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Surface Segmentation from Luminance and Color Differences (S03008.pdf)

Inventors
Donald MacLeod, Geoffrey Boynton and Ione Fine

Applications
Automatic Segmentation of Targets in Satellite Photos, Segmenting Different Tissue Types in Medical Imaging, Use of Color to Segment and Identify "Meaningful Regions" within a Scene.
A Bayesian model used to automatically segment scenes based on the luminance and color statistics of a particular image set.

The invention describes a plausible segmentation model based on luminance and color differences within natural scenes. Color and luminance differences show a striking lack of independence. When two points fall on the same surface, differences in luminance and color between the two points tend to be small. Conversely, when two points fall on different surfaces, the distribution of luminance and color differences tend to be larger. These statistics for color and luminance differences are not easily captured by correlation statistics or independent component analysis. However the Bayesian model of the invention captures these dependencies well. The model (with no free parameters) based on color and luminance pairwise differences, segments images similarly to human observers, both with an image set based on natural scenes and with a very different novel image set containing both natural and man-made environments. The model is based on the statistics governing differences in luminance and color between neighboring pixels in a given scene (such as a picture of a natural scene, a mammogram image or a satellite photo). For pixels of a given separation, differences in luminance and color are not independent, a change in luminance predicts a change in color and vice versa. Differences in luminance and color between nearby pixels can be modeled by assuming that the probability of belonging to the same surface decreases exponentially with the distance between the two pixels. The Bayesian model based on these statistics can be used to automatically segment scenes based on the luminance and color statistics of the particular image set..

References
J. Opt. Soc. Am. A., 20, No. 7, July 2003

Patent Status:
U.S. Patent Application published as 2005-0058351

License Terms:
Non-exclusive and Exclusive by Field of Use Licenses Negotiable

Reference_Number: S03008
Contact: Dave Odelson, Ph.D. o Senior Licensing Executive o 858.453.4100 x1223 o dodelson@salk.edu

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Assay for Integration Inhibitors Using Pre-Integration Complexes (S97022B.pdf)

Inventors
Frederic Bushman, Tal Kafri, Mark Hansen

Applications
Infection, HIV, Drug Discovery
A screen for viral integrase inhibitors

The invention describes an assay for viral integration inhibitors using pre-integration complexes (PICs). A cell line expressing high titers of HIV-based vectors has been developed. The vector particles produced have been used to generate PICs containing HIV integrase and other HIV proteins. This technique provides a source of PICs that are much safer to handle than live virus derived from Molt IIIB. Integrase is one of three enzymes encoded by HIV. Inhibitors of reverse transcriptase and protease have been shown to be effective in treatment of HIV infection. Similarly integrase is a promising, non-toxic target for drug therapy since there are no similar proteins known to be important for normal cell function. Despite extensive efforts, no clinically useful integrase inhibitors have been developed. In this invention, vector-based PICs were used to devise a microtiter plate-based assay for integration directed by PICs. The response to inhibitors by PICs is more authentic than purified recombinant integrase making them attractive for use in screens for inhibitors. Purified integrase protein can be inhibited by diverse compounds, complicating the identification of promising leads. However, assays with PICs are more resistant to inhibition and display a response that more closely matches the response of virus in vivo. Microtiter assay results can be obtained by PCR and gel analysis or use of the TaqMan gene quantification method..

References
Nat Biotechnol 17(6):578-82 (June 1999)

Patent Status:

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Method of Rapidly Identifying Inhibitors of Topoisomerase DNA Religation (S00014.pdf)

Inventors
Frederic Bushman and Young Hwang

Applications
Infection, Oncology, Antibacterials, Antifungal, Antiviral, Drug Discovery and Development
High throughput screen for compounds that modulate topoisomerase activity

Topoisomerases play a central role in nucleic acid metabolism and are important in a variety of biological processes related to cell division, DNA replication, chromosome structure and gene expression. Compounds that act as effective cellular inhibitors of topoisomerases are expected to act as cytotoxic agents through the disruption of the normal cell division process. Such compounds can be effective and selective antibacterial, antifungal and antiviral agents. And because cell division is an important characteristic of cancers and other proliferative diseases, agents that inhibit topoisomerases are also useful as antineoplastic agents. The invention provides methods for identifying topoisomerase activity modulators in both solid and liquid phase formats. High throughput screening methods, compositions, kits and integrated systems for performing the assays are provided. The invention represents an improvement over existing technology in several ways. Through the use of different nucleic acid substrates, the assays can be adapted to screen for inhibitors of numerous different classes of topoisomerase enzymes and assay multiple different topoisomerase enzymes in a single reaction, thus enhancing throughput. The assays can be run in a parallel fashion such that multiple different topoisomerase enzymes and/or modulators are assayed simultaneously. The assays can be performed in the liquid or solid phase and each of the formats is readily amenable for automation and high throughput screening. Further, the assays are are extremely sensitive relative to previous assay formats and only minimal quantities of reagents are required..

References
Nucleic Acids Res 28(24):4884-92 (December 2000)

Patent Status:

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Method for Site-specific Integration of Nucleic Acids and Related Products (S98028.pdf)

Inventors
Frederic Bushman

Applications
Gene Therapy
Useful for facilitating the identification (i.e., location and isolation) of desired genes.

