Abstract: Abstract of the Disclosure The invention is directed to a new class of biomarker in patient samples comprising dimers of ErbB cell surface membrane receptors. In one aspect, the invention includes a method of determining the status of a disease or healthful condition by correlating such condition to amounts of one or more dimers of ErbB cell surface membrane receptors measured directly in a patient sample, in particular a fixed tissue sample. In another aspect, the invention includes a method of determining a status of a cancer in a specimen from an individual by correlating measurements of amounts of one or more dimers of ErbB cell surface membrane receptors in cells of the specimen to such status, including presence or absence of a pre-cancerous state, presence or absence of a cancerous state, prognosis of a cancer, or responsiveness to treatment.

Abstract: Abstract of the Disclosure The invention is directed to a new class of biomarker in patient samples comprising dimers of ErbB cell surface membrane receptors. In one aspect, the invention includes a method of determining the status of a disease or healthful condition by correlating such condition to amounts of one or more dimers of ErbB cell surface membrane receptors measured directly in a patient sample, in particular a fixed tissue sample. In another aspect, the invention includes a method of determining a status of a cancer in a specimen from an individual by correlating measurements of amounts of one or more dimers of ErbB cell surface membrane receptors in cells of the specimen to such status, including presence or absence of a pre-cancerous state, presence or absence of a cancerous state, prognosis of a cancer, or responsiveness to treatment.

Abstract: The invention provides a method for detecting the presence of anti-therapeutic antibody antibodies in a patient being treated with a therapeutic antibody.

Abstract: The invention is directed to a new class of biomarker in patient samples comprising dimers of ErbB cell surface membrane receptors. In one aspect, the invention includes a method of determining the status of a disease or healthful condition by correlating such condition to amounts of one or more dimers of ErbB cell surface membrane receptors measured directly in a patient sample, in particular a fixed tissue sample. In another aspect, the invention includes a method of determining a status of a cancer in a specimen from an individual by correlating measurements of amounts of one or more dimers of ErbB cell surface membrane receptors in cells of the specimen to such status, including presence or absence of a pre-cancerous state, presence or absence of a cancerous state, prognosis of a cancer, or responsiveness to treatment.

Abstract: This invention relates to a novel microfluidic device and methods of using this device to conduct in vitro studies on the reaction and effects of various compounds on cells. More particularly, it relates to a method for using stop flow in a microfluidic system to study the effect of compounds on individual cells. It also provides a method for observing the effects of candidate compounds on leukocyte rolling.

Abstract: Methods are provided for detecting the formation of complexes of molecules, especially proteins, in a sample, such as a cell or tissue lysate. In one aspect, a cleaving probe specific for a first protein in a complex and one or more binding compounds specific for one or more second proteins in a complex are provided. Upon binding, the cleaving probe is induced to generate an active species, such as singlet oxygen, that cleaves molecular tags attached to the binding compounds only in the local region of the cleaving probe. The released molecular tags are separated from the assay mixture and from one another to provide a readout that is related to the number and types of proteins present in the complex.

Abstract: A photoactivation apparatus (200) separately delivers light to a plurality of wells of a multiwell plate (110). The device-includes a plurality of light emitting diodes (210) attached to a first surface of a substrate (220) such that when the photoactivation apparatus is positioned on the multiwell plate each of the light emitting diodes delivers light to one corresponding well. The light emitting diodes (210) may extend at least partially into the wells of the multiwell plate. A heat sink (250) and fan may be provided on the device to dissipate heat generated by the light emitting diodes. The components are preferably enclosed in a conveniently-sized housing (270). The housing may include one or more grips and air vents. The apparatus includes an interlocking lip (230) defining a recess which is sized to receive at least a portion of the multiwell plate. A power supply connected to the apparatus and configured to provide an equal voltage across each of the light emitting diodes.

