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...)

Rapid and efficient detection of mutagenic and carcinogenic potential in chemical materials has become a priority for the consumer, chemical, and pharmaceutical industries.  In fact, not detecting mutagenicity early in development is a major liability, particularly for drug companies.  As a result, in vitro carcinogenic assays – with the benefits of low cost, reduced use of animal tests, and faster results – are of significant interest to both companies and testing labs, and their use is expect to grow in the predictive toxicity testing market, which was valued at more than $1.3 billion globally in 2010. The Ames test, developed in the 1960s, is a widely adopted biological assay for the detection of mutagenic compounds and has been employed by the pharmaceutical, agricultural, and petro-chemical industries. However, the test has numerous limitations owing to its reliance on bacterial growth and is sub-optimal in predicting mutagenicity in higher organisms (high incidence of false-negatives).  As a result, other tests have been developed using human cell lines to detect DNA damage, the primary cause of mutagenicity. Yet these tests are limited by their inability to directly measure DNA damage, which also leads to a high false negative rate. Thus, an in vitro assay that can quickly and directly measure DNA damage would greatly improve the efficiency and reliability of carcinogen and mutagen testing of chemicals.     (more...)

 AIDS, the disease caused by the virus HIV, represents a devastating global pandemic. According to a United Nations report in 2010, HIV has killed nearly 30 million people worldwide, with over 2.5 million additional infections each year. Detecting HIV particles is critical not only to patient diagnosis, but also for basic and clinical research, the source of future therapies. Unfortunately, current methods are severely lacking. Phenotypic testing can take over a month to complete and only reports a single time point. Another system widely used for research employs cell lines that express CD4 and co-receptors at abnormally high levels, rendering results of questionable physiological relevance. Patients, physicians, and researchers alike would benefit greatly from a new method of detecting and characterizing HIV; one that is rapid, sensitive, adaptable, and most importantly, physiologically accurate.      (more...)

Using pulsed laser radiation, University of California, Irvine researchers have developed a novel methodology to provide a mechanical agonist to single or multiple cells and stimulate cellular mechanotransduction. These researchers have also shown this laser methodology can be used in a high-throughput assay format in 3D and 2D cell cultures. The UCI researchers have shown that this technology is highly effective in eliciting a mechanotransduction response that can be modulated by inhibitors or activators of mechanotransduction signaling axes. (more...)

UC Researchers have developed a Field-Programmable-Gate-Array (FPGA) based hardware implementation that utilizes the FM-Index for exact pattern matching for string searching.  This method of FM-Index string matching has a higher effective throughput than brute force due to the higher number of character comparisons per cycle performed by the FM-Index.  Further, the speed of this method is in the order of two orders of magnitude greater than Bowtie software tools and ten to seventy times faster than the traditional method using FHAST.   (more...)

DNA mutation events (gene rearrangements, base-pair substitutions) cause genomic instability, and can lead to cell death or cancer. These events also potentially lead to gene dysfunction and genetic disorders. DNA mutation events have many possible causes, such as inherited mutations in genes involved in genomic integrity, or exposure to environmental toxins. Human stem cell technology, in which stem cells can be differentiated into any cell type in the body, has the great potential to advance the discovery of therapeutics for unmet medical needs. However, recent reports indicate increased DNA mutation frequency in stem cells, which limits their potential use for discovery or therapeutic purposes. Therefore, technologies that enable the detection of the different types of DNA mutations would advance the characterization and selection of human stem cell lines for discovery or therapeutic purposes, and help characterize the mutagenic potential of environmental toxins. (more...)

As much as 15% of the adult population exhibits symptoms of irritable bowel syndrome (IBS), a disorder characterized by abdominal pain, diarrhea and/or constipation, bloating, and discomfort. Although IBS does not cause permanent harm, it can render sufferers unable to work, attend social events, or even travel short distances. IBS is also associated with significant health care costs and economic burden. Lacking well-defined and specific diagnostic criteria, physicians currently diagnose IBS on the basis of a complete medical history, physical examination, and other assays. These may include invasive procedures such as sigmoidoscopy or colonoscopy. As such, there is a need for a simple and reliable method to diagnose this condition, as well as a therapeutic target for drug development. (more...)

UCSD and Johns Hopkins University inventors have come up with a new microfluidic device with a flexible design intended to provide researchers with an additional tool to study non-adherent cells. The device is made of a single cast of a silicon elastomer polydimethylsiloxane, PDMS, and is essentially disposable. A single microfluidic chip contains a few hundreds of microscopic chambers, which are a few microns thick and fit the field of view of a high resolution objective lens. Colonies of motile bacteria (such as E. coli ) and other small non-adherent cells grow in the chambers under chemostatic conditions. The colonies grow exponentially and can be monitored at a single cell resolution. A colony can be started with a single cell and reach a dense packing. Medium in the chemostatic chambers can be redefined within less than a minute with no flow through the chambers and no disturbance to the cell environment. Chemical contents of the media can be varied between the chambers in a controlled way and colonies growing at different concentrations of a relevant chemical (e.g. antibiotics) can be studied on a single chip. (more...)

Mutations and duplication of the X-linked MeCP2 gene are observed in several disorders, such as Rett Syndrome (RTT), Autism, severe neonatal encephalopathy, schizophrenia and X-linked mental retardation. As MeCP2 plays an important role in the pathogenesis of multiple mental disorders, the investigation of MeCP2 function and regulatory pathways may show promise for developing broad-spectrum therapies. (more...)