The invention relates to chimeric proteins useful for targeting and integrating donor nucleic acids at specific locations on target nucleic acids. The invention proteins are also useful for facilitating the identification (i.e., location and isolation) of desired genes. Also provided are nucleic acid constructs encoding invention chimeric proteins, recombinant retroviruses comprising such nucleic acid constructs and methods for site specific control of donor nucleic acid integration into target nucleic acid. Recombinant retroviruses of the invention are useful as attenuated viral vaccines or as vectors for gene therapy methods..

References
Proc. Natl. Acad. Sci. USA 91: 9233-9237
Journal of Virology 71: 458-464

Patent Status:

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Compositions and Methods for Producing Recombinant Membrane-Associated Proteins (S04009B.pdf)

Inventors
Tarmo Roosild, Jason Greenwald, Senyon Choe, Roland Riek, Mark Vega

Applications
Research Tool, Drug Discovery and Development, Membrane Protein Production
A 'partner' molecule called Mistic makes widespread production of large quantities of membrane proteins possible for the first time, allowing scientists to determine their atomic structure and design drugs that interfere with disease processes involving crucial proteins such as ion channels and GPCRs.

Membrane proteins are crucially important in medical research and drug discovery, but until now human membrane proteins have been virtually impossible to produce in large enough amounts to study. Out of approximately 10,000 human genes dedicated to integral membrane proteins, such as receptors and ion channels, only a small handful of proteins have been made available from natural sources in the quality and quantity needed to study them successfully in isolation. The discovery of Mistic, which facilitates the integration of cloned membrane proteins into the E. coli cell membrane, gives medical researchers a new tool that could revolutionize membrane biology. Mistic is an unusual Bacillus subtilis integral membrane protein, with a structure that consists of a bundle of four helices that fold autonomously into place within the cell membrane, bypassing the cellular translocon machinery. This self-integrating, or auto-inserting, ability of Mistic facilitates the rest of the molecule, the "cargo" protein, to undergo the folding and integration process. Mistic allows scientists for the first time to produce large quantities of crucial membrane proteins for structural study or therapeutic research, such as ion channels and the vast family of receptors called G-protein coupled receptors (GPCRs). More than half the blockbuster drugs in the pharmaceutical industry target these two classes of proteins. Salk researchers have successfully created dozens of such important human membrane proteins in the cell membrane of E. coli using Mistic. _ In addition, experiments suggest that Mistic can be used for high-level production of other membrane proteins in their native conformations, including many eukaryotic proteins that have previously been intractable to recombinant bacterial expression.

References
Science 307:1317-8

Patent Status:
U.S. Patent Application Published as US-2006-0211087 A1

License Terms:
Exclusive or Non-Exclusive Licenses available by Field of Use

Reference_Number: S04009B
Contact: Dave Odelson, Ph.D. o Senior Licensing Executive o 858.453.4100 x1223 o dodelson@salk.edu

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DAS5, a P450 Protein Involved in the Brassinosteroid Biosynthesis Pathway of Plants (S01015.pdf)

Inventors
Joanne Chory and Zhiyong Wang

Applications
Plant Biology, Agriculture, Horticulture
Genetic modifications of plants to increase the expression of DAS5 results in a variety of useful phenotypes such as increased fresh weight and increased overall plant size.

The invention provides identification of nucleic acid molecules encoding proteins involved in the synthesis of brassinosteroids in plants, methods of increasing endogenous levels of brassinosteroids, insect protection and methods of increasing biomass by modulating levels of brassinosteroid pathway components. These molecules appear to modulate brassinosteroid response pathways at the level of their biosynthetic enzymes, therefore altering brassinosteriod-related responses and signaling pathways. An altered gene, DAS5 is disclosed which is involved in the synthesis of brassinolides. The DAS5 gene encodes a member of the P450 family of proteins. The das5-D mutant was generated using an activation tagging approach. The activation tagging procedure often produces dominant mutations, whereby the gene product of the altered gene is produced at high levels. By "das5-D" is meant the DAS5 gene additionally containing upstream activation sequences which cause a high level of DAS5 transcript and, consequently, high levels of DAS5 protein production in cells containing this construct. Transgenic plants carrying this altered gene are expected to have high levels of DAS5 gene expression and high levels of active DAS5 protein compared to widltype. Both overexpression of the DAS5 gene and expression of the dominant activation-tagged das5-D mutation in this invention resulted in increased brassinosteroid levels throughout the plant and produce the das5-D mutant phenotype. For example, when das5-D was expressed in wild type Arabidopsis plants, the fresh weight increased by 26%. It is expected that the increase in brassinosteroid levels and plant biomass produced in response to an increase in DAS5 gene expression may increase disease resistance, thermotolerance and general stress protection..

References
No publications to date

Patent Status:

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Genes Involved in Brassinosteroid Hormone Action in Plants (S01014.pdf)

Inventors
Joanne Chory and Zhiyong Wang

Applications
Plant Biology, Agriculture, Horticulture
Methods of altering plant phenotypes including plant size by altering the genes encoding the Brassinozole Resistant 1 (BZR1) Polypeptide.

