2254 results about "Expression gene" patented technology

The present invention provides methods for monitoring disease states in a subject, as well as methods for monitoring the levels of effect of therapies upon a subject having one or more disease states. The methods involve: (i) measuring abundances of cellular constituents in a cell from a subject so that a diagnostic profile is obtained, (ii) measuring abundances of cellular constituents in a cell of one or more analogous subjects so that perturbation response profiles are obtained which correlate to a particular disease or therapy, and (iii) determining the interpolated perturbation response profile or profiles which best fit the diagnostic profile according to some objective measure. In other aspects, the invention also provides a computer system capable of performing the methods of the invention, data bases comprising perturbation response profiles for one or more diseases and / or therapies, and kits for determining levels of disease states and / or therapeutic effects according to the methods of the invention.

The present invention provides methods for enhanced detection of biological response patterns. In one embodiment of the invention, genes are grouped into basis genesets according to the co-regulation of their expression. Expression of individual genes within a geneset is indicated with a single gene expression value for the geneset by a projection process. The expression values of genesets, rather than the expression of individual genes are then used as the basis for comparison and detection of biological responses with greatly enhanced sensitivity.

The present invention provides methods and compositions for the analysis of gene expression in single cells or in a plurality of single cells. The invention provides methods for preparing a cDNA library from individual cells by releasing mRNA from each single cell to provide a plurality of individual mRNA samples, synthesizing cDNA from the individual mRNA samples, tagging the individual cDNA, pooling the tagged cDNA samples and amplifying the pooled cDNA samples to generate a cDNA library. The invention also provides a cDNA library produced by the methods described herein. The invention farther provides methods for analyzing gene expression in a plurality of cells by preparing a cDNA library as described herein and sequencing the library.

The invention relates to a double-stranded ribonucleic acid (dsRNA) for inhibiting the expression of the Eg5 gene (Eg5 gene), comprising an antisense strand having a nucleotide sequence which is less that 30 nucleotides in length, generally 19-25 nucleotides in length, and which is substantially complementary to at least a part of the Eg5 gene. The invention also relates to a pharmaceutical composition comprising the dsRNA together with a pharmaceutically acceptable carrier; methods for treating diseases caused by Eg5 expression and the expression of the Eg5 gene using the pharmaceutical composition; and methods for inhibiting the expression of the Eg5 gene in a cell.

Presented herein are methods and compositions for multiplexed single cell gene expression analysis. Some methods and compositions include the use of droplets and / or beads bearing unique barcodes such as unique molecular barcodes (UMI).

This invention relates to the field of biotechnology or genetic engineering. Specifically, this invention relates to the field of gene expression. More specifically, this invention relates to a novel inducible gene expression system and methods of modulating gene expression in a host cell for applications such as gene therapy, large-scale production of proteins and antibodies, cell-based high throughput screetng assays, functional genomics and regulation of traits in transgenic plants and animals.

The present invention relates to non-invasive and minimally invasive techniques for evaluating the physical state of a subject, including diagnosing a disease, disorder, or physical state of the subject, determining the prognosis of the subject, determining a subject's susceptibility for a disease, disorder, or physical state and determining, developing and monitoring treatment for the same. The invention also relates to identifying genetic alterations contributing to, or susceptibility for, development of a disease, disorder, or physical state, and for diagnosis, prognosis and treatment of the disease, disorder, or physical state.

A variety of elastomeric-based microfluidic devices and methods for using and manufacturing such devices are provided. Certain of the devices have arrays of reaction sites to facilitate high throughput analyses. Some devices also include reaction sites located at the end of blind channels at which reagents have been previously deposited during manufacture. The reagents become suspended once sample is introduced into the reaction site. The devices can be utilized with a variety of heating devices and thus can be used in a variety of analyses requiring temperature control, including thermocycling applications such as nucleic acid amplification reactions, genotyping and gene expression analyses.