High-throughput, automated, large-scale mircoarry format assay in a short time frame and at low cost. (more...)

The reconstitution of ion channels and transmembrane proteins in planar lipid bilayer membranes allow for functionality testing in highly controlled environments. Recent work with lipid bilayers formed from mechanically joined monolayers has shown their potential for wider technological applications, including automation and parallelization. Although fully automated formation and measurement of functional planar lipid bilayers is currently possible using the contacting monolayer technique; automated formation of such 'droplet' lipid bilayers having consistent and repeatable sizes, however, has not been demonstrated. Further, bilayer areas are highly sensitive to variations in mechanical positions and the bilayers themselves cannot withstand significant perfusion of adjacent solutions. (more...)

Complex mixtures of aroma compounds are often responsible for the overall aroma of a food, beverage, cosmetic or other product.  Two or more odorants can frequently lead to an aroma that is not similar to any of its components.  A new method and apparatus allow for more precise and informative analysis and characterization of aromas and volatile constituents. (more...)

UCLA researchers have identified mutually exclusive mechanisms of acquired resistance to B-RAF inhibitors. By utilizing resistant melanoma sub-lines, patient-derived biopsies and short-term cultures they determined that a subset exhibit a mutation in N-RAS, a component of the MAPK signaling pathway. Another subset exhibits activation of PDGFRβ, a receptor tyrosine kinase involved in additional cell proliferation and survival pathways. Knockdown of N-RAS or PDGFRβ significantly reduced the growth of the resistant melanomas. Importantly, the acquired resistance develops not from secondary B-RAF mutations, but through reactivation of MAPK signaling or activation of alternate survival pathways. These findings offer assays to stratify patients for sequential treatment strategies. (more...)

Centrifugal microfluidic devices find extensive use for in vitro diagnostics. One of the most important considerations in developing a microfluidic device is determining how the liquids will be transferred in a controlled manner. The discovery of new methods for controlled release of liquids is an area of significant importance in the future development of microfluidic technologies. Researchers at the University of California, Irvine have developed a method for controlled release of liquids on a centrifugal platform. This invention has the ability to store liquid on a centrifugal microfluidic platform and, when needed, is able to transfer this liquid to any location on the platform independent of its proximity to the center of rotation. The invention is a non-contact method, uses stable materials, and would be easy to assemble in a mass manufacturing setting. (more...)

The Human Immunodeficiency Virus (HIV) has evolved a number of mechanisms of evading the human immune system.  One way is through a high level of mutation, which makes it difficult to develop a vaccine that stimulates protective immunity against all of the different HIV variants.  Therefore, scientists are searching for a general surrogate maker that could be used to target any HIV-infected cell regardless of its mutational status. In this regard, scientists have recently focused their attention on so-called cryptic peptides of HIV.  Cryptic peptides are non-functional HIV proteins that are produced due to translational errors that occur in HIV-infected cells.  Because these cryptic peptides are commonly produced and then presented on the surface of the HIV-infected cells, it is thought they may be good surrogate markers and targets for any HIV-infected cell. (more...)

Researchers at the University of California, Davis campus have discovered a novel metabolic pathway in human breast and propose this pathway as a new paradigm in molecular etiology of breast cancer. (more...)

Immunoassays have a tremendous range of uses in the diagnosis of diseases, pharmaceutical drug development studies, and therapeutic drug monitoring.They are highly popular due to their high specificity and sensitivity for a variety of analytes in biological samples.However, immunoassays can be labor intensive, time consuming, and require expensive reagents.An immunoassay method that is rapid, inexpensive, and highly effective would be practical and may have widespread use.Researchers at the University of California, Irvine have developed a fluoroimmunoassay chip that can be used for improving the detection of low concentration (approx. 1 nM) biological agents.The method is rapid, inexpensive, and provides a fluorescence enhancement that is approximately 30-fold greater than glass.In addition, this method does not use the principle of metal enhanced fluorescence to enhance the signal, so the fluorophore is not distance dependent in order to achieve enhancements. (more...)

The T-maze is a common laboratory test used to assess working memory in rodents. Conventional T-mazes are often built and operated by hand, which can introduce variation between experimenters. This device allows for standardization of the experiments, increases productivity, and eliminates the errors and distractions of animals inherent to manually operated devices. (more...)

Cyanide is a highly toxic and rapidly acting poison that is infamous due to its use in murders, suicides, wars and attempted genocide.In the present day, cyanide may be responsible for up to 10,000 deaths annually in the United States due to smoke inhalation.Cyanide may also be used as a terrorist weapon. Prior methods to measure cyanide in the blood have involved acidifying the blood after lysis of red blood cells.However, this method is time consuming (takes at least a few hours) and tedious, and thus, inadequate for rapid detection of cyanide toxicity in field or hospital settings.Field or laboratory devices capable of rapidly measuring cyanide levels in blood or body fluids are not currently available, however such field or laboratory devices would be highly useful. Researchers at the University of California, Irvine have developed a method to rapidly measure cyanide in biological samples, which can be carried out in field settings.This method is based on measuring cyanide based on spectral changes that occur when cyanide binds to the reagent.Advantages of this method are its ease of use, stability, and applicability across a wide range of cyanide concentrations and may be used with ease in the field or on laboratory devices. (more...)

