Glaucoma is the second-leading cause of blindness internationally, with a prevalence projected to reach nearly 60 million by 2020. Anti-glaucoma products took in approximately $5.8bn in revenue in 2009, with industry analysts projecting this figure to rise to $6.6bn by 2014. Precisely and accurately assessing the stage of the disease is crucial to determining which of the many classes of medications would be most effective for a given patient. Currently, staging is done largely by combining structural, functional, and clinical data of the patient. However, the addition of a genomic profile, a rich source of patient-specific data, would empower physicians to perform evidence-based risk assessment, thereby greatly improving glaucoma staging and patient outcomes.  (more...)

With the cost of sequencing the human genome dropping exponentially it will soon be economical for individuals to get the results of paternity tests, personal medicine analyses and even genetic matching or compatibility tests without the expense or trouble of elaborate laboratory procedures. Additionally, researchers from UCI’s Genomics and Computer Science departments have developed a safe and secure methodology and infrastructure to conduct these tests, safely and securely and all done via mobile devices. (more...)

Rapid, efficient, and low cost detection and identification of microorganisms including pathogenic bacteria, viruses, and fungi is a challenge facing plant and animal health. Current technologies such as Q-PCR rely on multiple assays and amplification methods to identify bacteria and viruses. Traditional optical detection methods also require fluorescent markers. These multiple independent steps and tests increase the processing time and cost for detection and identification. Researchers at the University of California, Davis, have developed a technique that uses nanotechnology to electrically detect and identify bacterial and viral RNA sequences without the necessity of using enzymatic amplification methods or fluorescent markers. In cases where microbe densities are particularly low, the technique provides additional sensitivity that allows for the target molecules to be detected in small quantities. Furthermore, the technique may be scaled into large multiplexed arrays for high-throughput and rapid screening. The implementation is further able to differentiate closely related variants of a given bacterial or viral species or strain. This technique addresses the need for a quick, efficient, and inexpensive bacterial and viral detection and identification system. (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...)

In seeded plants, successful fruit set and development are dependent on pollination, which can be highly sensitive to environmental conditions. Generating fruit without a requirement for physical pollination (parthenocarpy) allows extensive improvements in fruit crop productivity and yield. Presently, it is known that adding gibberellic acid (GA) or auxin promotes parthenocarpy as well as eventual fruit size. However, this mode of intervention requires physical treatment of fruit crops with these chemicals and the mechanisms through which these hormones promote fruit development remains unknown. Creation of fruit bearing plants capable of undergoing parthenocarpy without a requirement for exogenous treatment with plant hormones would allow fruit growers to produce seedless varieties without the limitations of pollination or spraying crops with plant hormones. Alternatively, some varieties of citrus fruits are naturally seedless and can develop without pollination. Pollination in this case can be an impediment to production of the desired fruit and in this case generating plants less susceptible to pollination would be advantageous. (more...)

Throughout development, cells and tissues differentiate and change as the organism ages. Both differentiation of tissues and ageing effects are at least partially caused by chemical modifications of the genome, such as DNA methylation. It was previously shown that significant DNA methylation differences are associated with specific age-related disorders, such as late-onset Alzheimer's disease. Measuring the methylation level at relevant sites in the genome could be used in routine medical screening to predict the risk of age-related diseases and increase our understanding of ageing in patient health. (more...)

MicroRNA (miRNA) is a gene expression regulator performing a critical role in epigenetics. Despite its importance in biology, the detection of miRNA at the single-molecule level has not been reported because it is difficult to detect due to its small molecular weight, fast dynamics, and low dehibridization temperature (melting point). Researchers at the University of California, Berkeley, have designed systems for both intracellular detection of single molecule miRNA of living single human cancer cells employing surface-enhanced upconversion using nanoparticles and locked nucleic acid (LNA)­ DNA/LNA-RNA hybridization. They have designed and synthesized gold nanoparticles for non-phototoxic wavelength tuning, and a huge surface enhancement, and finally inject into living single cells of drug-resistant human epithelial lung cancer cells. When they meet the target miRNAs, they will be disassembled which brings a dramatic change of signal measured by a home-built, multi-channel dark field imaging system.  (more...)