The invention includes the nucleic acid molecules encoding the Brassinazole Resistant 1 (BZR1) polypeptide and variants thereof, including the protein product of the dominant mutant bzr1-D, all of which are involved in the regulation of cell expansion in plants through effects on brassinosteroid response pathways. The BZ1 protein and bzr1-D protein appear to act downstream of the brassinosteroid receptor, so their action involves the brassinosteroid response pathway rather than the brassinosteroid biosynthetic pathway. The invention includes methods of modulating brassinosteroid-related responses, methods of identifying compounds involved in signaling pathways and methods of altering plant phenotypes by altering the genes encoding the BZR1 polypeptides. Plants with altered responses to brassinosteroids may be of particular economic interest to agriculture. For example, modification of brassinosteroid response pathways may produce larger plants with higher crop yields. Also, these response pathways may be modified in specific tissues or at specific developmental stages, to increase desirable qualities in agricultural products. It may be possible to produce crops with increased fruit size by linking fruit-specific promoters to genes with modified brassinosteroid responses..

References
Dev Cell 2(4):505-13 (April 2002)

Patent Status:

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Expression of Flavin-Containing Monooxygenases in Plants (S00015.pdf)

Inventors
Yunde Zhao, Joanne Chory, Christian Fankhauser, Detlef Weigel and John Cashman

Applications
Plant Biology, Agriculture, Horticulture
A gene to increase plant growth and yield by increasing endogenous auxin levels.

The invention describes the YUCCA gene, a flavin-containing monooxygenase (FMO) gene from Arabidopsis. Enhanced expression of the YUCCA gene or its homologues leads to a phenotype characterized by increased hypocotyl elongation, increased root thickness, increased root hair development, increased lateral root initiation, increased apical dominance, epinastic leaf growth, increased flowering node formation, increased fruit yield, increased endogenous auxin levels, parthenocarpic fruit production, altered gene expression, altered pathogen resistance, altered pest resistance, and altered herbicide resistance. The invention provides methods to alter these plant traits by transforming a plant with an expression vector encoding the YUCCA FMO or its homologues..

References
Science 291(5502):306-9 (January 2001)

Patent Status:

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Modulation of Flowering Time by the PFT1 Locus (S02023.pdf)

Inventors
Joanne Chory and Pablo Diego Cerdan

Applications
Plant Biology, Agriculture, Horticulture
A gene useful in protecting crops from shade-avoidance resulting in increased yields

When plants are grown at high densities in agricultural fields, the presence of neighboring plants decreases the red to far-red light ratios triggering shade-avoidance responses. These include stem elongation , restricted leaf development and early flowering and decreased seed set. The result is decreased plant biomass and decreased seed yield. We have isolated and characterized mutants of the gene PFT1. Plants expressing these mutants lack the protein called "phytochrome and flowering time 1"(pft1). This protein is part of a distinct shade-avoidance pathway. Crossbreeding experiments with mutants in the light sensing molecule phytochrome B revealed that the pft1 protein acted "downstream" of phytochrome B to regulate the expression of the gene called "flowering locus T" FT which governs flowering time. The pft1 protein is localized in the plant cell nucleus and is a presumed gene activator. Manipulating pft1 levels can be used to avoid productivity losses associated with shade avoidance as well as a tool to control flowering time..

References
Nature 423, 881-885, June 19, 2003

Patent Status:
U.S. Patent Application Published as WO04/113499

License Terms:
Non-exclusive and Exclusive by Field of Use Licenses Negotiable

Reference_Number: S02023
Contact: Mike White, Ph.D., CLP o Director, OTM o 858.453.4100 x1703 o mwhite@salk.edu

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Novel Plant Kinases and Methods of Modulation of Their Activity in Plants (PID1) (S99004.pdf)

Inventors
Susan Christensen, Joanne Chory, and Detlef Weigel

Applications
Plant Biology, Agriculture, Horticulture
A plant kinase is identified, the PINOID (PID) gene, which encodes an auxin signaling and /or response protein.

The PINOID (PID) gene encodes a member of a newly identified plant-specific serine-theronine protein kinase family (DFD kinase). PID is predominately expressed in lateral primordia, consistent with PID affecting downstream events in auxin signaling. PID overexpression results in shoot and root phenotypes similar to those of auxin-insensitive mutants. The invention provides a method of producing a genetically modified plant characterized as having early or increased loss of apical dominance, such as increased branching and/or lateral root growth as compared to a wild type plant. The method includes transferring at least one copy of a DFD kinase encoding polypeptide, including members of the PINOID gene family, operably linked to a promoter to a plant cell to obtain a transformed plant cell and producing a plant from the transformed plant cell. In addition, transcription factors or chemical agents may be used to increase expression of DFD kinase in a plant in order to provide plants having increased branching for more homogeneous fruit maturation, dwarf varieties, grass with little need of mowing and the like..

