Current systems used to perform sample preparations that integrate with digital microfluidics use liquid valves, rotary valves, or small volume injection loops that are expensive and often require a large apparatus to operate. Other digital microfluidic systems require operators to directly pipette sample reagents into the platform which can incorporate human error and the potential exposure to hazardous chemicals. In order for automated and consistent benchtop chemical synthesis using digital microfluidics to exist, a compact and inexpensive system must be able to interface with the external environment to allow efficient chemical delivery and retrieval. (more...)

Researchers at University of California, Davis have discovered a nanophotonic device that reduces limits of detection of an immunoassay by orders of magnitude. (more...)

A novel technique for the integration of small complementary metal-oxide semiconductor (CMOS) chips into a large area substrate. (more...)

CE-Combinatorial Extension, Algorithms and Computer Programs for Comparing the 3-dimensional Structures of Protein Molecules.   Download Site License. (more...)

A high quality nanometer scale electrical circuit with a single protein attached to a carbon nanotube that allows for the detailed study of the kinetics and dynamics of single proteins. (more...)

Head and Neck Squamous Cell Carcinomas (HNSCC) are usually treated with radiotherapy (RT), alone or in combination with surgery and chemotherapy. While many patients with HNSCC are cured by RT, acute side effects from RT can reduce the quality of life for these patients and may lead to increased co-morbidity. In some patients the side effect are so severe that they may even interrupt radiation treatment, reducing its efficacy and thereby increasing the probability of treatment failure. In some patients, a mechanism termed accelerated repopulation occurs, where the re-growth rate of a tumor during a treatment gap exceeds that of its initial growth rate. The result is a marked decrease in local tumor control rates. Major causes for treatment gaps are severe normal tissue side effects like mucositis of the oral mucosa. While most patients experience mild grade 2 and 3 mucositis at the end of treatment, a subgroup of patients develop severe early onset mucosistis that requires treatment interruption, often leading to accelerated repopulation. Identification of the patients at risk of developing severe side effects would be highly desirable. However, aside from very rare cases of genetic disorders that correlate with DNA repair defects, it is currently impossible to prospectively identify patients at risk for developing these complications during RT. (more...)

The ability of natural products and other compounds to act as proteasome inhibitors has attracted significant interest because of the wide range of cellular substrates and processes controlled or affected by the ubiquitin-proteasome pathway.UCR Researchers have achieved the synthesis of novel compounds useful for regulating the ubiquitin-proteasome pathway. They can be prepared in just a few steps, in high efficiency, and in good quantity, as would be needed for a manufacturing process.  Due to the role of the ubiquitin-proteasome pathway in important cellular processes such as apoptosis, and cellular proliferation , the inhibition of the proteasome has been recognized as a useful property for the development novel anti-cancer therapeutics. In addition to cancer therapy, it is envisioned that molecules that specifically inhibit the proteasome such as those in this invention could have other uses, including as drugs for autoimmune diseases or as agrochemical and possibly antibacterial agents.   (more...)

Researchers at the University of California, Irvine have developed a new controllable method to fabricate functionalized carbon nanowires that can then be covalently bound to antibodies, proteins, mRNA, DNA or other reagents. These antibodies and reagents may then bind with analytes of interest in solution causing a measurable change in the electrical current. Additionally, interdigitated electrode arrays may also be fabricated by using nanowires made from this method. (more...)

UCSF researchers have developed a high-performance miniaturized bioreactor that fits inside a standard 5mm tube NMR spectrometer.  This bioreactor is ideal for growth of small, valuable cell samples, including stem cells and biopsies and for metabolomics in living cell samples.  Applications would include rapid metabolic testing of valuable new chemical entities and personalized medicine.    (more...)

This invention relates to the areas of the biochemical and chemical analysis of molecules in cells, and in particular to an assay and method for measuring the activation of internal chemical activity of a plurality of proteins in a single cell, a population of cells, or portion of a cell. The activity of multiple proteins in a single living cell, portion of a cell or in a group of cells is simultaneously measured by introducing reporter molecules into the cell(s) or a portion thereof, chemically modifying the reporter(s) by the enzyme of interest, terminating the modification reactions, removing the reporter(s) and modified reporter(s), and determining the amount of enzyme activity present by measuring or comparing the amount of reporter(s) and modified reporter(s) present. By performing a series of experiments at different time points, conditions, and varieties of cell types, a database is developed for molecular cellular mechanisms in health and disease states. By exposing cells to a variety of compounds data for drug development and screening is provided. (more...)