     The transfer of sequence information by nucleic acid replication is central to all of biology. This reaction has been incorporated into important biotechnology applications such as the polymerase chain reaction (PCR). All such replication reactions are catalyzed by complex enzymatic systems, so it would be useful if a non-enzymatic process could be established. However, the only previous method has been to use activated ribonucleotides and an RNA template (Inouye and Orgel, 1983).      In earlier studies, it has been demonstrated that anhydrous lipids form a lamellar matrix that can organize monomers within planar two-dimensional structures composed of lipid head groups. Rajamini et al. (2008) reported that one or more drying - rehydration cycles at moderately elevated temperature ranges provide sufficient chemical potential to drive the synthesis of phosphodiester bonds between nucleoside monophosphates. As a result, low yields of RNA-like polymers were observed, typically 50 nucleotides in length and ranging from 10 to 100 nucleotides. This reaction is described in US Patent 7,772,390. (more...)

Researchers at the University of California, Irvine have developed a novel method to continuously pattern nanofibers on 2D and 3D substrates. A unique polymer ink formulation provides the right balance of viscosity and elasticity necessary to enable controlled, seamless near-field electrospinning of nanofibers at very low voltages. (more...)

Researchers at the University of California San Francisco (UCSF) have identified a specific biomarker set for accurately detecting oral squamous cell carcinomas that are unlikely to metastasize and thus these patients could avoid major surgery. (more...)

Researchers at the University of California, Irvine have developed a Laplace pressure trap that can fuse droplets from different inlets and fuse droplets generated at different frequencies. The device traps and fuses droplets passively by balancing the driving hydrostatic pressure with increasing Laplace pressure imposed by the device’s design geometry. Above are video frames showing the Laplace pressure trap and of a single droplet fusion event at the Laplace trap. Frame A - Reference droplet can be seen waiting for its fusion partner. Excess partner droplets can be seen exiting towards the outlet. Frames B and C show the reference droplet and its fusion partner fuse and move toward the outlet. Frame D shows the next reference droplet approaching the trap. (more...)

In the areas of diagnostic and discovery applications surface bioaffinity sensing using either SPR sensors or LSPR sensors is currently being used for the detection of proteins, antibodies and nucleic acids. By combining the advantages of both SPR and LSPR, researchers at UCI have developed Nanoparticle-Enhanced Diffractions Grating biosensors (NEDG) that are able to detect unmodified DNA at a concentration of 10fM. (more...)

It is often advantageous to ascertain the biological purpose of a gene product by "knocking out" that gene and observing the phenotypic consequence(s). This is most often accomplished in whole animal experiments that are costly and take long periods of time related to the gestation period of the animal system. Here we divulge a system where this goal can be accomplished in a short period of time in laboratory cultured animal cells. (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...)

The availability of complete genome sequences from many organisms allows scientists to create genomic collections where each encoded protein can be analyzed individually in high throughput applications. The yeast one and two-hybrid systems are the most widely accepted genetic assays used to identify and characterize novel protein-DNA and protein-protein interactions. Yeast hybrid screening systems that are commercially available in high throughput format are optimized for use with random or pooled libraries and typically use lacZ as a reporter.However, these systems have several limitations when used with individually arrayed libraries. Multiple, time-consuming steps, the need for polyethylene glycol, and the disruption of the cells to assay the reporter activity all limit the adaptability to automated formats. Therefore, there is a need for an improved protocol that can be used for the screening of individually arrayed libraries and is also compatible with robotic applications. (more...)

Normal 0 0 1 95 543 UC Berkeley 4 1 666 11.1282 0 0 0 This invention relates to genes and methods to control eukaryotic mechanisms responsible for both the genesis and maintenance of heritable phenotypic variation. Paramutations represent specific types of epigenetic alterations that can be stably inherited without altering the DNA sequence. Several genes are known to be involved in regulating the paramutant state in maize plants. It is currently thought that these allelic interactions cause structural alterations to the chromatin. This invention relates to the use of the rmr1 gene for reducing or mitigating gene silencing in a transgenic maize plant and also to reduce or mitigate inbreeding depression (more...)

