Cloning of cytochrome p450 genes from Nicotiana
Publication Number: US 8658856 B2 Publication Date: Feb 25, 2014 Inventor: Dongmei Xu
Abstract: The present invention relates to p450 enzymes and nucleic acid sequences encoding p450 enzymes in Nicotiana, and methods of using those enzymes and nucleic acid sequences to alter plant phenotypes.
Contribution: Genome Explorations generated data used in support of patent and application. Hybridization experiments were conducted by Genome Explorations, Inc. (Memphis, Tenn.). The RNA samples used in hybridization consisted of six pairs of nonconverter/converter isogenic lines that were induced by ethylene treatments…Twelve sets of hybridizations were successful as evidenced by the Expression Report generated using detection instruments from Genome Explorations…
Tissue-specific differentiation matrices and uses thereof
Publication Number: US 20130195814 A1 Publication Date: Aug 1, 2013 Inventor: Xiao-Dong Chen
Abstract: In some aspects, this invention provides a method of making a bone marrow-derived tissue-specific stem cell proliferation, expansion, isolation and rejuvenation extracellular matrix. In other aspects, this invention provides a method of making a tissue-specific fibroblast-derived stem cell differentiation extracellular matrix. Also provided are methods of using such a cell-derived preservation or differentiation matrices to induce tissue-specific differentiation of pluripotent cells, repair damaged tissue, and treat a subject having a physiologic deficiency using the same.
Contribution: Genome Explorations generated data used in support of patent and application. After pooling, RNA was sent to Genome Explorations (available on the world wide web at qenomeexplorations.com). There, RNA was converted to DNA and the labeled cRNA was prepared, which were hybridized onto Affymetrix Human Genome U133 Plus 2.0 chips. The chips were scanned, and data were pre-analyzed using Affymetrix MAS 5.0. Gene expression levels on “Plastic” chips (Plastic-A, Plastic-B, and Plastic-C) were compared…
Use of emt gene signatures in cancer drug discovery, diagnostics, and treatment
Publication Number: US 20120302572 A1 Publication Date: Nov 29, 2012 Inventor: Julie Kan, Stuart Thomson, Gretchen M. Argast, Matthew E. O’Connor, Murray Robinson, Bin Feng, Joerg Heyer, Maria I. Chiu, Richard Nicoletti
Abstract: The present invention provides diagnostic methods for assessing the EMT status of tumor cells, and for predicting the effectiveness of treatment of a cancer patient with an EGFR or IGF-1R kinase inhibitor, utilizing an EMT gene signature index score. The present invention further provides methods for treating patients with cancer that incorporate these methods.
Contribution: Genome Explorations generated data used in support of patent and application. On experimental day 7, the cells were trypsinized, washed, pelleted, and snap frozen. Cell pellets were sent to Genome Explorations (Memphis, Tenn.) or Expression Analysis (Durham, N.C.) for isolation of RNA. mRNA was then processed to cDNA, amplified and labeled for hybridization to Affymetrix U133 Plus 2.0 mRNA microarrays. After hybridization and washing,..
Methods and Compositions for Tissue Engineering
Publication Number: US 20120148539 A1 Publication Date: Jun 14, 2012 Inventor: Moulay Hicham Alaoui-Ismaili
Abstract: Disclosed herein are methods and compositions for promoting endochondral bone formation. The invention includes methods of promoting endochondral bone formation by down-regulating the expression of the DIO2 gene or the activity of the deiodinase protein. The invention also includes methods of up-regulating the activity of the FGFR3, ADAMTS9, HEY1, HAS3, and/or MFI2 genes and/or the activity of the expression products of those genes to promote endochondral bone formation. The invention also includes compositions of BMP-7 and agonists of FGFR3, ADAMTS9, HEY1, HAS3, and/or MFI2 proteins. Compositions can further include mesenchymal stem cells.
Contribution: Genome Explorations generated data used in support of patent and application. Data analysis was performed by Genome Explorations, Inc. (Memphis, Tenn.). Data were normalized using two different methods, the Affymetrix Statistical Algorithm MAS 5.0 (GCOS v1.4) and RMA (Lockhart et al., (1996), Nat Biotechnol…Each normalized data set was subjected to ANOVA and independent t-tests at each time point (treated versus control) using the Benjamini-Hochberg FDR correction method…
Methods for the identification of agents that inhibit mesenchymal-like tumor cells or their formation
Publication Number: US 7951549 B2 Publication Date: May 31, 2011 Inventor: John D. Haley, Stuart Thomson, Julie Kan, Salam A. Shaaban
Abstract: The present invention provides tumor cell preparations for use as models of the EMT process for use in the identification of anti-cancer agents, wherein said tumor cell preparations comprise cells of the epithelial tumor cell line H358, which are stimulated by receptor ligands to induce EMT, or which have been engineered to inducibly express a protein that stimulates EMT. The present invention also provides methods of identifying potential anti-cancer agents by using such tumor cell preparations to identify agents that inhibit EMT, stimulate MET, or inhibit the growth of mesenchymal-like cells. Such agents should be particularly useful when used in conjunction with other anti-cancer drugs such as EGFR and IGF-1R kinase inhibitors, which appear to be less effective at inhibiting tumor cells that have undergone an EMT.