The use of antibodies to target tumor cell-associated antigens for diagnostic and therapeutic purposes has been a critical step forward in cancer research. As protein engineering capabilities grow, researchers modify antibodies to alter inherent characteristics, such as affinity and immunogenicity, for enhanced imaging and tumor response. One example of this is in the conjugation of various radionuclides to small recombinant antibody fragments (i.e. diabodies and minibodies) for in vivo tumor cell targeting applications. However, it is not always advantageous to use radioactivity, and thus alternative detection systems are necessary. To that end, the search for high-sensitivity and high-specificity probes that circumvent the limitations of organic dyes and fluorescent proteins has led to the discovery and utilization of quantum dots, nanometer-sized semiconductor particles. Quantum dots are brighter than traditional chromophores, have greater stability, and can be used in multiplex imaging due to size-tunable emission wavelengths. To date, bioconjugates with quantum dots are coupled to intact antibodies whose large size makes it difficult to penetrate tissues and tumors. Therefore, it would be advantageous to monitor tumors with a robust, but small, bioconjugate for tandem in vivo monitoring and treatment. (more...)

Researchers at the University of California, Irvine have developed a novel micron-sized hybrid particle complex, consisting of an AAL linked to SPIO particles, that can be used as a multimodal imaging agent, as well as a drug delivery vehicle. (more...)

Researchers at UC San Diego have invented a method of optically encoding porous silicon photonic crystals for use in high throughput screening and bioassays. The method allows for large libraries of unique particle types to be manufactured. The process is distinct from existing methods of encoding, such as fluorescent molecules, core-shell quantum dots, and photonic crystals formed using Rugate or Bragg reflectivity approaches, in that it does not strive to create spectral lines that act as bits-and are limited by the number of codes that can be generated. In contrast, this invention for data extraction and analysis utilizes all the complexity of the spectrum which results from the reflectivity properties of the photonic crystals. Unlike bioassay systems that couple fluorescent encoding methods with fluorescent assay, the method does not suffer from spectral overlap of the encoding method with the assay readout. These photonic crystals may be used as integral parts of randomly assembled microarrays. These microarrays could be applied in the field of gene expression, genotyping, proteomics, as well as real time chemical and biological sensing. (more...)

Combinatorial chemistry is arguably the most important development in the drug discovery process in over a decade. However, the detection of significant biological events in high throughput screening involves many burdensome tasks, and often includes the separation of the products of reaction before detection can take place. (more...)

Most optical transducers for label-free biosensing involve measurement of a change in the refractive index of a material induced upon analyte binding. While surface plasmon resonance (SPR) films, resonant and nonresonant diffraction gratings, reflectometric interference (RIFS) layers and Fabry-Perot interferometers show very sensitive responses to small changes in refractive index, these methods are all limited by zero-point-drift arising from changes in temperature, matrix composition, or nonspecific binding to the analytical surface. A double-beam (Michelson-type) interferometer, in which one optical path acts as a reference channel, provides an excellent means of compensating for such effects. Various implementations of double-beam correction have been employed in micro-scale biosensor systems, generally involving two spatially distinct regions of a chip. However, because the sample and reference channels are separated in the X-Y plane, such designs pose significant alignment and manufacturability challenges, especially upon incorporation into high-throughput arrays. (more...)

University researchers have written powerful software for the molecular modeling of protein. The Fast Atomic Density Evaluation (FADE) and Pairwise Atomic Density Reverse Engineering (PADRE) programs deduce molecular shape using the local density of atoms at points within a few Angstroms of the molecular surface. FADE uses Fast Fourier Transforms and convolution integrals to rapidly calculate the distribution of atomic neighbors. PADRE poses the question of atomic density as an inverse problem based on a one-dimensional integral of Lennard-Jones potentials. A primary advantage of atomic density methods is their computational efficiency. FADE can analyze molecular shape in seconds, while other methods may take minutes or hours. FADE and PADRE can deduce surface shape features, such as crevices and protrusions. FADE is also able to do detailed analysis of shape complementarity for docked complexes. The ability to determine regions of strong shape match or mismatch in an interface is very useful to computer-aided drug design. In addition to research, atomic density methods offer an ideal tool for learning about the shape features of molecules. The basic ideas underlying density methods can be understood intuitively, and integration within existing packages for molecular visualization would be a great aid to students studying protein structure-function relationships. For more information please see the website http://www.sdsc.edu/CCMS/FP/ (more...)