This approach abandons the classical "overlap-layout-consensus" approach in favor of a new Eulerian splicing graph approach that, for the first time, resolves the problem of repeats in fragment assembly. The splicing graph approach, in contrast to the Celera assembler, does not mask repeats but uses them instead as a powerful fragment assembly tool. UC San Diego is interested in commercializing its rights in the fragment assembly modules (see below). The research-quality software modules available are listed below. For general information about the EULER project, see Pevzner, et al, PNAS, 98, 2001 and http://nbcr.sdsc.edu/euler. EULER-Compare (SD2002-818) consists of a Java user interface and a C server backend. It compares different sets of contigs, aligns them, and outputs information about the similarities between contig sets of different DNA sequence assemblies. The web-based Java user interface visualizes the comparison data as a contig-comparison graph.EULER-Connect (SD2002-819) is software that may be used to find some useful reads from the discarded reads to improve the assembly result and expedite the sequence finishing. EULER-connect can also verify chimeric reads.EULER-EC (SD2002-820) corrects errors in sequencing reads. For each read, it determines other overlapping reads and builds a multiple alignment. Using his multiple alignment, EULER-EC detects and corrects errors in the reads.EULER-PCR (SD2002-821) designs finishing multiplex PCR experiments for resolution of repeats that could not be resolved by sequence assemblers due to their length. Based on the repeat graph generated by EULER assembler (Pevzner, et al, PNAS, 98, 2001), the software identifies repeats and estimates their multiplicities. Every individual repeat is resolved by placing forward and reverse PCR primers at such distance from the beginning and the end of a repeat, so that all possible PCR products have different length. Thus, deducing the correct pairing between sequences outside of a repeat becomes a matter of measuring PCR product length by gel electrophoresis. EULER-PCR optimizes the number of reactions by pooling repeats that can be resolved simultaneously in a single multiplex PCR experiment.EULER-TR (SD2002-822) is software that improves the assembly result of EULER. Based on the repeat graph generated by the EULER assembler (Pevzner, et al. PNAS, 98, 2001), EULER-TR can resolve tangle edges (repeat edges) by inspecting the differences between reads fitted onto the tangled edge. (more...)

UC San Diego researchers have developed a method for assembling live biological cells using electrokinetic addressing for functional genomics studies. The method employs rapid, single-cell arraying with real-time fluorescence monitoring in a non-well format and without using harsh cell sorting procedures. This low cost technology can be fabricated on various types of substrates such as silicon, polymer, or glass, and can be integrated with microfuidics and optical controls. The technology can be used for rapid, simultaneous electronic arraying of libraries of live, single cells for functional clonal assays, such as mitosis, migration, or morphology. Individual cells can be selected and captured for further testing by non-destructive methods. (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...)

Comparative genomics has, historically been limited to the study of changes that occurred over millions of years. Evolution, however, is a dynamic and recurring reality, which can be responsible for such vexing realities as the emergence of new pathogens and the acquisition of drug-resistance. From a more proactive stance, the ability to design, manipulate and evaluate the consequences of specific stressors could dramatically improve the ability to design beneficial mutations for industrial processes that use bacteria for anything from food and chemical production to the clean-up of oil spills. (more...)

The equalizer is a custom application that uses rank-order similarity in gene expression intensity to construct non-linear equalization vectors that are then used to linerize the data matrix to a consistent slope of 1. In addition, the equalizer rationally eliminates "negative" values of expression seen in Affymetrix data. Use of the equalizer greatly facilitates downstream data analysis. This software has been used for Affymetrix chip analysis but has applications to other microarray systems as well. See also: Robert O. Stuart, Kevin T. Bush, and Sanjay K. Nigam. 2001. Changes in Global Gene Expression Patterns During Development and Maturation of the Rat Kidney. PNAS. 98:5649-54). (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...)