References
Cell 100(4):469-478 (February 2000)

Patent Status:

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Receptor Kinase, BIN1 (S97020.pdf)

Inventors
Joanne Chory and Jianming Li

Applications
Plant Biology, Agriculture, Horticulture
Genetic modification of plants to increase BIN1 expression results in a variety of useful phenotypes such as increased yield, enhanced disease resistance, and increased biomass

The brassinosteroids are a unique class of biologically active natural products that possess plant steroidal hormone activity. The brassionosteroids can be used as plant protectants from both pesticide and environmental adversity and appear to be useful in insect control. Further, brassionsteroids can regulate some stage of the reproductive cycle of plants, thereby providing means to increase or decrease the reproductive process. They also appear to stimulate root growth. Historically brasinosteriods have not been used in actual agricultural applications due to the expense of producing them and difficulties in purification. The invention describes a novel steroid receptor kinase, Bin1, which is involved in the pathway for synthesis of the plant brassiosteroid, brassinolide. Overexpresiion of Bin1 in transgenic plants provides plants characterized as having enhanced disease resistance, increased plant yield or vegetative biomass and increased seed yield..

References
Li et al., Cell, vol. 90, 929-938,1997

Patent Status:
U.S. Patent No. 6,765,085 Issued July 20, 2004

License Terms:
Exclusive and Non-Exclusive Licenses Available

Reference_Number: S97020
Contact: Mike White, Ph.D., CLP o Director, OTM o 858.453.4100 x1703 o mwhite@salk.edu

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Compositions, Cells, and Plants that Include BK11, A Negative Regulator of BRI1-Mediated BR Signaling (S06016.pdf)

Inventors
Xuelu Wang, Joanne Chory

Applications
Plant Biology, Growth and Yield
The BRI1 gene encodes a receptor serine/threonine kinase. Loss-of-function mutations in BRI1 result in dwarf plants that resemble steroid-deficient plants.

Earlier studies provided evidence that the action of a steroid hormone, brassinolide (BL), may be involved in light-regulated gene expression and cell elongation responses in plants. BL-deficient plants display many defects throughout development. In the dark, these mutants develop as light-grown plants and inappropriately express light-regulated genes. In the light, BL-deficient mutants are dwarfs, have reduced male fertility, and display a significant delay in the senescence program. In the absence of hormone, Arabidopsis plants do not respond properly to fluctuations in their light environment. The inventors have dicovered mutations in a gene, BRI1, that encodes a receptor serine/threonine kinase. Loss-of-function mutations in BRI1 result in dwarf plants that resemble steroid-deficient plants. Using a photoaffinity-labeled ligand, it was shown that BRI1 binds BL directly through a 94-amino acid region that includes the 70-amino acid subdomain in the extracellular domain. Moreover, BRI1 functions as a homodimer and in close proximity with BAK1, a second LRR-kinase. BRI1 is kept in a basal state by BKI1, a negative regulator whose function is to prevent the interaction of BRI1 with BAK1 in the absence of ligand. Other studies, using full-genome microarrays, indicate that BL and another plant hormone, auxin, regulate the expression of scores of overlapping target genes, and that the two signaling pathways act in close proximity, especially in terms of growth responses regulated by light..

References
The Plant Cell, Vol. 19: 1709-1717, May 2007
Genes & Dev. published online Jun 19, 2007

Patent Status:
U.S. Patent Application filed January 10, 2007

License Terms:
Non-exclusive and Exclusive by Field of Use Licenses Negotiable

Reference_Number: S06016
Contact: Mike White, Ph.D., CLP o Director, OTM o 858.453.4100 x1703 o mwhite@salk.edu

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Plant steroid 5 alpha Reductase, DET 2 (S96011.pdf)

Inventors
Joanne Chory and Jianming Li

Applications
Plant Biology, Agriculture, Horticulture
Increased plant yield using a novel gene, DET2 involved in brassinolide synthesis.

The invention describes a novel steroid 5alpha-reductase, DET2, which is involved in the synthesis of the plant steroid hormone, brassinolide. Overexpression of DET2 reductase in transgenic plants causes such plants to become significantly larger and more robust than their wild-type counterparts, thus increasing plant growth, crop growth and/or increased biomass. The invention provides for methods to produce a genetically modified plant characterized as having increased yield as compared to a wild-type plants. The method can include transferring a copy of a DET2-encoding polynucleotide operably associated with a promoter to a plant cell to obtain a transformed plant cell and producing a plant from the transformed plant cell. Also provided is a method of contacting a plant with a native DET2 gene operably linked to its native promoter, with a promoter-inducing amount of an agent which induces DET2 gene expression..

References
Science 272(5260):398-401 (April 1996)
PNAS 94(8):3554-9 (April 1997)
Plant Cell 9(11):1951-62 (November 1997)
Plant Physiol 120(3):833-40 (July 1999)

Patent Status:
U.S. Patent No. 6,143,950 issued November 7, 2000
Australian Patent No. 720,590 issued June 8, 2000

License Terms:
Non-exclusive and Exclusive by Field of Use Licenses Negotiable

Reference_Number: S96011
Contact: Mike White, Ph.D., CLP o Director, OTM o 858.453.4100 x1703 o mwhite@salk.edu

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Methods and Compositions to Modulate Ethylene Sensitivity (S01009.pdf)

Inventors
Joseph Ecker, Anna Stepanova

Applications
Plant Biology, Agriculture, Floriculture
Novel transcription factors affecting ethylene sensitivity in plants