Cell adhesion is an essential function that mediates the physical interaction betweeen cells and their microenvironment and plays an important role in tissue formation.  Chemical control of cell adhesion allows for temporal and spatial manipulations of cell-cell and cell-surface interactions with high resolution for therapeutic and research purposes.  Recent reports show that cell-surface grafted nucleic acids can serve as adhesion molecules that have the benefits of minimal cross reactivity with endogenous cell-surface receptors and combinatorial encoding of interactions.  Cell surfaces can be modified with DNA either covalently or non-covalently through direct linkage of oligonucleotides to hydrophobic molecules such as lipids and steroids.  Current labeling approaches have several disadvantages, including manufacturing difficulties, inability to stably integrate into the cell surface under typical culture conditions, interfering with cellular function, and failure to display adhesive sequence at controlled distances from the cell surface. (more...)

There is a broad interest in targeting kinases for drug discovery and patient diagnosis. For example, kinases are important biomarkers in cancer diagnostics and treatment, or their activity can be monitored to determine the state of a cell (e.g. via PET imaging). This interest led to the development of numerous kinase assay technologies. Generally, radiometric assays are adopted as the primary technology used by companies that provide kinase profiling services. However, they suffer from several limitations. The input amounts required for these assays make it difficult to study kinase activity on a small level. Also, these assays are labor-intensive, expensive, and are potentially hazardous to those handling the radioactive materials. Further, regulations that control the levels of a specific radioisotope that can be used may limit the desired work pace. (more...)

The invention provides methods and devices in which microscopic particles or cells within a fluid flowing in microfluidic channels are selectively manipulated, normally by being pushed with optical pressure forces at branching junctions in the channels so as to enter into selected downstream branches, thereby realizing particle switching and sorting. Transport of the particles thus transpires by microfluidics while manipulation in the manner of optical tweezers arises either from pushing due to optical scattering force, or from pulling due to an attractive optical gradient force. Whether pushed or pulled, the particles within the flowing fluid may be optically sensed, and highly-parallel, low-cost, cell- and particle-analysis devices thus may be efficiently realized, including as integrated on bio-chips. (more...)

The ability to capture and study circulating tumor cells is an emerging field with implications for early detection, diagnosis, determining prognosis, and monitoring of cancer, as well as for understanding the fundamental biology of metastasis. Current techniques of identifying and isolating such cells usually involve flowing cells in a chip across an antibody coated surface. However, these devices usually require complex geometries to ensure effective contact of the target cells with the functionalized surfaces. Such a problem can be avoided by using micro/nanoscale motors that can be programmed to scower an entire static sample as many times as needed. Further, the movement of the nano/microscale motor increases the solution convection thereby improving the diffusion of the target antigen, making for a quicker and more favorable recognition reaction. This also helps eliminate non-specific binding of the antigen while on its way to a clean environment for post-capture analysis. (more...)

Lymphatic dysfunction has been found in many disorders from transplant rejection to cancer metastasis, but there is little effective treatment for lymphatic diseases. The cornea is an ideal site for lymphatic research due to its accessible location, transparent nature, and lymphatic-free but –inducible features. Because there are no pre-existing vessels to consider at this site, it is exceptionally straightforward and accurate to evaluate new lymphatic events in the cornea. Since lymphatic vessels are not easily visible, previous studies using the cornea have relied on traditional immunohistochemistry assays with dead tissues. Currently, there is no means of direct and harmless visualization of lymphatic vessels within live cornea.   Investigators at University of California at Berkeley have addressed this challenge by developing the first live imaging of corneal lymphatic vessels. Lymphatic specific dye is injected into the subconjunctival space to visualize lymphatic vessels at various stages in the cornea under a fluorescence stereo-, confocal, or two-photon microscope. Lymphatic vessels can be labeled in different colors to produce two-, three-, and four-dimensional images or live videos at a molecular level. The investigators have demonstrated a proof of principle in live mouse cornea. The technique allows time course tracking of dynamic lymphatic processes within the same tissue or subject over a short or long period of time. Live imaging of corneal lymphatic vessels allows visualization of lymphatic vessels in their natural morphology, state, and interactions with the local environment. Live imaging of corneal lymphatic vessels is readily applicable to patient examination as the lymphatic dye of dextran is bio-degradable and harmless to human health. (more...)

Understanding protein interactions within a cell allows one to probe the mechanisms that control its growth, maintenance, and death. This would help lead to the development of more specific and powerful drugs to combat disease. Several methods currently exist for studying protein-protein interactions. The yeast two-hybrid (Y2H) system is the most popular one. However, this method has several limitations, including complications associated with the use of protein fusions, incorrect protein folding, incorrect post-translational modification, and potential toxicity of the proteins of interest in yeast. Also, Y2H is based on DNA transcription, and thus, is not well suited for the study of DNA transcription factors or DNA binding proteins. Finally, Y2H is not instantaneous and cannot provide the accurate characterization that a homogenous, equilibrium binding assay can provide. Meanwhile, ultrahigh sensitivity fluorescence detection methods have been developed that allow for the study of molecular interactions in extremely small volumes. These methods extract information regarding brightness and/or diffusion for detecting properties such as ligand-protein binding and cleavage of DNA hybrids by restriction enzymes. However, these analytical methods often fail to take advantage of all the information available in the data. (more...)