Various methods exist for the quantification of disease related biomarkers; however, measurement of enzyme activity could be a better indicator of certain disease states when those disease states are caused by the activity of particular enzymes.  Proteases are enzymes that cleave proteins and account for approximately two percent of all proteins in humans.  Dysregulation of protease activity has been linked to a wide range of diseases including cancer and heart disease.  A new method of measuring protease activity and inhibition has been developed through the use of microcantilevers, which are nanomechanical transducers that convert intermolecular reaction forces into measurable cantilever deflections measured by optical methods.  Studies using a model protease (Trypsin) have shown that microcantilever arrays can measure protease activity over a varying substrate concentration and can measure inhibition of protease activity.  These devices and methods could be useful for measuring protease-substrate interactions, protease-substrate turnover, and for identifying protease inhibitors. (more...)

The expression of a cloned gene to isolate large quantities of its protein product demands a highly efficient expression system in which protein can be purified to homogeneity, especially for crystallographic and therapeutic purposes. It is often difficult to achieve high-level expression of biologically active recombinant proteins from eukaryotes. Several systems have emerged that involve fusing the gene of interest downstream of a second gene to produce a fusion protein. A major drawback of this approach is the covalent linkage of the two proteins, where the presence of the fusion partner may prevent or interfere with subsequent use of the desired protein. To overcome this problem, a protease recognition site can be constructed between the two fused proteins; however, this involves altering the N terminus of the desired product and resulting in the expression of an unauthentic protein. Furthermore, cleavage of the fusion protein is rarely complete, causing a reduction in protein yield, and it may also occur nonspecifically within the fused protein. Ubiquitin (Ub), the fusion partner, is a small eukaryotic protein that offers a natural yield enhancement, and uniquely, allows the Ub moiety to be removed by highly specific proteases known as deubiquitylating enzymes. A related system using WT ubiquitin for the production of soluble proteins has been reported. However, in many cases it is desirable to have the protein produced in an insoluble form for 1) reduced toxicity, 2) protection from proteolysis, and 3) ultimately higher yield. (more...)

In the pharmaceutical industry, synthetic chemists often alkylate starting compounds to generate compounds that have more desirable properties. However, the current reagents used in this modification process can be expensive or harmful to the chemist. (more...)

University of California, Irvine researchers have discovered SKCa3-1b and SKCa3-1c, two novel isoform variants of the SK3 (also known as KCNN3) gene. The SK3 gene is located on human chromosome 1q21 in a region containing a major susceptibility locus for familial schizophrenia and familial hemiplegic migraine associated with permanent cerebellar ataxia. Researchers have also found that these two novel isoforms dominantly-negatively suppress SKCa3-1A currents. Suppressing SKCa3-1A currents creates a concomitant increase in dopamine release, characteristic of schizophrenia. (more...)

Preservation of posttranslational modifications during purification is crucial for successful mass spectrometric analyses of protein modifications. Current tandem-affinity purification strategies require native conditions and are therefore susceptible to loss of posttranslational modifications during cell lysis and purification because modifying as well as de-modifying enzymes remain active under these conditions. (more...)

A Chemically Inducible Cucumber Mosaic Virus Amplicon Expression System for Production of Recombinant Proteins in Plant-Based Systems (more...)

Novel single chain variable fragment (scFV) antibodies against human Mucin-1 (MUC-1) have been developed by researchers at University of California, Davis to diagnose and treat adenocarcinoma cells, such as human breast, prostate and ovarian cancer cells. This method is superior to current methods for optimal diagnosis and treatment of these cancers. For example, while radioimmunotherapy using intact monoclonal antibodies (MoAbs) has been utilized in the treatment of breast cancer and other solid tumors, therapeutic success has been limited by the large size of the MoAb (150 kD) inhibiting blood clearance and retarding accumulation of the radiopharmaceutical at the tumor site(s). This powerful method utilizes small peptide antibodies that are specifically targeted to MUC-1, one of the epithelial mucin family of molecules that has received considerable interest as an antigen target because it is widely expressed on a large number of epithelial cancers and is aberrantly glycosylated, making it structurally and antigenically distinct from that expressed by non-malignant cells. These targeted antibodies make it possible to both image and treat primary and metastatic tumors associated with breast, prostate and ovarian cancer by killing only cancerous cells. New methods using these antibody peptides can be superior to current methods in that: Identification of cancer cells is achieved through anti-MUC-1 peptide antibody binding profiles to select the scFv to the type of cancer by large tissue arrays (eg prostate and breast cancers); and, Targeted therapy to MUC-1 positive cells is possible resulting in the death of only cancerous cells. Targeted imaging (eg PET or SPECT) for sensitive detection and treatment of cancerous cells can be made ideal using these innovative reagents. Efficient cost-effective production of the small cancer-specific peptide antibodies is possible using standard techniques. Focused, hyperimmune libraries of single chain Fvs against the tandem repeat region of the MUC1 antigen upregulated on most epithelial cancers, e.g., prostate, breast, ovarian, etc. Rigorously screened against the antigen and highly characterized tissues from patients with prostate and breast cancers. Screened for relationship to cancer grade; Screened for high affinity; Directly screened using biotinylated discFvs recombinantly engineered using methods in complementary patent pending invention. Evidence for xenograft uptake in mice and not in normal tissues including gastrointestinal tissue. Images Anti-MUC-1 MAb compared to anti-MUC1 scFv E1 and G1 binding to human prostate cancer (grade 3) (A-C) and not to normal human colon (D). A) BrE-3 MAb B) E1 scFv C) G1 scFv and D) G1 scFv on human colon (more...)