Contribution: Explorations generated data used in support of patent and application. On experimental day 7, the cells were trypsinized, washed, pelleted, and snap frozen. Cell pellets were sent to Genome Explorations for mRNA isolation and analysis by Affymetrix Human Genome 133 Plus 2.0 Array. On experimental day 7, cells were harvested for protein. For analysis of total protein, nuclear, membrane and cytosol fractions were prepared using PROTEOEXTRACT® reagent (EMD #444810). Proteins were then precipitated using …
Compositions and methods of use of EPB1, and ErbB3 binding protein
Publication Number: US 7838495 B2 Publication Date: Nov 23, 2010 Inventor: Yuexing Zhang, Anne Hamburger
Abstract: Inhibition of the proliferation of hormone refractory prostate cancer cells is achieved by administering EPB1, an ErbB3 binding protein, in combination with another anti-proliferation therapy such as administration of antiandrogens, other anticancer agents, radiation therapy, or surgery. Administration of EPB1 reverses the phenotype of hormone-resistant prostate cancer cells to hormone-sensitive prostate cancer cells.
Contribution: Genome Explorations generated data used in support of patent and application. First and second strand cDNA were synthesized from 5-15 μg of total RNA at Genome Explorations (Memphis, Tenn.) using the SuperScript Double-Stranded cDNA Synthesis Kit…Microarray processing and data analysis was performed at Genome Explorations (Memphis, Tenn.). U133A oligonucleotide arrays (Affymetrix) containing ˜33,000 full length annotated genes together with additional probe sets designed to represent EST sequences were used for the analysis…
Nucleotide sequences coding plant monooxygenase for use in identifying modulators of nornicotine levels in tobacco
Publication Number: US 7812227 B2 Publication Date: Oct 12, 2010 Inventor: Dongmei Xu
Abstract: The present invention relates to p450 enzymes and nucleic acid sequences encoding p450 enzymes in Nicotiana, and methods of using those enzymes and nucleic acid sequences to alter plant phenotypes.
Contribution: Genome Explorations generated data used in support of patent and application. Hybridization experiments were conducted by Genome Explorations, Inc. (Memphis, Tenn.). The RNA samples used in hybridization consisted of six pairs of nonconverter/converter isogenic lines that were induced by ethylene treatments…Twelve sets of hybridizations were successful as evidenced by the Expression Report generated using detection instruments from Genome Explorations…
ErbB3 binding protein compositions and methods of use
Publication Number: 7,718,626 Publication Date: May 18, 2010 Inventor: Yue-xing Zhang, Anne W. Hamburger
Abstract: A method of repressing a cell-cycle gene, which is regulated by an E2F transcription factor, in a cell, wherein the method comprises contacting the cell with a cell-cycle gene-repressing amount of ErbB3 binding protein (Ebp1); a method of inhibiting prostate cancer in a mammal, wherein the method comprises administering to the mammal a prostate cancer-inhibiting amount of Ebp1; a composition comprising an Ebp1-expressing viral vector that expresses a cell-cycle gene-repressing amount of Ebp1; and a composition comprising polymer-packaged DNA comprising and expressing a cell-cycle gene-repressing amount of Ebp1.
Contribution: Genome Explorations generated data used in support of patent and application. Microarray Analysis: First and second strand cDNA were synthesized from 5-15 μg of total RNA at Genome Explorations (Nashville, Tenn.) using the SuperScript Double-Stranded cDNA Synthesis Kit (Gibco Life Technologies, Gaithersburg, Md.) and an oligo-dT24-T7 (5′-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3′) (SEQ ID NO: 3) primer according to the manufacturer’s instructions…
Nicotiana nucleic acid molecules and uses thereof
Publication Number: US7700834 B2 Publication Date: Apr 20, 2010 Inventor: Dongmei Xu, Mark T. Nielsen
Abstract: The present invention features Nicotiana nucleic acid sequences such as sequences encoding constitutive, or ethylene or senescence induced polypeptides, in particular cytochrome p450 enzymes, in Nicotiana plants and methods for using these nucleic acid sequences and plants to alter desirable traits, for example by using breeding protocols.