Lipid bilayers have previously been fabricated through droplet methods difficult to scale up and control in bulk fabrication processes. Although these methods have been inventive in their formation technique, they pose problems when attempting to transition to an automated system, and they also do not allow for simultaneous characterization, and instead rely on additional tools for that process. (more...)

The field of the invention generally relates to methods of constructing high surface area structures using photoresist patterning in combination with electrochemical polymer deposition.The methods described herein can be used to create structures for a wide variety of applications including, but not limited to, micro-reactors, electrodes, and sensors (e.g., biosensors). (more...)

A novel DNA-based switch that enables the one-step quantitative detection of antibodies in complex samples (such as whole blood) and effectively reduces analysis time from a few hours to less than 5 minutes. (more...)

Conventional diagnosis of tuberculosis (TB) and subsequent monitoring of response to treatment requires culturing of bacteria from sputum samples, which does not always test positive. UC Berkeley investigators have developed an inexpensive serological test platform that provides accurate and rapid results for monitoring tuberculosis treatment response. This could also be used to assess end-point in drug trials. Since antibody response to pathogen is a direct reflection of bacterial burden in a host, the biomarker assay focuses on host response to the infection and treatment, as opposed to the pathogen itself. Compared to a WHO approved PCR based technology Xpert®MTB/RIF (Cepheid) used for the diagnosis of TB, which could be relatively expensive ($17,000/module and $9.98/cartridge), the present invention could provide a competitive and an inexpensive alternative for monitoring TB, especially in developing countries.         (more...)

Researchers at the University of California, Irvine have developed a novel microfluidic device that is capable of encapsulating cells at a very high efficiency. The device integrates impedance measurement with a novel on-demand droplet generation process to enable the selective generation of droplets that contain encapsulated cells only when a cell is present. This ensures that a high percentage of cells are encapsulated rather than droplets that do not contain cells. The device consists of two main components – the impedance sensor and the on-demand droplet generator. When the sensing electrodes of the impedance sensor detects a change in impedance caused by a cell, the cell is coupled with a droplet. (more...)

UCSF inventors have developed a safe endovascular biopsy device for extraction of endothelial cells from the blood vessel wall. (more...)

A novel system and methods that provides efficient display and screening of peptide libraries at the cell surface, and enables rapid and quantitative characterization of the candidate peptides. (more...)

Researchers at the University of California, Irvine have developed a plasmid that expresses recombinant GST-RILP protein. RILP is a Rab7 effector protein and therefore selectively binds the GTP-bound form of Rab7. (more...)

The Ah receptor (AhR) is a ligand-dependent transcription factor that mediates the ability of dioxin and related halogenated aromatic hydrocarbons (HaHs) to induce gene expression and to produce toxicity. Cell-based bioassays for dioxin-like chemicals (commonly referred to as CALUX bioassays) respond to dioxins and related chemicals with the induction of luciferase in a time-, dose-, AhR-, and chemical specific manner.  A researcher at the University of California Davis has developed and characterized a new CALUX bioassay for the detection of lower concentrations of dioxins and dioxin-like chemicals within a sample. There is a need for rapid, inexpensive and accurate methods for the detection and quantification of HAHs, such as polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs) and biphenyls (PCBs) and related chemicals in environmental, biological, food and other matrices.  This invention provides an improved CALUX cell-based reporting system meeting this need. (more...)

During their lifetime, some form of cancer affects more than 40 percent of the U.S. population. It is known that the catch-all term “cancer” includes a variety of diseases with varying etiology and prognoses. It is also known that the progression to metastasis radically changes treatment options. Despite the trend toward better understanding of the nuances of various types of cancer, the critical aspect of effective therapy remains early detection. An early indicator of cancer would allow physicians to proactively test and choose appropriate treatments, before disease progression has ruled out the most effective, early options. (more...)

It has been shown recently that in addition to their classical role in desensitizing G protein coupled receptors (GPCR’s), beta-arrestins can act as signaling molecules themselves. Thus, it is now widely held that GPCR’s are able to signal through parallel G-Protein and beta-arrestin pathways. Next generation GPCR therapeutics will be advanced by fine-tuning the actions along these pathways. GPCR ligands that preferentially activate the latter pathway are called beta-arrestin “biased” agonists. Different biological responses have been observed with such beta-arrestin biased agonists, compared with traditional GPCR therapeutics designed to activate G-proteins. (more...)

Surface-enhanced Raman spectroscopy (SERS) is an analytical chemistry technique for rapid and accurate detection of chemicals and bioagents by scattering laser light from a sample. The Raman signals are enhanced tremendously when samples are deposited onto specially prepared metal surfaces (substrates), which create localized amplification of the laser’s electromagnetic field. The result is an enhancement of the intensity of the spectral peaks by several orders of magnitude, bringing the level of detection down to a single molecule. A good nanostructure substrate is the key to SERS applications. Silver has optimal properties for Raman scattering, but is chemically unstable, requiring complex and expensive equipment for substrate fabrication. Current SERS substrates typically cost over $100 and are not reusable. For a wide range of commercial SERS applications, better methods are needed to make nanosubstrates that are inexpensive, stable, and easy to make. Scientists as UC Berkeley developed an easy and cost-effective way of producing substrates suitable for enhancement of Raman, fluorescent, or luminescent signals. The method allows for producing bulk amounts of silver dendrites in powder form that can be used as is, attached to adhesive substrate, or compressed into a tablet. The final cost of each substrate can be substantially less than $1 because of the simplicity of the process and the low cost of the materials and reagents used. (more...)