Abstract: The invention is directed to a new class of biomarker in patient samples comprising dimers of cell surface membrane receptors. In one aspect, the invention includes a method of determining the status of a disease or healthful condition by correlating such condition to amounts of one or more dimers of cell surface membrane receptors measured directly in a patient sample, in particular a fixed tissue sample. In another aspect, the invention includes a method of determining a status of a cancer in a specimen from an individual by correlating measurements of amounts of one or more dimers of cell surface membrane receptors in cells of the specimen to such status, including presence or absence of a pre-cancerous state, presence or absence of a cancerous state, prognosis of a cancer, or responsiveness to treatment. Preferably, methods of the invention are implemented by using sets of binding compounds having releasable molecular tags that are specific for multiple components of one or more types of receptor dimers.

Abstract: The invention is directed to a new class of biomarker in patient samples comprising heterodimers of Her cell surface membrane receptors. In one aspect, the invention includes a method of determining the status of a disease or healthful condition by correlating such condition to amounts of one or more heterodimers of ErbB, or Her, cell surface membrane receptors measured directly in a patient sample, in particular a fixed tissue sample. In another aspect, the invention includes a method of determining a status of a cancer in a specimen from an individual by correlating measurements of amounts of one or more heterodimers of ErbB cell surface membrane receptors in cells of the specimen to such status, including presence or absence of a pre-cancerous state, presence or absence of a cancerous state, prognosis of a cancer, or responsiveness to treatment.

Abstract: The invention provides a method for determining a disease status of a patient by measuring expression levels of selected intracellular complexes. In one aspect of the invention, the activation status of apoptotic pathways in a patient sample is determined by measuring relative amounts of protein-protein complexes that are characteristic of the apoptotic pathways. In particular, the invention provides a method of determining the activation status of the mitochondrial apoptotic pathway by simultaneously measuring relative amounts of complexes between 14-3-3 proteins and BAD proteins on the one hand and complexes of Bcl-2 proteins and BAD proteins on the other hand. Preferably, methods of the invention are implemented by using sets of binding compounds having releasable molecular tags that are specific for multiple components of one or more complexes formed within apoptotic pathways. After binding, molecular tags are released and separated from the assay mixture for analysis.

Abstract: The invention is directed to a new class of biomarker in patient samples comprising dimers of ErbB cell surface membrane receptors. In one aspect, the invention includes a method of determining the status of a disease or healthful condition by correlating such condition to amounts of one or more dimers of ErbB cell surface membrane receptors measured directly in a patient sample, in particular a fixed tissue sample. In another aspect, the invention includes a method of determining a status of a cancer in a specimen from an individual by correlating measurements of amounts of one or more dimers of ErbB cell surface membrane receptors in cells of the specimen to such status, including presence or absence of a pre-cancerous state, presence or absence of a cancerous state, prognosis of a cancer, or responsiveness to treatment.

Abstract: Methods for the multiplexed detection of the binding of, or interaction between, one or more ligands and target antiligands are provided. Detection involves the release of identifying tags as a consequence of target recognition. The methods include the use of electrophoretic tag probes or e-tag probes, comprising a detection region and a mobility-defining region called the mobility modifier, both linked to a target-binding moiety. In practicing the methods, target antiligands are contacted with a set of e-tag probes and the contacted antiligands are treated with a selected cleaving agent resulting in a mixture of e-tag reporters and uncleaved and/or partially cleaved e-tag probes. The mixture is exposed to a capture agent effective to bind to uncleaved or partially cleaved e-tag probes, followed by electrophoretic separation. In a multiplexed assay, different released e-tag reporters may be separated and detected providing for target identification.

Abstract: Families of compositions are provided as labels, referred to as eTag reporters for attaching to polymeric compounds and assaying based on release of the eTag reporters from the polymeric compound and separation and detection. For oligonucleotides, the eTag reporters are synthesized at the end of the oligonucleotide by using phosphiste or phosphate chemistry, whereby mass-modifying regions, charge-modifying regions and detectable regions are added sequentially to produce the eTag labeled reporters. By using small building blocks and varying their combination large numbers of different eTag reporters can be readily produced attached to the oligonucleotide of interest for identification. Protocols are used that release the eTag reporter when the target sequence is present in the sample.