A gene regulatory system controls gene therapy by emitting one or more forms of energy that regulate gene expression by triggering promoters. The system includes a sensor to sense a signal indicative of a need for the gene therapy as well as responses to the gene therapy. The regulation of the gene expression is controlled based on the sensed signal and / or a user command. In one embodiment, the system delivers one or more electrical therapies in conjunction with the gene therapy.

The present invention concerns a method for the oxidative refolding of a hepcidin polypeptide to a form that is mature, bioactive and folded as in the native configuration and molecular mass; a method for measuring the level of native, bioactive hepcidin in a vertebrate animal; a method for measuring the level of hepcidin gene expression in a vertebrate animal; and a method for regulating the production of native, bioactive hepcidin in a vertebrate animal in vivo. The present invention also concerns an antibody or fragment thereof that specifically binds to a continuous, discontinuous, and / or conformational epitope of a mature and bioactive hepcidin folded as in the native configuration; and a pharmaceutical composition that includes the antibody or a hepcidin polypeptide and that provides antimicrobial, agonistic, or antagonistic activities in vivo in a vertebrate animal.

A method and apparatus are provided for delivering an agent into a cell through the application of nanosecond pulse electric fields (“nsPEF's”). The method includes circuitry for delivery of an agent into a cell via known methods followed by the application of nanosecond pulse electric fields to said cell in order to facilitate entry of the agent into the nucleus of the cell. In a preferred embodiment, the present invention is directed to a method of enhancing gene expression in a cell comprising the application of nanosecond pulse electric fields to said cell. An apparatus for generating long and short pulses according to the present invention is also provided. The apparatus includes a pulse generator capable of producing a first pulse having a long duration and low voltage amplitude and a second pulse having a short duration and high voltage amplitude.

The present invention is directed to methods and compositions for use in screening nucleic acid populations for nucleic acid polymorphisms. The methods, referred to generally as ValiGeneSM Mutation Screening, Peptide-Linked (VGMS-PL) methods, are specifically designed for high-throughput genotype mapping and gene expression analysis of animal and plant nucleic acids without requiring a PCR amplification step. In particular, the methods of the invention utilize oligonucleotide probes labeled with distinguishable and identifiable peptide tags, that are captured on addressable antibody arrays.

A method for mimicking the effects of caloric restriction by administration of a food substrate having carnitine or a carnitine derivative and an antioxidant. The food substrate is capable of modulating gene expression in a way similar to caloric restriction.

Methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. This prediction model can be used to accurately predict the intrinsic subtype of a subject diagnosed with or suspected of having breast cancer. Further provided are compositions and methods for predicting outcome or response to therapy of a subject diagnosed with or suspected of having breast cancer. These methods are useful for guiding or determining treatment options for a subject afflicted with breast cancer. Methods of the invention further include means for evaluating gene expression profiles, including microarrays and quantitative polymerase chain reaction assays, as well as kits comprising reagents for practicing the methods of the invention.

The present invention provides methods for determining the level of protein activity in a cell by: (i) measuring abundances of cellular constituents in a cell in which the activity of a specific protein is to be determined so that a diagnostic profile is thus obtained; (ii) measuring abundances of cellular constituents that occur in a cell in response to perturbations in the activity of said protein to obtain response profiles and interpolating said response profiles to generate response curves; and (iii) determining a protein activity level at which the response profile extracted from the response curves best fits the measured diagnostic profile, according to some objective measure. In alternative embodiments, the present invention also provides methods for identifying individuals having genetic mutations or polymorphisms that disrupt protein activity, and methods for identifying drug activity in vivo by determining the activity levels of proteins which interact with said drugs.

The present invention relates to the field of plant molecular biology, more particularly to the root-specific gene expression in plants. The invention provides nucleic acids for a novel transcriptional regulatory root-specific promoter and nucleic acid and protein sequences coding for a new LRR receptor-kinase protein, further specified as a root clavata 1 homolog (RCH1). Further provided are compositions comprising nucleic acids, polypeptides, antibodies and vectors. The invention further provides for methods for modifying cell fate and / or plant development and / or plant morphology and / or plant biochemistry and / or plant physiology comprising the modification of expression in particular cells, tissues or organs of a plant of the novel LRR receptor-like kinase or comprising the expressing of a gene of interest under the control of the novel transcriptional regulatory root-specific promoter. Further are provided compounds interacting with the new polypeptides for use as herbicides or growth regulators.