Normal.dotm 0 0 1 182 1041 UC Berkeley 8 2 1278 12.256 0 false 18 pt 18 pt 0 0 false false false /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-ascii-font-family:Cambria; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Cambria; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Normal.dotm 0 0 1 182 1041 UC Berkeley 8 2 1278 12.0 0 false 18 pt 18 pt 0 0 false false false /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-ascii-font-family:Cambria; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Cambria; mso-hansi-theme-font:minor-latin;} Luminescent (including fluorescent and phosphorescent) markers find a wide variety of applications in science, medicine and engineering. In many situations, these markers provide competitive replacements for radiolabels, chromogens, radiation-dense dyes, etc. Moreover, improvements in fluorimetric instrumentation have increased attainable sensitivities and permitted quantitative analysis. We present the synthesis, properties, and biological applications of Ratio Coppersensor-1 (RCS1), a new water-soluble fluorescent sensor for ratiometric imaging of copper in living cells. RCS1 combines an asymmetric BODIPY reporter and thioetherbased ligand receptor to provide high selectivity and sensitivity for Cu+ over other biologically relevant metal ions, including Cu2+ and Zn2+, a ca. 20-fold fluorescence ratio change upon Cu+ binding, and visible excitation and emission profiles compatible with standard fluorescence microscopy filter sets. Live-cell confocal microscopy experiments show that RCS1 is membrane-permeable and can sense changes in the levels of labile Cu+ pools within living cells by ratiometric imaging, including expansion of endogenous stores of exchangeable intracellular Cu+ triggered by ascorbate stimulation in kidney and brain cells. (more...)

Aging is a natural state of development that reduces ones adaptivity and increases the incidence of disease. Several diseases, including cancer, atherosclerosis and neurodegeneration, occur as a direct result of aging. Resveratrol is a well known anti-aging chemical, but its molecular target is controversial, making it difficult to uncover other chemicals. It would be of interest to discover resveratrols target within the cell to allow a new class of anti-aging drugs to emerge. (more...)

Tyrosine kinases (TKs) are a diverse family of highly regulated enzymes that, upon activation, phosphorylate target proteins on the amino acid tyrosine. TKs are involved in many cellular functions such as cell division and cell proliferation, as well as in several diseases including cancer and diabetes. Active site TK inhibitors, such as Imatinib (Gleevac) and Dasatinib (Sprycel), are the primary treatment options for chronic myelogenous leukemia (CML) and some other malignancies. Unfortunately, TK point mutations can prevent the inhibitors from binding and lead to drug resistance and disease relapse. Thus, an alternative method of inhibiting TKs would lead to treatment options for TK inhibitor-resistant patients and should reduce the rate of resistance to TK inhibitors in patients beginning therapy. (more...)

The present invention involves a method of artificially introducing an allosteric site into a protein whereby an addition of an artificially designed or a natural modulator of that allosteric site leads to a mechanical tension onto the protein. This mechanical tension alters the proteins affinity for its substrate, and, in the case of an enzyme, the catalysis rate.In addition to the above-described method, the invention involves, but is not limited to, the following: 1. An allosteric protein, selected from a group of well-studied proteins, artificially engineered with an allosteric site, herein referred to as the chimera); 2. A modulator engineered to affect the specific allosteric site on the chimera to effectively affect the chimeras substrate affinity; 3. A well-known substrate for the chimera that can be implemented in an in vitro or an in vivo reporting system.This differential change in substrate affinity or catalysis rate caused by modulator binding can be used in multiple applications. One is the use of such chimera system as an amplified molecular probe, to detect the presence of a natural biological modulator specific to the chimera in an in vitro or in vivo assay. In addition, the chimera-modulator system can be used as a method to study protein conformation and the effect of modulating such conformation on a proteins function. (more...)

Proteases or enzymes with proteolytic activity are fundamental to many key biological processes such as cell growth, cell death, blood clotting, matrix remodeling and immune defense. A large number of pathogens, including viruses, bacteria and multi-cellular parasites also use proteases to infect host cells, complete their life cycle and degrade the host immune system. Proteases have also been found to play a role in the pathogenesis of hypertension, liver cirrhosis, Alzheimers disease, autoimmune diseases, rheumatoid- or osteoarthritis and cancer. There is considerable effort to understand the role of proteases in disease and to identify therapeutic agents targeting specific protease activities. A bottleneck for high throughput drug screening, however, is now at the level of bioassays. Many compounds initially identified using in vitro assays fail in later phases of drug development because they cannot be used in a biologically relevant environment. Therefore, drug discovery researchers are now aggressively looking for high-throughput in vivo assays using cells, or, ideally, whole organisms, to screen potential drugs.What are needed are efficient bioassays to (1) determine the role of proteases in normal and diseased cellular processes and (2) screen in biologically meaningful systems for pharmacologic modulators of proteases of interest. (more...)

