Prostate cancer is one of the most common cancers to affect men and is the second leading cause of death amongst cancer victims. For decades, primary cultures of malignant prostatic cells have provided a convenient model system to study prostate cancer and tumorigenesis. However, these cell lines do not adequately recapitulate the microenvironment that supports tumor development in vivo. Many of the available prostate cancer cell lines (PC3, DU145, and LNCaP) are derived from metastases and are not inclusive of all prostate cancer phenotypes. Thus, there is a need for cell culture model systems that more effectively recapitulate the genetic and environmental composition of tumors. Seminal work carried out by Dr. Garraway's research group at UCLA has provided crucial insight into the development of a novel cell line derived from human fetal prostate tissue for the study of prostate tumors and tumorigenesis.       (more...)

The fate of somatic cells can be reprogrammed to the pluripotent state by the combination of a few transcription factors, resulting in induced pluripotent stem cells (iPSCs). One of the most important aspects of somatic cell reprogramming is the possibility of using iPSCs to model human diseases in order to recapitulate their development, pathology and drug responsiveness. Although the field of iPSCs has advanced significantly in recent years, much still remains unclear in the reprogramming process itself, the differentiation potential of cells and their future use in clinical therapy. Recent evidence suggests that iPSCs can exist in alternative states, which can influence the potential of cells to make different cell types. Thus, it has become critically important to develop an efficient method to identify and isolate these alternative states, which will provide tremendous insights in the reprogramming process and differentiation potential of the cells. (more...)

Sequencing based approaches of gene expression analysis generate millions of sequence tags, thus providing the dynamic range required to investigate genes of low abundance. Currently available digital gene expression analysis systems offer the potential for high-throughput transcriptomic measurements, however truly quantitative data are routinely not obtained. The most widely used RNA-seq protocol relies upon fragmentation of mRNA generating a library of uniformly distributed fragments of mRNA. This protocol requires large amounts of starting material (100ng of mRNA) limiting its application in many fields such as in developmental biology, where it is impractical to get such large amounts. Furthermore, this protocol maintains the relative order of transcript expression resulting in poor representation of low abundance transcripts at current sequencing depths. Multireads and biases introduced by transcript length and random hexamer primer hybridization further restrict reliable quantitation of low abundance transcripts for large mammalian transcriptomes. While random priming strategies amplify starting material (mRNA or cDNA) by exploiting hybridization and extension potential of hexamer/heptamer primers, they often result in low yield of good quality reads arising out of mis-hybridization of primers and primer dimerization. In a recent experiment, the inventors used a widely available sequencer to generate sequence tags via random priming strategy. Only 18% of the reads mapped uniquely to the transcriptome and low abundant transcripts were significantly under-represented because of poor dynamic range. Since many genes (signal transduction, transcription factors) are only expressed at relatively low levels, currently available strategies fall short in statistically quantifying these genes. (more...)

Epilepsy is a debilitating disease of the central nervous system, which can cause severe seizures. Affecting around 1% of the population, this disease requires prolonged, and often life-long, drug treatments. Keppra, or Levetiracetam, is an important anti-convulsant drug used to treat seizures in patients with epilepsy. Keppra's patent rights in the US expired in 2009 opening up a large opportunity for generic production of the drug. Drug synthesis can be costly, however, due to laborious and expensive syntheses of starting materials. The ability to renewably produce the chiral-specific starting materials from simple molecules in bacteria could greatly reduce production costs. (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...)

For producing RNA viruses, applications such as drug screening or basic research require immortalized tissue cultures that enable efficient production of fully infectious viruses of a genotype of clinical interest and are easy to use. In the case of hepatitis C virus (HCV), however, existing tissue culture systems yield incompletely replicated viruses (which do not infect cells in vitro), work only transiently, or are not robust enough and otherwise yield viruses with less prevalent HCV genotypes such as genotype 2. Thus, there is a need for a continuous or semi-continuous HCV production system that overcomes these limitations with the generation of a fully infectious HCV of genotype 1. (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...)

Mycobacterium tuberculosis is a disease that infects millions of people each year; in addition, the related bacterium, Mycobacterium bovis, infects domesticated animals, resulting in substantial economic losses. Currently, humans are administered Bacille Calmette-Guerin (BCG) vaccine to prevent tuberculosis. However, BCG vaccines have variable efficacy - on average about 50%. Recombinant BCG vaccines have been developed that express a key antigen of M. tuberculosis and are more potent than BCG. However, these recombinant BCG vaccines contain antibiotic resistance markers; regulatory authorities want vaccines to be free of such antibiotic resistance markers to diminish their dissemination to other pathogens in the environment. Unmarked vaccine vectors (i.e. those lacking an antibiotic resistance marker) have been produced by various means, but these methods have resulted in low levels of expression of recombinant proteins. Preferably, unmarked strains would not only express large amounts of the recombinant proteins, but express them from genes integrated into the chromosome because such constructs tend to be more stable than when the genes are expressed from a plasmid. Due to safety, potency, regulatory, and stability issues, there is a need for a better vaccine that can prevent and treat tuberculosis in humans and animals. (more...)