A small family of novel transcription factors, termed "Ethylene-Response DNA-Binding Factors" (EDFs) were found to be involved in transcriptional regulation of ethylene-inducible genes and pathways. Mutant or transformed plants having inactivated or partially inactivated EDF genes (i.e. edf1, edf2, edf3, or edf4) may have a decreased sensitivity to ethylene. The invention includes the genetic modifications of EDF proteins and the genes that encode them to alter plant sensitivity and responsiveness to ethylene. Plants having reduced sensitivity to ethylene could be useful in the floral industry. These modified plants may have longer flower longevity. Further, EDF genes could be used to create vegetative crops that do not bolt or flower easily. For example, lettuce, spinach, and other leafy vegetables or certain herbs may have higher yields due to decreased floral initiation. Other plants may benefit from decreasing ethylene sensitivity at fruit ripening , by linking a modified EDF gene to a fruit-ripening-specific promoter. Yet another use would be to linking the EDF modified gene to a darkness-inducible promoter which could be useful in the long term storage of certain crops between the time of harvest and sale..

References
Publishec PCT Application WO02/089555

Patent Status:
U.S. Application pending

License Terms:
Non-exclusive and Exclusive by Field of Use Licenses Negotiable

Reference_Number: S01009
Contact: Mike White, Ph.D., CLP o Director, OTM o 858.453.4100 x1703 o mwhite@salk.edu

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Ethylene Insensitive Plants (S01008.pdf)

Inventors
Joseph Ecker, Ramlah Nehring, Robert McGrath

Applications
Plant Biology, Agriculture, Horticulture, Floriculture
Mutants conferring ethylene insensitivity on plants

The gaseous plant hormone ethylene modulates a diverse array of biological processes in plants including cell elongation, senescence and abscission of leaves and flowers, fruit ripening and responses to a wide variety of biotic and abiotic stresses. The ability to genetically manipulate ethylene production will provide agriculture with new tools to prevent detrimental effects (senescence) or provide the beneficial properties of ethylene responsiveness, such as controlling fruit ripening. The invention describes a mutated form of the EIN6 gene (ein6) that results in an altered response to ethylene including an ethylene insensitive root (EIR) phenotype. A double mutant consisting of the mutant EIN6 gene and a mutated form of the een gene results in ethylene insensitivity throughout the plant in contrast to the EIR phenotype found in the ein6 single mutant..

References
No publications to date

Patent Status:
U.S. Application Published as 2006-0005278

License Terms:
Non-exclusive and Exclusive by Field of Use Licenses Negotiable

Reference_Number: S01008
Contact: Mike White, Ph.D., CLP o Director, OTM o 858.453.4100 x1703 o mwhite@salk.edu

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Genetic Control of Organ Abscission (NEVERSHED) (S01002.pdf)

Inventors
Sarah Liljegren, Joseph Ecker and Marty Yanofsky

Applications
Plant Biology, Agriculture, Horticulture, Floriculture
Mutation in the NEVERSHED family resulting in decreased plant organ abscission. NEV provides opportunities to increase crop yield and to control shedding.

It has been discovered that genetic modification of particular genes in a plant can result in modulation of organ abscission (the natural separation of flowers, fruit, or leaves from plants). Thus, the genes and methods of this technology can be used to control the timing and development of the abscission (separation) zones on plants. Accordingly, plants can be designed to maintain structures (e.g., fruit, grains, vegetables, flowers etc.) for a longer period of time on the plant or, conversely, to selectively shed such structures earlier or at a pre-selected time. The ability to genetically manipulate abscission zone differentiation in agronomically important plants will provide valuable opportunities to improve crop yield and to simplify harvesting as well as applications in the floral industry. The invention identifies NEVERSHED (NEV), a gene responsible for controlling abscission via mutation of ARF-GAp domains. In Arabidopsis, modulation of NEV results in inhibiting abscission of flowers and, to a lesser extent, of leaves. Therefore, NEV has the potential of controlling abscission of commercially-relevant crops. Foe example, NEV may be used to regulate abscission in cotton and prevent the shedding of cotton balls until ready for harvest. Similarly, NEV may be used to inhibit abscission in corn, rice, or to control shedding of fruits and vegetables like peaches or tomatoes..

References
No publications to date

Patent Status:
U.S. Application Published as 2004-0143872

License Terms:
Exclusive or Nonexclusive licenses available

Reference_Number: S01002
Contact: Mike White, Ph.D., CLP o Director, OTM o 858.453.4100 x1703 o mwhite@salk.edu

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Method of Regulating Transcription in a Cell and Methods of Modulating Gene Expression (S00004.pdf)

Inventors
Beverly Emerson and Shilpa Kadam

Applications
Drug Discovery, Regulation of Gene Expression, Chromatin Remodeling
Chromatin based technology to define novel and highly specific protein targets for selective gene modulation