Prior to translation, transcription generates a precursor molecule (pre-mRNA) that contains both introns (intervening sequences) and exons (protein coding regions). Alternative splicing pathways vary the production of a mature mRNA strand by modifying the introns removed and the exons joined. Depending on the splice sites, these mRNA variances give rise to proteome diversity by changing the encoded protein structure, which in turn can affect ligand binding, allosteric regulation, protein localization, etc. Although mutations in splice signals account for 15% of genetic diseases caused by point mutations indicating a pressing need for research into the mechanisms controlling alternative splicing, experimental efforts to discover compounds targeting splicing are hampered by a lack of reliable, reproducible, and high-throughput techniques. (more...)

Internal ribosome entry site (IRES)-mediated translation initiates and assembles translation machinery at a site close to the start codon in a manner that does not require the traditional eukaryotic 5 nucleotide cap or eIF4E (cap-binding protein). Initially discovered in picornaviruses (poliovirus, encephalomyocarditis virus, rhinovirus, etc.), viral IRES-mediated translation relies on virus-specific combinations of transcription factors, trans-acting factors that help stabilize the IRES structure and the IRES elements themselves, which can span hundreds of nucleotides in length and have complicated secondary and tertiary structures. The complex way in which the IRES elements mediate translation is of great importance to researchers seeking insight into viral gene expression and ultimately, anti-viral therapeutics. (more...)

Targeted drug delivery is often critical in clinical treatments. Ideally, such delivery would be automatically responsive to physiologic parameters. ALZA, Durect, and other companies have made considerable investments toprovide such responsive dosing. More recently, monoclonal antibodies tagged with radioactive cancer treatment moieties have been developed to provide more focused treatment of cancers, sparing normal cells from these potent toxins. Implantable insulin pumps have been developed to provide a more natural philological level of insulin to diabetics. Investigators at University of California at Berkeley have developed a nanozippering device that can both detect and transduce molecular signals. Theforces of antibody binding exert strain on the delivery vehicle and subsequently release an encapsulated secondary species. The device is in
highly miniaturized form, which provides advantages over implanted insulinpumps, slow release materials, osmotic pumps, and other 
currently employed drug release devices. This new nanomachine provides biomolecularconcentration dependent release of signaling molecules, drugs, or imaging
agents. This new nanomachine, which uses the binding forces of an analyte to bend a component in a nano-device, will detect with great specificity anyantigenic bimolecular and transduce that signal into the release ofsecondary species. The secondary species need not be antigenic 
and couldinclude proteins, small molecules, haptens, imaging agents, nanoparticles,polymers, etc. The antigenic nature of the detection makes the devicebroadly applicable. The device is capable of operation in physiologicsolutions and requires no external power source. This fundamentalarchitecture exerts mechanical forces on a coupled delivery vehicle that contains a secondary species when the presence of a biomolecular species is detected. (more...)

The present invention relates to a method for determining cancer susceptibility by quantifying DNA damage-induced mRNA in whole blood. (more...)

UC San Diego researchers have developed a new nanotechnology, smart dust, that has state-of-the-art applications in almost every field of use, including biological sensing, screening, and communications technology. The invention utilizes micron-sized particles of silicon that have been etched and then chemically modified in such a way that each individual particle has its own addressable identity. This feature allows one to use thousands of the particles together, each with its own “tag,” for high-sensitivity chemical or biological sensing, diagnostics, and low- and high-throughput screening of biomolecular compounds. (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...)

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...)

Single-cell analysis has generated a wealth of information in cell population studies. The characteristics of cells in a heterogeneous population can be analyzed without the loss of information that would result from averaging the population as a whole. Until now, most single-cell analysis has been focused on the surface properties since limited markers exist that can penetrate the plasma membrane into the cytosol and allow measurement of the cellular contents in single cells. Most cytosolic components can only be measured after disruption of the plasma membrane and report on the composition of the population as a whole rather than on individual cells in a heterogeneous cell population. Using a multi-disciplinary approach, combining biomedical science and nanotechnology developed by micromechanical engineering, the Microfluidics Flow Lysometer (MFL) team is developing a novel technique, flow-lysometry, which measures cytosolic components of single cells. The team envisions that this technology can be applied to various types of cells measuring many different cytosolic components including antibodies, RNA levels and enzyme production. The flow-lysometry technology when combined with commercially available flowcytometer capabilities will be capable of correlating individual cell morphology and surface characteristics with the cell's internal biochemistry.  Flow cytometry is currently used in numerous applications in basic research, clinical research, drug discovery and clinical diagnostics testing. With the extension of flow-lysometry, this proprietary technology provides a more robust cell analysis capability.  (more...)

Integrins are found throughout the animal kingdom where they play important roles in cell adhesion, migration, proliferation, and survival. In humans, integrins play critical roles in development. Aberrant activation is implicated in several disease states, including cancer and heart disease. Thus, drugs aimed at disrupting this specific interaction could lead to therapies for these conditions. (more...)

The success of gene therapy methods such as small fragment homologous recombination and cDNA-based gene therapies is often difficult to quantify. These methods often lack an endogenous selection mechanism that can be used to differentiate and quantify targeted cells. Therefore, it is difficult to monitor and map the success of gene therapy in patients. UCSF investigators have developed methods and compounds enabling the measurement of expression of mutated and non-mutated alleles in the tissue or cells of a human subject. The method, an in situ RT-PCR assay, can be used for diagnosis of allelic variation and the monitoring of gene therapy for a variety of gene-based diseases, especially cystic fibrosis. (more...)

