus mitigating the harmful side effects from nuclease based 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.

Monoclonal Antibody against ATR-IP (Clone 11)

Mouse monoclonal antibody against the human ATR-interacting protein (ATR-IP). This antibody has been tested for use in immunocytochemistry/immunofluorescence, immunoprecipitation, and western blot.

Monoclonal Antibody Against CEP164 (Clone 13)

Mouse monoclonal antibody against the human centrosomal protein 164kDa (Cep164). This antibody binds to the phosphorylation site of Cep164 and has been tested for use in immunocytochemistry/immunofluorescence, immunoprecipitation, and western blot.

Monoclonal Antibody Against CEP164 (Clone 17)

Mouse monoclonal antibody against the human centrosomal protein 164kDa (Cep164). This antibody binds to the phosphorylation site of Cep164 and has been tested for use in immunoprecipitation and western blot.

Monoclonal Antibodies Against Chk2 (Clone 4B8)

Mouse monoclonal antibody (clone 4B8) against the human Serine/threonine-protein kinase Chk2. This antibody has been tested for use in immunoprecipitation and western blot.

Monoclonal Antibodies Against Mtpap (Clone 1D3)

Mouse monoclonal antibody against the human Poly (A) RNA polymerase, mitochondrial (mtPAP). This antibody has been tested for use in immunocytochemistry/immunofluorescence, immunoprecipitation, and western blot.

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.

Fluorescent Biosensor for Methyltransferase Assay

Correct epigenetic regulation is essential to cellular development, and methyltransferases are enzymes important for epigenetic regulatory processes. They add methyl groups to their substrates, which can be DNA, proteins, or small-molecule secondary metabolites. Methyltransferases have been implicated in a number of diseases, including cancer, HIV infection, and diabetes, yet many remain uncharacterized.S-adenosyl methionine (SAM) is used as a methyl group donor by a majority of methyltransferases. Use of SAM by a methyltransferase results in the production of S-adenosyl homocysteine (SAH). SAM is found across all branches of life, and therefore represents a useful biological marker for methyltransferase activity. Researchers at UC Berkeley have developed a sensitive and selective means of assaying methyltransferase activity. This assay monitors the presence of SAH, and can be used for high-throughput screening.

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.

Monoclonal Antibody Against mtPAP (Clone 3D2)

Mouse monoclonal antibody against the human Poly (A) RNA polymerase, mitochondrial (mtPAP). This antibody has been tested for use in immunocytochemistry/immunofluorescence, immunoprecipitation, and western blot. .

Monoclonal Antibody Against PNPase (Clone 3H5)

Mouse monoclonal antibody against the human mitochondrial polyribonucleotide nucleotidyltransferase 1 (PNPase). This antibody has been tested for use in immunocytochemistry/immunofluorescence, immunoprecipitation, and western blot.

Improved Generation of Terpene and Other High-Value Bioproducts from Cyanobacteria and Microalgae

Cyanobacteria and other microalgae can be used as photosynthetic platforms to heterologously generate terpene hydrocarbons and other high-value bioproducts. In addition to being a renewable and biological means of synthesis, cyanobacteria can be grown in high-volume liquid cultures; and terpenes are key ingredients in synthetic chemistry, medical products, cosmetics, and potentially fuels. However, current approaches to generating terpene using microalgae exhibit slow rates of production.   To address these low production levels, researchers at UC Berkeley have developed a method to increase transgenic terpene synthase expression resulting in high rates and yields of terpene hydrocarbon synthesis.   In proof-of-principle experiments, this Berkeley method yielded 20-fold higher amounts of terpene product, which could be easily harvested by siphoning off the top of the culture.

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