Appropriate differentiation and development of higher organisms require precisely regulated expression of multiple genes. The packaging of DNA into chromatin within the eukaryotic nucleus is highly organized and plays a critical role in regulating gene expression. The various types of chromatin structures that form on individual genes determine whether a gene is turned on or off. Regulation of chromatin structure is a critical component of gene regulation which affects tissue differentiation and cell function related to aging, cancer and a variety of diseases caused by changes in gene expression. Drug discovery related to modulation of gene expression, either to down regulate an overexpressed gene or to up regulate a silenced gene cannot be done at the DNA level alone. Chromatin based assays allow for the natural state of DNA regulation and provide optimal targets for therapeutic intervention. One important family of mammalian chromatin remodeling complexes, SWI/SNF (switch/sniff) is targeted to individual genes to specifically regulate its expression. SWI/SNF interacts with only certain classes of transcription factors and this property enables SWI/SNF to be selectively recruited to particular promoters. For example, proteins containing zinc finger DNA-binding domains (ZF DBDs), which is the largest class of eukaryotic transcription factors, interact with the BRG1 subunit of human SWI/SNF complex and recruit this complex to target promoters rather than the other catalytic subunit of SWI/SNF, BRM complexes. One invention provides for screening assays that identify small molecules that enhance or block the association between chromatin remodeling complexes and the specific transcription factors with which they interact. Specifically, the assays utilize several families of chromatin remodeling complexes which play key roles in facilitating the binding of specific transcription factors to nucleosomal DNA in diverse organisms from yeast to man. These in vitro assays can be developed for high-throughput screening to identify small molecule drugs that alleviate specific diseases caused by gene over or under expression. The second invention relates to three new findings of commercial potential. First, ZF DBDs or peptides are sufficient to direct SWI/SNF to a repressed promoter and create an accessible chromatin structure which enables other transcription factors to interact and activate the gene. In the absence of the ZF DBD, SWI/SNF and the other factors do not interact and the gene remains silent. Second, SWI/SNF BRG1 complexes, but not BRM, bind to the CREB transcription factor only when phosphorylated. CREB is the critical regulator of cAMP-response genes and thus a direct link between this signaling pathway and targeted chromosomal binding and gene activation by a specific form of SWI/SNF is established. Third, the opposite specificity exists for another type of signaling pathway. In this case, BRM SWI/SNF, but not BRG1, interacts with critical regulators of the Notch signaling pathway and is recruited to Notch target genes. Thus it is possible to identify drugs that selectively inhibit one type of pathway without affecting others..

References
S00004: Cell 95(1):93-104(October 1998)
S02019: Molecular Cell 11:377-389 (February 2003)

Patent Status:
U.S. Patent Application published as 2002-0022021
U.S. Patent Application published as 2005-0079512

License Terms:
Non-Exclusive Licenses Negotiable

Reference_Number: S00004
Contact: Dave Odelson, Ph.D. o Senior Licensing Executive o 858.453.4100 x1223 o dodelson@salk.edu

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Compounds Useful for the Modulation of Processes Mediated by Nuclear Hormone Receptors, Methods for the Identification and Use of Such Compounds (S97012.pdf)

Inventors
Ronald Evans and Laszlo Nagy

Applications
Oncology, Drug Discovery and Development
Compositions for treatment of cancer, comprised of a ligand for a member of the steroid/thyroid hormone superfamily of receptors and a histone deacetylase inhibitor

It has been discovered that histone deacetylase associates with hormone receptor complexes and contributes to the repression thereof. It has further been discovered that exposure of a repressed system to histone deacetylase inhibitors relieves this repression. Thus, histone deacetylase inhibitors have been found to be useful for the activation of genes responsive to hormone receptors. The invention includes compositions for the treatment of cancer, which are made up of a ligand for a member of the steroid/thyroid hormone superfamily of receptors and a histone deacetylase inhibitor. Preferred ligands are ligands for retinoid receptors (e.g., all-trans retinoic acid, 9-cis retinoic acid), ligands for thyroid hormone receptors or ligands for vitamin D3 receptor. Preferred inhibitors included histone deacetylase inhibitors (e.g., Trichostatin A, Trapoxin), and chromatin remodeling machinery inhibitors..

References
Cell 1997 May 2;89(3):373-80
Nature 1998 Feb 19;391(6669):811-4
Published PCT application WO98/48825

Patent Status:

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Products Useful for Modulating Expression of Exogenous Genes in Mammalian Systems (S98001.pdf)

Inventors
Ronald Evans and David No

Applications
Gene Expression
Modulation of exogenous gene expression in mammalian and other systems using modified ecdysone receptors

This invention relates to various methods for modulating the expression of an exogenous gene in a mammalian subject employing modified ecdysone receptors. The invention method is useful in a wide variety of applications where inducible in vivo expression of an exogenous gene is desired, such as in vivo therapeutic methods for delivering recombinant proteins into a variety of cells within a patient. Advantages of ecdysteroid use include the lipophilic nature of the compounds, short half-lives, and favorable pharmacokinetics that prevent storage and expedite clearance. The invention also relates to modified ecdysone receptors, nucleic acids encoding modified ecdysone receptors, modified ecdysone response elements, gene transfer vectors, recombinant cells, and transgenic animals containing nucleic acids encoding modified ecdysone receptor..

References
Proc. Natl. Acad. Sci. 93: 3346-3351 (1996)

Patent Status:

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Selective Modulators of PPAR-gamma and Methods for the Use Thereof (S95031.pdf)

Inventors
Ron Evans and Barry Forman

Applications
Cardiovascular, Obesity, Drug Discovery and Development
Use of PPAR-gamma-selective compounds for the treatment of obesity and diabetes.