Researchers at the University of California, Irvine, have developed a method for the computational optimization of DNA sequences that encode their own correct self-assembly. (more...)

Knowledge of DNA gene sequences and other parts of the genome of organisms has become indispensable when studying biological processes, diagnostic research, and forensic research. Following the development of dye-based sequencing methods with automated analysis, DNA sequencing has become easier and faster by a magnitude of orders. The prominent rapid high-throughput DNA sequencing methods include Genome Sequencer using pyrosequencing by Roche/454, SOliD technology by Applied Biosystems, and the sequencing by synthesis technology employed by Ilumina/Solexa. Methods for real-time direct sequencing from single DNA molecules are also emerging. These include the SMART technology being developed by Pacific Biosciences and the FRET-based sequencing method by VisiGen Biotechnologies (a part of Life Technologies Incorporated). The use of fluorescent-labeled nucleotides in almost all current single molecule-sequencing methods with optical imaging presents numerous problems, including background fluorescence and the requirement for a polymerase capable of incorporating labeled nucleotides. (more...)

Transcriptional regulation involves a large number of protein complexes specifically assembled at a given promoter to activate or suppress RNA synthesis. In a specific tissue or cell type, a promoter can be turned on by a sequence of specific recognition events. Transcription factors bind cis-acting regulatory sequences and allow these DNA binding proteins to recruit co-activator complexes that further recruit the core transcription machinery. Similarly, a gene can be turned off by the recruitment of transcription co-repressor complexes through sequence-specific DNA binding proteins during repression-involved chromatin remodeling factors that modify histones. A long-term molecular memory may be established by epigenetic modification of a specific chromatin region(s) via DNA methylation. (more...)

Gene therapy via viral vector technology has been associated with dangerous complications and risks. UCSF investigators have discovered a process that permits defective genetic sequences to be replaced with greater efficiency and potentially fewer side effects. The process, small fragment homologous replacement (SFHR), allows genes to be repaired in a site specific fashion and does not require the insertion of new genetic material into the genome. Thus, the SFHR approach should be applicable to a wide variety of gene therapy applications requiring the repair of specific mutations in DNA sequence. Furthermore, assay methods have been developed to monitor and quantify gene targeting frequency and to differentiate between cells carrying modified and unmodified DNA. (more...)

Currently, many induced gene expression systems (pTet, pBAD, pTrc, etc) are used commercially for variety of applications that require some control of gene expression. These systems are chosen over other expression systems for their ability to give the user control over the timing and the level of expression after induction. All of the existing systems, though, have the following limitation: the stronger the expression after induction, the leakier (less tight) the control during un-induced state. There have been many attempts to overcome this limitation to give both very tight un-induced expression and strong induced expression, many of them commercialized. This invention solves the problem completely. The invention is a gene expression system using two promoters, one located within an invertible segment recognized by the Fim invertases, and another that is located elsewhere. By utilizing these two promoters and the Fim intervase mechanism, this gene expression system allows a complete shutoff of the expressed gene and achieves a high level of expression by using a strong promoter. This invention will be invaluable to those who desire controlled all-or-none expression. It has many applications in research settings (easy gene complimentation studies, functional studies, toxicity studies), as well as industrial (protein/drug production, metabolic engineering, bio-sensor) applications. (more...)

The invention provides methods and compositions for normalizing and amplifying RNA populations. The methods generally comprise the steps OF : (a) copying MRNA to form first ss-cDNA; (b) converting the first ss-cDNA to first ds-cDNA; (C) linearly amplifying the first ds-cDNA to form first ARNA ; (d) tagging the 3'end of the first ARNA with a known sequence to form 3'-tagged first ARNA ; (e) copying the 3'-tagged first ARNA to form second ss-cDNA; and (F) normalizing the MRNA AND/OR the first aRNA. Note that the normalizing step (f), may be implemented prior to step (a), prior to step (d), or prior to both. The invention also provides kits for practicing the subject methods and protocols. These generally comprise one or more reagents used in the methods and instructions describing protocols embodying the subject methods. In a particular embodiment, the kits include premeasured portions of oligo dT T7 biotinylated primer, T7 RNA polymerase, annealed biotinylated primers (used to make Driver pool #1, see Fig. 3), streptavidin beads, polyadenyl transferase, reverse transcriptase, RNase H, DNA pol I, buffers and nucleotides (more...)