Background   Since the human genome has been sequenced, researchers are now focusing on defining the roles of each the ~30,000 genes in development and disease. As most human genes have homologs in the mouse genome, many researchers study the function of mouse genes to model the function of related human genes.       To study all aspects of gene function, one must be able to manipulate a single gene to generate many kinds of mutations: deletions, point mutations, insertion of exogenous DNA, etc. In mice, such site-directed mutagenesis is commonly achieved by homologous recombination of embryonic stem cells, which can be laborious, time-consuming, and inefficient. Thus, there is a need for technologies that allow for high-throughput, site-directed mutagenesis.   Description   UCSF investigators have designed vectors and methods for high-throughput genetic modification of an existing collection of gene trap insertions in mouse embryonic stem cells. The collection is publically available from the Sanger Gene Trap Consortium and currently consists of ~20,000 random insertions in ~4,500 genes in the mouse genome.   The vectors designed by UCSF investigators make use of recombinase activity to drive three recombination steps at the site of the gene trap insertion. The first step allows for reversion of the original gene trap insertion, resulting in the generation of an internal control. The final two steps allow for the insertion of new DNA of interest, resulting in the desired mutant or allele. Each recombination step can be selected easily using a visible genetic marker.   This system allows one to generate any number of mutations repeatedly into the same genomic site, with efficiencies as high as 80%. Additionally, because the insertions are controlled by the same endogenous promoter elements, position effects, which can create artifacts by misexpression or overexpression, are effectively eliminated. Using these vectors and methods, one could generate with relative ease a variety of site-directed mutations in any of the 4,500 genes for which there is an available enhancer trap insertion.     (more...)

Her2/neu is over-expressed in various types of tumor cells, including 20-30% of breast cancers, adenocarcinomas of the ovary, salivary gland, stomach and kidney, colon cancer, and non-small cell lung cancer. Passive immunotherapeutics like Herceptin control and prevent further tumor cell growth. Unlike active immunotherapeutics, Herceptin does not mediate the immunological cellular destruction. Active immunotherapeutics such as vaccines elicit T helper-1 (Th1) and Cytotoxic T lymphocytes (CTL) biased immune responses and are generally observed for proteins expressed in the intracellular compartment, and less prominently with extracellular or secreted proteins. Rapid degradation of a protein containing polyepitopes can contribute to establishing a bias in the immune response, facilitate antigen presentation and, perhaps assist in establishing specificity of the immune response. This type of immunological response should result in immunological cellular destruction. (more...)

The ability to resist nonspecific protein adsorption (protein resistance) is an indicator of a material's biological inertness or biocompatibility. Protein resistant biomaterials such as the commonly used poly(ethylene glycol) (PEG) have been used in a number of applications such as prostheses, contact lenses, implanted devices, microfluidic systems, drug delivery, and substrates for assays. However PEG has two major limitations. First PEG can only be functionalized at the chain ends, and second PEG is not biodegradable. (more...)

The development of multifunctional, high throughput lab-on-a-chip depends heavily on the ability to measure flow rate and perform quantitative analysis of fluids in minute volumes. Traditionally, there have been many microelectromechanical system (MEMS) based flow sensors for gaseous flows. In recent times, there is some advancement in measuring micro flows of liquids. Examples of sensing principles explored in the measurement of microfluidic flow are heat transfer detection molecular sensing, atomic emission detection, streaming potential measurements, electrical impedance tomography, ion-selective field-effect transitor and periodic flapping motion detection. Flow sensors based on sensing the temperature difference require a complicated design and the integration of the heater, temperature sensors and membrane shielding is difficult to implement. Most other methods are not capable of measuring very low flow rates. (more...)

Cell encapsulation is a highly useful tool in cell culturing, assay, and cell-based therapy applications. Encapsulation has traditionally been accomplished by extrusion through a nozzle, forming an air/water emulsion, into a bath containing a polymerizing agent. However, this batch processing technique is characterized by its inability to trap cell droplets before or without polymerization and non-uniform polymerization times across droplet population. Furthermore, minimum droplet size is limited to 400um and size dispersion is pronounced for small droplet geometries. (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...)

The highly abundant GTP binding protein elongation factor Tu (EF-Tu) fulfills multiple roles in bacterial protein biosynthesis. EF-Tu also binds other ligands, including four structurally distinct families of antibiotics. The lack of sequence homology among the identified EF-Tu ligands demonstate promiscuous peptide binding by EF-Tu. (more...)

Sodium/potassium ATPases (Na+/K+-ATPases), a family of multi-subunit ion pumps, are the most important active transporters in animal cells. They are required for maintaining the electrochemical gradient responsible for resting membrane potentials in neuronal cells and for the function of other transport proteins in a variety of cell types. The important regulatory activities of Na+/K+-ATPases make them an attractive therapeutic target for the treatment of neurodegenerative, cardiac, and other diseases. To date, there are unmet medical needs for the treatment of these diseases, and it is desirable to discover and develop novel therapeutic agents aimed at treating ion pump related disorders. (more...)