Because obesity is associated with the development of serious medical conditions, including noninsulin-dependent diabetes mellitus, hypertension, coronary artery disease, hyperlipidemias and certain malignancies, it is important that compounds to control adiposity are identified. The conversion of fibroblasts into cells of the adipose lineage is induced by expression of the orphan nuclear receptor PPAR-gamma. Accordingly, an endogenous PPAR-gamma ligand may be an important regulator of adipogenesis. This invention reveals PPAR-gamma as a drug target and relates to a class of compounds which are capable of selectively modulating processes mediated by PPAR-gamma. The identification of such compounds makes possible the selective intervention in PPAR-gamma mediated pathways, without exerting inadvertent effects on pathways mediated by other PPAR isoforms..

References
Cell 1995 Dec 1;83(5):803-12.

Patent Status:
U.S. Patent No. 6,830,882 issued December 14, 2004

License Terms:
Exclusive or Nonexclusive licenses available

Reference_Number: S95031
Contact: Mike White, Ph.D., CLP o Director, OTM o 858.453.4100 x1703 o mwhite@salk.edu

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Treatment of Disease States which Result from Neoplastic Cell Proliferation Using PPAR-gamma Activators and Compositions Useful Therefor (S96024A.pdf)

Inventors
Ron Evans, Laszlo Nagy, and Peter Tontonoz

Applications
Oncology, Drug Discovery and Development
Administration of PPAR-gamma agonists, optionally in combination with RXR specific agonists, can block neoplastic cell proliferation

Neoplastic cell proliferation is the underlying cause of a wide variety of diseases, e.g., breast cancer, leukemia, colon cancer, prostate cancer. Traditional approaches to treatment of neoplastic cell proliferation include surgery, chemotherapy and radiotherapy. Induction of terminal differentiation represents a promising alternative to conventional methods of treatment for certain malignancies. It has been discovered that PPAR-gamma is expressed consistently in tissues associated with a variety of disease states which result from neoplastic cell proliferation. Maximal activation of PPAR-gamma with exogenous ligand promotes terminal differentiation of primary cells which are otherwise subject to neoplastic cell proliferation. Thus, cells undergoing neoplastic cell proliferation can be induced to differentiate, thereby blocking further proliferation. It has also been discovered that RXR-specific ligands are potent agents for induction of differentiation of cells expressing the PPAR-gamma/RXR-alpha heterodimer and that simultaneous treatment of cells subject to neoplastic cell proliferation with a PPAR-gamma-selective ligand, in combination with an RXR-specific ligand, results in an additive stimulation of differentiation. The invention includes compounds and compositions which could be useful for the treatment of breast cancer, leukemia, colon cancer and prostate cancer..

References
PNAS USA 1997 Jan 7; 94(1):237-41

Patent Status:

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Treatment of Liposarcomas Using a Combination of Thiazolidinediones and Retinoid X Receptor Selective Agonists (S96023A.pdf)

Inventors
Ron Evans, Peter Tontonoz, and Barry Forman

Applications
Oncology, Drug Discovery and Development
Compositions useful for the treatment of liposarcomas

Liposarcoma is the most common soft tissue malignancy in adults, accounting for at least 20% of all sarcomas in this age group. Localized disease is treated primarily with surgery, often in combination with radiotherapy. Metastatic liposarcoma is associated with an extremely poor prognosis, with average five year survival ranging from 70% to 25%, depending on the type of tumor. The development of effective, noninvasive methods for treating liposarcomas would represent a significant advancement in the therapeutic arts. It has been discovered that PPAR-gamma is expressed consistently in each of the major histologic types of human liposarcoma. Maximal activation of PPAR-gamma with exogenous ligand (a thiazolidinedione or derivative thereof) promotes terminal differentiation of primary human liposarcoma cells, thereby blocking further proliferation. It has also been discovered that RXR-specific ligands are potent adipogenic agents in cells expressing the PPAR-gamma/RXR-alpha heterodimer and that simultaneous treatment of liposarcoma cells with a thiazolidinedionyl moiety (a PPAR-gamma-selective class of compounds) and an RXR-specific ligand results in an additive stimulation of differentiation. The invention includes compositions useful for the treatment of liposarcomas..

References
PNAS USA 1997 Jan 7; 94(1):237-41

Patent Status:

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Use of RAR Antagonists as Modulators of Hormone Mediated Processes (S96028.pdf)

Inventors
Ron Evans, Laszlo Nagy, and Peter Tontonoz

Applications
Cardiovascular, Obesity. Drug Discovery and Development
RAR Antagonists are capable of modulating processes mediated by other members of the steroid/thyroid hormone receptor superfamily, including permissive receptors such as PPARs.

Retinoic acid receptor (RAR) antagonists are capable of modulating processes mediated by non-RAR members of the steroid/thyroid hormone receptor superfamily including permissive receptors such as PPARs (e.g., PPAR-alpha, PPAR-delta and PPAR-gamma). It has been discovered that RAR antagonists, in combination with agonists for members of the steroid/thyroid hormone receptor superfamily, are capable of inducing and/or enhancing processes mediated by such members. Such compositions will modulate the activity of permissive heterodimers. Permissive heterodimeric members of the steriod/thyroid hormone receptor superfamily include PPAR:RXR, LXR:RXR, NGFI-B:RXR, NURR1:RXR, FXR:RXR, BXR:RXR, SXR:RXR. For example, PPAR regulates genes involved in fatty acid degradation. This is blocked by retinoid agonists. In contrast, an RAR antagonist can stimulate PPAR signalling. Accordingly, a composition composed of an RAR antagonist and a PPAR agonist could represent a unique approach to treat PPAR controlled syndromes such as cardiovascular disease, hyperlipidemia, obesity or insulin resistance which are characterized by altered levels of fatty acids or their metabolites..