The present invention provides methods and compositions for isolating and detecting rare cells from a biological sample containing other types of cells. In particular, the present invention includes a debulking step that uses a microfabricated filters for filtering fluid samples and the enriched rare cells can be used in a downstream process such as identifies, characterizes or even grown in culture or used in other ways. The invention also include a method of determining the aggressiveness of the tumor or of the number or proportion of cancer cells in the enriched sample by detecting the presence or amount of telomerase activity or telomerase nucleic acid or telomerase expression after enrichment of rare cells. This invention further provides an efficient and rapid method to specifically remove red blood cells as well as white blood cells from a biological sample containing at least one of each of red blood cells and white blood cells, resulting in the enrichment of rare target cells including circulating tumor cells (CTC), stromal cells, mesenchymal cells, endothelial cells, fetal cells, stem cells, non-hematopoietic cells etc from a blood sample. The method is based upon combination of immuno-microparticles (antibody coated microparticles) and density-based separation. The final enriched target cells can be subjected to a variety of analysis and manipulations, such as flowcytometry, PCR, immunofluorescence, immunocytochemistry, image analysis, enzymatic assays, gene expression profiling analysis, efficacy tests of therapeutics, culturing of enriched rare cells, and therapeutic use of enriched rare cells. In addition, depleted plasma protein and white blood cells can be optionally recovered, and subjected to other analysis such as inflammation studies, gene expression profiling, etc.

Methods and compositions are generally provided for treating metabolic disorders, e.g., obesity. One aspect discloses methods and compositions for obtaining a biological sample from the subject, evaluating the sample for the presence or absence of a genetic indicator, wherein the genetic indicator is selected from a single nucleotide polymorphism and a level of gene expression, and performing a first metabolic procedure if the genetic indicator is present, or performing an alternative second metabolic procedure if the genetic indicator is absent. One aspect discloses methods and compositions for obtaining a sample including deoxyribonucleic acids (DNA) from the subject, evaluating the DNA for an absence or presence of one or more genetic indicators and performing a first metabolic procedure or an alternative second metabolic procedure based on the absence or presence of the genetic indicator(s). Other aspects are also disclosed.

Pluri-differentiated human mesenchymal progenitor cells (MPCs) are isolated. A method isolates and purifies human mesenchymal progenitor cells from Dexter-type cultures for characterization of and uses, particularly therapeutic uses for such cells. Specifically, isolated MPCs can be used for diagnostic purposes, to enhance the engraftment of hematopoietic progenitor cells, enhance bone marrow transplantation, or aid in the treatment or prevention of graft versus host disease.

The present invention provides sets of genes the expression of which is important in the prognosis of cancer. In particular, the invention provides gene expression information useful for predicting whether cancer patients are likely to have a beneficial treatment response to chemotherapy.FHIT; MTA1; ErbB4; FUS; BBC3; IGF1R; CD9; TP53BP1; MUC1; IGFBP5; rhoC; RALBP1; STAT3; ERK1; SGCB; DHPS; MGMT; CRIP2; ErbB3; RAP1GDS1; CCND1; PRKCD; Hepsin; AK055699; ZNF38; SEMA3F; COL1A1; BAG1; AKT1; COL1A2; Wnt.5a; PTPD1; RAB6C; GSTM1, BCL2, ESR1; or the corresponding expression product, is determined, said report includes a prediction that said subject has a decreased likelihood of response to chemotherapy.

The present invention relates to a method for visualizing GFP expression in callus, various tissue and organ of the transgenic plants as image and system using the same. The said method needs no other additional genetic product, substrate or cofactor and can detect very simply and quickly GFP expression by using the said system of the present invention consisting of a CCD camera, a light source, band-pass filter and data processing computer, so it provides many advantages for selection of transgenic seeds, for studying of gene expression in the tissue or organ of plants, or for studying of specificity of each development step.