The saturated fat content of non-human animals and their by-products, such as milk, can be lowered by a new method that has been developed by researchers at the University of California, Davis. This new method introduces a transgene into non-human animals, resulting in the conversion of saturated fatty acids into unsaturated fatty acids by anywhere from 5% to 50%. In addition, transgenic animals exhibit increased levels of conjugated linoloeic acids (CLAs). Food products containing a reduced level of saturated fatty acids may: Contribute to the lowering of serum cholesterol; and Help prevent some forms of cardiovascular disease Increased levels of CLAs may: Stimulate the immune system; Reduce inflammation; and Reduce the risks of cancer Over one half of the saturated fat in the human diet comes from meat and dairy consumption. Researchers at the University of California, Davis offer a means to lower those levels through transgenic non-human animals and their derivative food products. (more...)

Method for Cryopreservation of Human Tissue and Cells (more...)

University of California researchers have developed a family of antibody fusion proteins with a potential for various therapeutic applications. These inventions represent both novel technologies and products with novel applications. These UC fusion proteins combine an antibody with various cytokines. While these cytokines have been used previously as direct antitumor agents, these antibody-cytokine fusion proteins can be employed in a novel therapeutic strategy. In this role, the fusion proteins enhance the immune response to a particular tumor marker. Studies in an animal model have demonstrated that these fusion proteins lead to significant anti-proliferative activity against a murine tumor expressing a breast cancer antigen; the results suggest that both humoral and cell-mediate responses contribute to the observed anti-tumoral activity. It is expected that these fusion proteins will lend themselves to both prophylactic and therapeutic vaccinations; they may be used separately or in combination to achieve an additive or synergistic anti-proliferative effect. (more...)

Beta-1 integrin is a critical member of the large family of integrin proteins necessary for cell-extracellular matrix adhesion and bi-directional signaling across the cell membrane. Conventional deletion of beta-1 integrin from the mouse genome results in embryonic death soon after implantation of the blastocyst. Thus, analysis of beta-1 integrin function beyond post-implantation embryogenesis is not possible in a classic deletion model. (more...)

Fusobatcerium nucleatum is an anaerobic Gram-negative microorganism that is commonly found in the mouth. For example, Fusobacterium nucleatum is the most frequently isolated pathogen from periodontal disease sites and is believed to be an initiator of periodontal diseases. Moreover, this bacterium is commonly found in abscesses and other infections in the abdomen, blood, chest, lung, sinuses, and female genital tract. Several F. nucleatum proteins that are believed to be associated with F. nucleatum pathogenesis have been identified, but their evaluation has been hampered by a lack of systems for genetic manipulation of this microbe. Therefore, there is a need for reliable gene transfer and expression systems for F. nucleatum. (more...)

Hospital-borne bacterial infections present a major challenge in patient care due to the rising number of strains resistant to multiple antibiotics in recent years. Gram-positive bacteria, such as Staphylococci, Streptococci and Pneumococci, are the most common cause of these often fatal infections and are particularly more difficult to treat in immunocompromised patients. Therefore, there is an urgent need for identifying novel targets sites in these pathogens for the development of antibiotics. A unique characteristic of these pathogens, including Staphylococci, is the presence of surface proteins anchored to the cell wall, many of which are essential for pathogenesis. The anchoring process involves secretion of the protein through the cellular membrane, followed by its cleavage at a C-terminal sorting signal and anchoring of the cleaved protein to the cell wall peptidoglycan. This two-step transpeptidation reaction is catalyzed by the enzyme sortase. Since these final processes catalyzed by sortase are crucial in the presentation of biologically active surface proteins and the enzyme is conserved in gram positive bacteria but absent in humans, sortase is an attractive novel target for the development of effective and safe antibiotics directed towards many gram positive pathogenic bacteria. (more...)