References
No publications to date

Patent Status:

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Hormone Receptor Functional Dimers and Methods of Use (S98032.pdf)

Inventors
Fred Gage, Steven Suhr, Elad Gil and Marie-Claude Senut

Applications
Gene Expression.


This invention relates to chimeric proteins comprising at least two functional protein units. The chimeric proteins can fold under crystallization conditions to form functional entities. The DNA binding characteristics of the invention functional entities differ from those of wild-type complexes formed between "monomeric" receptors and their binding partners. Some functional entities, e.g. dimers expressed as fusion proteins, transactivate responsive promoters in a manner similar to wild-type complexes, while others do not promote transactivation and function instead essentially as constitutive repressors..

References
Published PCT Application WO01/36447

Patent Status:
U.S. Application pending, PCT filed Oct. 2000

License Terms:
Exclusive, Partial Exclusive or Nonexclusive license negotiable

Reference_Number: S98032
Contact: Mike White, Ph.D., CLP o Director, OTM o 858.453.4100 x1703 o mwhite@salk.edu

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Modular Assembly Retroviral Vectors and Uses Therefor (S96013.pdf)

Inventors
Fred H. Gage and Steven T. Suhr

Applications
Gene Expression/Gene Therapy
Gene transfer vectors with the capacity for prolonged or modulated transgene expression

This invention relates to novel retroviral vectors containing modified long terminal repeats (LTR) which enable high level and ligand-modulatable expression of a desired gene product, even after prolonged periods of cellular quiescence. These novel vectors overcome proviral transcriptional inactivation which occurs in cultured primary cells that are growth arrested due to environmental constraints such as contact inhibition and/or nutrient starvation. These vectors represent a class of retroviral vectors in which LTR-promoted proviral expression in infected cells may be maintained or increased, even in situations generally considered to be non-permissive for retroviral vectors. This invention can be applied: as gene transfer vectors with the capacity for prolonged or modulated transgene expression for either in vivo or ex vivo gene therapy; as gene transfer vectors for efficient production of transgenic animals; as vectors for efficient gene transfer to developing embryos; and as vectors with inducible high titers..

References
No publications to date

Patent Status:

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Regulation of Tyrosine Hydroxylase Expression (S98035.pdf)

Inventors
Kazuhiro Sakurada, Theo Palmer and Fred H. Gage

Applications
Gene Expression, CNS
Nurr1 polypeptide upregulates tyrosine hydroxylase activity and promotes expression of DOPA, norepinenephrine and epinephrine.

The invention describes methods to regulate tyrosine hydroxylase expression and the treatment of catecholamine-related diseases including Parkinson's disease, manic depression and schizophrenia. The basis for the invention is the discovery that expression of Nurr1 polypeptide induces tyrosine hydroxylase in both undifferentiated and differentiated mammalian cells including adult hippocampal progenitor cells. Specifically, the invention provides cells that contain exogenous nucleic acid as well as methods and materials for inducing tyrosine hydroxylase expression, treating catecholamine-related deficiencies and identifying tyrosine hydroxylase-related deficiencies. Neural progenitor cells, neural cells and neural stem cells which contain the exogenous nucleic acid and express the Nurr1 polypeptide are upregulated for tyrosine hydroxylase activity and thus promote the expression of DOPA, norepinephrine and epinephrine. These cells can be used to treat catecholamine deficiency diseases directly. In addition, these diseases can be treated by transfection using the genetic construct for Nurr1 expression..

References
Development. 126(18): 4017-26 (Sept. 1999)

Patent Status:

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Transcription Factor Regulating FGF-2 and Variants Thereof (S98015.pdf)

Inventors
Fred H. Gage and Tetsuya Ueba

Applications
Oncology, Diagnostic, Drug Discovery
Genes which encode polypeptides that are FGF-2 regulators of transcription

This invention is based on the discovery of genes which encode polypeptides that are FGF-2 regulators of transcription (RFT). RFT-A, a negative regulator of transcription and RFT-A' and RFT-B, positive regulators of FGF-2 transcription are provided. The invention also relates to methods for diagnosis of prognosis for a subject having or at risk of having a disorder associated with FGF-2 and for treatment of cell proliferative disorders associated with FGF-2, such as neoplasia, atrocytoma, glioma, glioblastoma, medulloblastoma, colon cancer, lung cancer, renal cancer, leukemia, testicular cancer, breast cancer, prostate cancer, endometrial cancer and neuroblastoma. Screening methods for identifying a compound which affects RFT-A polypeptide or a variant of RFT-A polypeptide and for identifying proteins that bind to RFT-A polypeptide or a variant of RFT-A are also provided..

References
J Biol Chem 274(15): 10382-7 (April 1999)

Patent Status:

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Orphan Receptor TLX and Uses Therefor (S04004.pdf)

Inventors
Yanh