The immunoglobulin secretory IgA (sIgA) is found in mucosal surfaces is often the first line of defense against infectious agents. Normally, sIgA is the product of two different cell types with heavy, light, and J chains produced by plasma cells, whereas the secretory component (SC) is added by cellular enzymes during transit of the dimeric IgA through the epithelial cell layer.The SC component of sIgA provides for stability at the mucosal surfaces. Currently available monoclonal IgA which lacks SC, while protective, is rapidly degraded. Attempts have been made to create sIgA in vitro by either co-culturing IgA producing cells with polarized epithelial cells or by adding SC exogenously to purified IgA, however, both methods provide very low yields of sIgA. (more...)

UC San Diego inventors have developed strategies and methods for exertion of combinatorial control on gene expression by integrating multiple transcription signals directly in the regulatory region without the need for additional genes and their expressions. (See White Paper PDF below for additional details.) (more...)

UC San Diego researchers have developed a perfusion bioreactor system with a directional oxygen gradient and a method to determine the effect of oxygen gradients on cellular functions. Cellular components exhibit different functional characteristics based on the local oxygen availability. Graded oxygen environments have functional consequences in both normal cellular and disease processes, such as development, regeneration, wound healing, iscehmia-reperfusion injury, toxicity, and cancer. In the perfusion bioreactor system, the formation of oxygen gradients is achieved by optimizing parameters such as cell seeding density, flow rate, inlet oxygen concentration, and reactor dimensions. Use of this in vitro platform system allows for molecular analysis of cellular responses including changes in gene expression, protein synthesis, and cellular damage in response to oxygen gradients. The invention has applications in the following: For liver: Platform for evaluating novel drug candidates, including but not limited to drug metabolism, toxicity, and adverse xenobiotic interactions. Model system for the study ischemia on liver tissue and its implications, such as cellular hypoxic response and organ preservation. For other tissues: Platform for evaluating potential cancer drugs in variable oxygen environments.Platform for engineering artificial organs. (more...)

UCSF scientists have developed a method to engineer a synthetic, feedback-regulated MAPK signaling pathway using scaffold-mediated feedback loops. This method can be used to systematically re-program MAPK signaling responses, allowing one to engineer and modify the MAPK signaling pathway to optimally control dynamic and complex behaviors in living cells. Many potential applications exist, including engineering of metabolic processes for optimal biofuel production. (more...)

Ectopic activation of the Wnt signaling pathway leads to increased cellular growth and division in experimental organisms and mutations in the Wnt pathway. Wnt pathway genes are tightly linked to the genesis of certain cancers in humans, such as colon cancer. (more...)

Cancer is genetic disease which is originated due to multiple genetic alterations, including mutation or loss of tumor suppressor genes and amplification of oncogenes, and consequently alteration of gene expression profile which alters the phenotype of normal cells. It is composed with genetically heterogeneous cell subgroups and normal cells. Information on the degree of loss of tumor suppressor genes or amplification of oncogene genes cancer mass can play important role to prognosis of patient response to therapy, as well as survival. (more...)

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A novel transformation method for transforming many commercial genotypes of cereals has been developed. The method incolves using meristematic tissues which include vegetative shoot meristems and young leaf bases as initial explants and the induction of a direct organogenesis pathway for in vitro proliferation and plant regeneration. Use of this pathway results in less impact and destabilizaton of the methylation state of the genomic DNa during invitro growth and reduces the impact of somaclonal variation and instability of transgene expression. References; S. Zhang, et al. 1999. Genetic transformation of commercial cultivars of oat (Avena sativa L.) and barley (Hordeum vulgare L.) using in vitro shoot meristem cultures derived from germinated seedlings. Plant Cell Reports. 18:959-66. S. Zhang, et al., 1998. Expression of CDC2Zm an dknotted 1 during in=vitro axillary shoot meristem proliferation and adventitious shoot meristem formation in maize (Zea mays L.) and barley (Hordeum vulgare L.). Planta. 204:542-9 (more...)

This invention makes available plasmids designed to express derivatives of Saccharomyces cerevisiae Ste5 protein tagged with an N-terminal in-frame (His)6 tract and a c-Myc epitope recognized by the monoclonal antibody, 9E10, and /or fused in-frame at either its N- or C-terminus to the Aequoria victoria Green Fluorescent Protein (GFP), or mutant derivatives of Ste5 in these contexts. References: Hasson et al. 1994. Mol. Cell Biol. 14:1054-65 Inouye et al. 1997. Science 278:103-6 Inouye et al. 1997. Genetics 147:479-92 Sette et al. 2000. Mol Biol. Cell 11:4033-49 Bardwell et al. 2001. J. Biol. Chem. 276:10374-86 Kunzler et al. 2001. Genetics 157:1089-105 (more...)

To assay transcription from promoters under the control of Filamentous Response Elements (FREs) which comprise binding sites for the transcription factors Ste7 and Tec1, investigators at UCB constructed a plasmid (YEpU-FTyZ) in which expression of the E. coli lacZ gene is driven by the FRE of the transposon Ty1. Reference; Cook et al. 1997 Nature 390:85-8. (more...)

Purified native phycobiliproteins and their subunits fluoresce strongly and, since 1982, have been widely used as labels for cell sorting and analysis, and in a wide range of other fluorescence based assays. This invention embodies the use of phycobiliproteins and phycobiliprotein fusions as in vivo fluorescent protein probes. (more...)

Plasmid vectors (pV-alpha-11-GH and pLCRc) have been developed for the expression of transgenic proteins in immature and mature T cells. Research using these vectors has been published: Diaz et al. Immunity 1:207 (1994) Ortiz et al. EMBO J. 16:5037 (1997) Kabra et al. J. Immunol. 162:2766 (1999) (more...)