BRCA2/RAD5 1 interaction is essential for DNA repair mechanisms and play significant role in tumor resistance to irradiation and chemotherapy treatments. Effective strategies to selectively interfere with BRCA2/RAD5 1 interaction in the context of treatment and chemoprevention of neoplastic diseases are described. (more...)

Angiogenesis drugs act to inhibit survival of newly formed blood vessels required for tumor growth and progression. These drugs have recently shown good activity in the clinic for breast, lung, colon and kidney cancer. However, these drugs can be toxic and even cause death. Only about half of patients benefit from this treatment approach. It would therefore be of value to be able to predict in advance if a patient has a better or worse probability of responding in order to avoid this treatment if the chances for success are low. (more...)

Prokineticin 2 (PK2) is a signaling molecule that is critical for transmitting circadian rhythms from the suprachiasmatic nucleus, the master pacemaker that drives circadian rhythms in animals. It is known that disrupted circadian rhythms are strictly associated with many mood disorders, such as bipolar disorders, depression, and seasonal affective disorder. The functional role of PK2 in anxiety and depression-like behaviors was investigated and provide a new therapeutic target and system for the discovery of treatments for mood disorders and stress. (more...)

Bone Morphogentic Proteins (BMP)s are involved in various developmental processes, but are most famous for the activity to stimulate bone formation. BMP signaling is one of the most extensively studied growth factor signaling pathways. This is partly because it is involved in so many different biological progresses (neurogeneisis, apoptosis, stem cell maintenance and differentiation, various organogenesis ,etc). Despite the importance, it has been rather difficult to determine the precise onset of BMP signaling during these processes and what they do in the tissues or cells where the signaling is active. A UC Irvine inventor has developed an easy reporter gene assay that can not only monitor the level of BMP signaling in vivo, but also allows isolation of the BMP responding cells. (more...)

Chlamydia trachomatis is the most common cause of sexually transmitted diseases worldwide; yet, there remains a need for a rapid and economical diagnostic test. Such an assay must be economical, readily standardized among laboratories, objective, quantitative, rapid, easy to use, and capable of detecting serovariant-specific responses. Work at UC Berkeley has lead to development of peptide antigens useful for producing such an immunoassay test. (more...)

A novel recombinant streptavidin-protein A chimeric protein which allows conjugation of antibody molecules with biological materials. The chimeric protein is efficiently expressed in Escherichia coli and is purified by simple procedures. The purified chimetic protein can bind one biotin molecule and one to two immunoglobulin molecules per subunit. (more...)

Precise control of gene interference in living cells is in critical demand for studying cellular signaling pathways, quantitative cell biology, systems biology, and molecular cell biology. Nanoscale intracellular transmitter and receiver systems are required for the remote manipulation of biological systems and the advancement cellular research. However, current intracellular transmitter and receiver systems do not enable precise control of the spatial and temporal resolution of optical activation, nor selective coupling of optical transmission frequency to different nanoscale transmitters. To address this problem, UC Berkeley researchers have developed a remote optical switch of gene interference with unprecedented spatial and temporal control in living cells. The Nanoparticle optical switches carry gene interfering oligonucleotides into cells and are activated to thermally release oligonucleotides using light by converting optical energy to thermal heat at the surface of the nanoparticle. Nanoparticles are tuned such that optical activation can be achieved at a specific wavelength with a longer penetration depth and where cellular photo-damage is minimized. This technology will be valuable in any endeavor in which precise special and temporal control of gene interference is beneficial. (more...)

Scientific progress is often associated with the invention of a new experimental apparatus. New tools can increase the ease and efficiency of routine experiments as well as provide the means to make new discoveries by making possible novel experiments. The development of Lab on Chip (LOC) devices is playing an important role in the progression of many different areas of research ranging from point of care diagnostics to the search for life on Mars. LOC devices hold promise to replace existing techniques with processes that are not only more automated and consistent but also require less time and valuable reagents. Researchers at the University of California have developed an integrated LOC for cell-based studies/analysis/research. The device has integrated biological fluidic circuits with the capability of culturing cells inside of a microfluidic ?chip?, the ability to lyse the cells on demand, and the ability to perform on chip analysis of the lysate, which contains both genetic and proteinaceous material. The device is essentially a completely integrated cell-based platform capable of performing practically all of the common cell-based studies currently employed in laboratories across the world. (more...)

Fluorescence detection is widely used as a bioassay technique in laboratories. If this technique could be functionally?integrated in a microsystem format, then its lower cost and improved portability would broaden the applications of fluorescence for both bioassay and chemical detection in the field as well as in the lab. To address this opportunity, researchers at the University of California at Berkeley have developed a microsystem and corresponding fabrication process that integrates photodetection, filtering and excitation. This Si-based microsystem performs the same functions as a bench-top fluorescence detection system by replacing the bench-top system's gas laser with a thin-film LED, and replacing the bench-top's grating, bulk glass and/or DBR filter with a single-layer thin-film filter. In comparison to bench-top systems, this fluorescence detection microsystem is less expensive and more compact, making it better-suited to applications in the field. The Berkeley microsystem combines all of its nondisposable components on a single substrate, and hygienically isolates its disposable microfluidic component, enabling the device to sequentially evaluate many samples. Moreover, multicolored LEDs with matching filters can be integrated in a single microsystem, enabling it to simultaneously perform multiple bioassays and chemical detections. (more...)