Alpha-4 Beta-1 Ligands as Targeting Agents for Cancer and Autoimmune Diseases (more...)

Production of Excreted Recombinant Proteins Using Metabolically-Regulated Transgenic Plant Cell Cultures (more...)

The hormone prolactin (PRL) exerts various effects in a wide range of physiological processes. Research suggests that PRL may promote cellular proliferation in both breast cancer and prostate cancer cells. University of California researchers have developed a modified PRL analog (S179D) that acts as a strong antagonist to PRL in cell proliferation assays. S179D consists of a wild-type PRL with a single amino acid substitution. This substitution alters the activity of the molecule such that it antagonizes the growth-promoting effects of unmodified PRL in experimental breast cancer and prostate cancer cell lines. Research results indicate that the modified S179D retains some functions of normal PRL. In other words, S179D may be a selective inhibitor of cell proliferation in certain systems, which suggests that it could potentially be used as a cancer therapeutic that did not wholly disrupt PRL metabolism throughout the body. The University of California holds a soon-to-issue United States Patent claiming S179D and related PRL mutants. The University is searching for commercial partners that are interested in investigating the potential of S179D as a therapeutic. Examples Figure 1.  Effects of S179D on the proliferation of MCF-7 breast cancer cells Normal MCF-7 cells produce PRL, making it difficult to study the effects of exogenous PRL. In this study, MCF-7 breast cancer cells were developed that are deficient in PRL production so that the effects of exogenously applied hormone could be elucidated. Cells were cultured in media containing wild-type human PRL at 100 ng/ml. Cell numbers were measured at 48 hours, and the percent increase over the number of cells in the vehicle only control was calculated. In the absence of S179D, wild type PRL induced a near doubling in the number of MCF-7 cells. When treated with either of two forms of S179D (A or B), the growth-promoting effects of PRL were significantly reduced in a dose-dependent manner. Figure 2.  In one experiment, the administration of S179D prior to cancer cell injection was effective in decreasing both the incidence and size of tumors in mice injected with prostate cancer cells (A and B). In a second experiment, mice previously injected with prostate cancer cells were treated with S179D, which was effective in reducing tumor size (C). 2A.  At day 1, nude mice were implanted with minipumps administering control vehicle, wild type PRL, or S179D. On day 4, mice were injected with DU145 human prostate cancer cells. On day 22, mice were assayed for tumor incidence and size. S179D significantly reduced the incidence of tumors. 2B.  PRL slightly increased tumor size while S179D significantly reduced tumor size. 2C.  In a separate experiment, mice were injected on day 1 with DU145 human prostate cancer cells. At day 18, mice were implanted with minipumps administering control vehicle, wild type PRL, or S179D. On day 42, tumor size was measured. PRL promoted increased tumor size while S179D significantly reduced the size of well-established tumors. References X. Xu, E. Kreye, C.B. Kuo, and A.M. Walker. A molecular mimic of phosphorylated prolactin markedly reduced tumor incidence and size when DU145 human prostate cancer cells were gown in nude mice. Cancer Research 61:6098 (2001) M.D. Schroeder, J.L. Brockman, A.M. Walker, and L.A. Schuler. Inhibition of Prolactin (PRL)-Induced Proliferative Signals in Breast Cancer Cells by a Molecular Mimic of Phosphorylated PRL, S179D-PRL. Endocrinology 144: 5300 ' 5307 (2003) T.J. Chen, C.B. Kuo, F.F. Tsai, J.W. Liu, D.Y. Chen, and A.M. Walker. Development of Recombinant Human Prolactin Receptor Antagonists by Molecular Mimicry of the Phosphorylated Hormone. Endocrinology 139: 609-616 (1998).   (more...)