Contribution: Genome Explorations generated data used in support of patent and application. All 14 sets of hybridizations were successful as evidenced by the Expression Report generated using detection instruments by Genome Explorations, Inc. (Memphis, Tenn.). The main reports included analyses of Noise, Scale factor, background, total probe sets, number and percentage of present and absent probe sets, signal intensity of housekeeping controls…
Method of Regulating Gene Expression
Publication Number: US 2009⁄0099259 A1
Publication Date: Apr 16, 2009
Inventor: Zeina Jouni, Joshua Anthony, Steven C. Rumsey, Deshanie Rai, Kumar Sesha Kothapalli, James T. Brenna
Abstract: The present invention is directed to a novel method for modulation the expression of one or more genes in a subject by administering an amount of DHA and ARA to the subject.
Contribution: Genome Explorations generated data used in support of patent and application RNA preparations and array hybridizations were processed at Genome Explorations, Memphis, Tenn. http://www.genome-explorations.com. The completed raw data sets were downloaded from the Genome Explorations secure ftp servers. Data are expressed as mean±SD. Statistical analysis was conducted using analysis of variance (ANOVA) to test the hypothesis of equivalent means for measures taken at 12 weeks…
Use of dha and ara in the preparation of a composition for regulating gene expression
Publication Number: WO2007100566 A2 Publication Date: Sep 7, 2007 Inventor: Zeina Jouni, J Thomas Brenna, Joshua C Anthony, Kumar Sesha Durga Kothapalli, Steven C Rumsey, Deshanie Rai
Abstract: The present invention is directed to a novel method for modulating the expression of one or more genes in a subject by administering an amount of DHA and ARA to the subject.
Contribution: Genome Explorations generated data used in support of patent and application. (One hybridization was performed for each animal (12 chips total). RNA preparations and array hybridizations were processed at GenomeExplorations, Memphis, TN. The completed raw data sets were downloaded from the Genome Explorations secure ftp servers. Statistics ### [00064] Data are expressed as mean±SD. Statistical analysis was conducted using analysis of variance (ANOVA)…
Method for increasing the expression of pulmonary surfactant protein-B
Publication Number: US 20070202052 A1 Publication Date: Aug 30, 2007 Inventor: Thomas Brenna, Kumar Sesha Durga Kothapali, Zeina Jouni, Joshua C. Anthony, Steven C. Rumsey
Abstract: The present invention is directed to a novel method for increasing the expression of pulmonary surfactant protein-B in an infant. The method comprises administration of a therapeutically effective amount of DHA and ARA, alone or in combination with one another, to the infant.
Contribution: Genome Explorations generated data used in support of patent and application. RNA preparations and array hybridizations were processed at Genome Explorations, Memphis, Tenn. http://www.genome-explorations.com. The completed raw data sets were downloaded from the Genome Explorations secure ftp servers…
Mammalian cell modified with genes encoding plant late embryogenesis protein HVA1, trehalose transport protein, or a trehalose synthesis pathway; freezing and/or drying organs for storage prior to use
Publication Number: US 20070202052 A1 Publication Date: Aug 25, 2005 Inventor: Paul Conrad, Lynn Allen-Hoffmann
Abstract: The present invention relates generally to compositions and method for freezing and/or drying organs for storage prior to use. In particular, the present invention relates to the genetic modification of cells used to form organs so that organs formed from the genetically modified cells can be dried. According to the invention, mammalian cells may be modified with genes encoding plant late embryogenesis protein HVA1, trehalose transport protein, or a trehalose synthesis pathway. The invention also provides methods of treating patients with organs that have been preserved by freezing and/or drying.
Contribution: Genome Explorations generated data used in support of patent and application. Gene array analysis is used to monitor global changes in gene expression following recovery from the dried state, RNA from rehydrated and control (not preserved) tissue is submitted to Genome Explorations, Inc., which will perform gene expression array hybridization and data analysis. Biotinylated cDNA probes is generated from the RNA samples and is hybridized to the U133 GeneChips from …
Mammalian cell modified with genes encoding plant late embryogenesis protein HVA1, trehalose transport protein, or a trehalose synthesis pathway; freezing and/or drying organs for storage prior to use
Publication Number: US 20050186185 A1 Publication Date: Aug 25, 2005 Inventor: Paul Conrad, Lynn Allen-Hoffmann
Abstract: The present invention relates generally to compositions and method for freezing and/or drying organs for storage prior to use. In particular, the present invention relates to the genetic modification of cells used to form organs so that organs formed from the genetically modified cells can be dried. According to the invention, mammalian cells may be modified with genes encoding plant late embryogenesis protein HVA1, trehalose transport protein, or a trehalose synthesis pathway. The invention also provides methods of treating patients with organs that have been preserved by freezing and/or drying.
Contribution: Genome Explorations generated data used in support of patent and application. Gene array analysis is used to monitor global changes in gene expression following recovery from the dried state, RNA from rehydrated and control (not preserved) tissue is submitted to Genome Explorations, Inc., which will perform gene expression array hybridization and data analysis…