Abstract: Families of compositions are provided as labels, referred to as eTag reporters for attaching to polymeric compounds and assaying based on release of the eTag reporters from the polymeric compound and separation and detection. For oligonucleotides, the eTag reporters are synthesized at the end of the oligonucleotide by using phosphite or phosphate chemistry, whereby mass-modifying regions, charge-modifying regions and detectable regions are added sequentially to produce the eTag labeled reporters. By using small building blocks and varying their combination large numbers of different eTag reporters can be readily produced attached to a binding compound specific for the target compound of interest for identification. Protocols are used that release the eTag reporter when the target compound is present in the sample.

Abstract: Cytochrome P-450 assay methods and kits for the methods are provided employing a cytochrome P-450 enzyme, substrates characterized by having an oxidizable methylene group oxidized to an aldehyde and a fluorescent hydrazine. A fluorescent hydrazine is added to the reaction mixture and the resulting hydrazone analyzed by capillary electrophoresis. The method finds use in evaluating compounds for enzyme modulating activity.

Abstract: Methods, compositions and kits are disclosed for determining one or more target polypeptides in a sample where the target polypeptides have undergone a post-translational modification. A mixture comprising the sample and a first reagent comprising a cleavage-inducing moiety and a first binding agent for a binding site on a target polypeptide is subjected to conditions under which binding of respective binding moieties occurs. The binding site is the result of post-translational modification activity involving the target polypeptide. The method may be employed to determine the target polypeptide itself. In another embodiment the presence and/or amount of the target polypeptide is related to the presence and/or amount and/or activity of an agent such as an enzyme involved in the post-translational modification of the target polypeptide.

Abstract: Compositions for the multiplexed detection of the binding of, or interaction between, one or more ligands and target antiligands are provided. The compositions include one or more uncleaved or partially cleaved electrophoretic tag (e-tag) probes from a set of e-tag probes, at least one e-tag reporter out of a possible set of e-tag reporters and a capture agent. Detection involves the release of identifying tags as a consequence of target recognition. The e-tag probes comprise a detection region and a mobility-defining region called the mobility modifier, both linked to a target-binding moiety. Target antiligands are contacted with a set of e-tag probes and the contacted antiligands are treated with a selected cleaving agent resulting in a mixture of e-tag reporters and uncleaved and/or partially cleaved e-tag probes. The mixture is exposed to a capture agent effective to bind to uncleaved or partially cleaved e-tag probes, followed by electrophoretic separation.

Abstract: Cytochrome P-450 assay methods and kits for the methods are provided employing a cytochrome P-450 enzyme, substrates characterized by having an oxidizable methylene group oxidized to an aldehyde and a fluorescent hydrazine. A fluorescent hydrazine is added to the reaction mixture and the resulting hydrazone analyzed by capillary electrophoresis. The method finds use in evaluating compounds for enzyme modulating activity.

Abstract: Methods for the multiplexed detection of the binding of, or interaction between, one or more ligands and target antiligands are provided. Detection involves the release of identifying tags as a consequence of target recognition. The methods include the use of electrophoretic tag probes or e-tag probes, comprising a detection region and a mobility-defining region called the mobility modifier, both linked to a target-binding moiety. In practicing the methods, target antiligands are contacted with a set of e-tag probes and the contacted antiligands are treated with a selected cleaving agent resulting in a mixture of e-tag reporters and uncleaved and/or partially cleaved e-tag probes. The mixture is exposed to a capture agent effective to bind to uncleaved or partially cleaved e-tag probes, followed by electrophoretic separation. In a multiplexed assay, different released e-tag reporters may be separated and detected providing for target identification.

Abstract: An improved absorbance or detection cell for a microfluid device, and in accordance with an aspect of the invention, the absorbance cell comprises a bottom plate having a channel bearing surface in which a channel having a fluid inlet and fluid outlet is defined, a top plate having a channel facing surface bound to the channel bearing surface of the bottom plate and first and second reflecting elements formed on opposed sides of the channel to form a waveguide through which the channel extends such that radiation propagating along the waveguide makes multiple passes across the channel, the waveguide having a radiation input end and a radiation output end.