The present invention relates to the identification of a novel role of Nr-CAM in cell transformation and aberrant cellular proliferation. In particular, the present invention relates to the altered gene expression of Nr-CAM in a number of primary tumors and cell lines derived from tumors, in addition to, the altered gene expression of ligands for Nr-CAM. Further, the present invention relates, in part, to the Applicants' surprising discovery that the inhibition of Nr-CAM gene expression or the inhibition of Nr-CAM activity in transformed cells reverses the transformed phenotype.

The invention provides chimeric proteins having at least two functional protein units, each containing the dimerization domain of a member of the steroid / thyroid hormone nuclear receptor superfamily. The chimeric proteins can fold under crystallization conditions to form functional entities. The functional entities optionally contain a novel flexible peptide linker of variable lengths between at least two of the protein units. In a preferred embodiment, the linker is designed to be increased in increments of 12 amino acids each to aid in preparation of variant chimeric proteins. 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. The invention further provides nucleotide sequences encoding the invention chimeric proteins, cells containing such nucleotide sequences, and methods for using the invention chimeric proteins to modulate expression of one or more exogenous genes in a subject organism. In addition, isolated protein crystals suitable for x-ray diffraction analysis and methods for obtaining putative ligands for the invention chimeric proteins are provided.

The present invention relates to the discovery, identification and characterization of nucleotides that encode Ob receptor (ObR), a receptor protein that participates in mammalian body weight regulation. The invention encompasses obR nucleotides, host cell expression systems, ObR proteins, fusion proteins, polypeptides and peptides, antibodies to the receptor, transgenic animals that express an obR transgene, or recombinant knock-out animals that do not express the ObR, antagonists and agonists of the receptor, and other compounds that modulate obR gene expression or ObR activity that can be used for diagnosis, drug screening, clinical trial monitoring, and / or the treatment of body weight disorders, including but not limited to obesity, cachexia and anorexia.

Provided is a novel nucleic acid molecule that can be produced easily and efficiently and can inhibit the expression of a gene. The nucleic acid molecule is a single-stranded nucleic acid molecule including an expression inhibitory sequence that inhibits expression of a target gene. The single-stranded nucleic acid molecule includes: a region (X); a linker region (Lx); and a region (Xc). The linker region (Lx) is linked between the regions (Xc) and (Xc). The region (Xc) is complementary to the region (X). At least one of the regions (X) and (Xc) includes the expression inhibitory sequence. The linker region (Lx) has a non-nucleotide structure including at least one of a pyrrolidine skeleton and a piperidine skeleton. According to this single-stranded nucleic acid molecule, it is possible to inhibit the expression of the target gene.

A computer-based system and method are provided for retrieving information from a number of data sources on a computer network containing biological data. The network database is organized in a b-tree configuration having a plurality of sample nodes. Each sample node includes a curated data set of pre-formatted and pre-computed summary biological data obtained from at least one biological sample. The plurality of sample nodes are organized in a hierarchical arrangement according to clinical relevance. A set of attributes is assigned to each sample node to facilitate navigation through the database using a browser accessible through a graphical user interface. The set of attributes including at least one taxonomy designation selected from the group including tissues, diseases, medications and sample parameters. Search results that are produced include automated reports of the summary biological data stored in the sample nodes and custom reports generated using the summary biological data.

The present invention concerns prognostic markers associated with EGFR positive cancer. In particular, the invention concerns prognostic methods based on the molecular characterization of gene expression in paraffin-embedded, fixed tissue samples of EGFR-expressing cancer, which allow a physician to predict whether a patient is likely to respond well to treatment with an EGFR inhibitor.

The present invention relates to non-steroidal ligands for use in nuclear receptor-based inducible gene expression system, and a method to modulate exogenous gene expression in which an ecdysone receptor complex comprising: a DNA binding domain; a ligand binding domain; a transactivation domain; and a ligand is contacted with a DNA construct comprising: the exogenous gene and a response element; wherein the exogenous gene is under the control of the response element and binding of the DNA binding domain to the response element in the presence of the ligand results in activation or suppression of the gene.