Abstract: The present invention relates to compositions and methods for detection and quantification of individual target molecules in biomolecular samples. In particular, the invention relates to coded, labeled probes that are capable of binding to and identifying target molecules based on the probes' label codes. Methods of making and using such probes are also provided. The probes can be used in diagnostic, prognostic, quality control and screening applications.

Abstract: Concentrations of certain miRNA, mRNA and/or protein markers in the biological fluids and/or tissues of a subject are used to determine the probability that the subject does or does not have Posttraumatic Stress Disorder (PTSD). The concentrations of these markers in fluids and/or tissues are different in subjects with PTSD as compared to subjects who do not suffer from this disorder.

Abstract: Point of care methods to detect the probability or status of tuberculosis infection in individuals by determining presence or absence of one or more peptide of SEQ ID NOS:1-22 in a biological fluid of a subject are described. These methods may be assays based on affinity reagents specifically reactive with these peptides.

Abstract: A signature of proteins occurring in glioblastoma multiforme (GBM) tissue comprised of 33 cell surface proteins (GBMSig) that distinguish subjects with GBM from healthy controls with more than 98% accuracy is described. In addition, four of the members of this signature are particularly useful as blood-borne markers of GBM. Certain other members of the signature are indicators of the possible efficacy of the use of TGF-?1 inhibitors in the treatment of this condition. Methods to treat and to stratify GBM based on GBMSig proteins are also disclosed.

Abstract: Improved methods to quantitate RNA in biological or other analytical samples employ extended RNAs containing adaptors at the 5? end and polyA sequences coupled to a tag at the 3? end. The invention method is particularly useful in quantitating microRNAs as primers can be used that need not complement the non-conserved 3? ends of these molecules.

Abstract: The invention provides an unbiased method to assess the binding of a test compound to a multiplicity of proteins in the same sample, including samples from living cells by applying the unbiased determination technique of SWATH-MS or the biased technique of SRM-MS to a thermal shift assay to evaluate drug target interactions. In addition, the results created by SWATH-MS can be analyzed by SRM-MS in a biased manner to assess the binding of a test compound to a multiplicity of proteins in the same sample, including samples from living cells.

Abstract: The invention provides a method to detect an abnormal condition or disease state by assessing a characteristic response pattern of responder cells to indicators contained in a biological fluid of a subject. A characteristic disease-associated pattern can be obtained by determining the response pattern of responder cells to that of bodily fluids or fractions thereof from subjects known to exhibit a particular abnormal condition optionally comparing said pattern to such pattern elicited by fluids or fractions from normal subjects and identifying elements that differ. The identified elements constitute a characteristic or differential pattern which can then be used to identify the presence or stage of a disease in a test subject.

Abstract: Methods to detect amyotrophic lateral sclerosis (ALS) or presymptomatic Alzheimer's disease (PSAD) using an indicator cell assay platform (iCAP) in a test subject are described. Specifically, the disclosure provides a method comprising contacting a biological fluid of said test subject with indicator cells and assessing said indicator cells for the level of expression of an exon of CKIgamma2 that encodes the C-terminal palmitoylated region of said CKIgamma2, to determine the probability that a test subject is afflicted with amyotrophic lateral sclerosis (ALS). Further disclosed are methods of using indicator cells that are pan neuronal populations of glutamatergic (and/or GABAergic) neurons to determine the probability of the presence of presymptomatic or symptomatic Alzheimer's disease (PSAD) in a test subject.

Abstract: The present invention relates to compositions and methods for detection and quantification of individual target molecules in biomolecular samples. In particular, the invention relates to coded, labeled probes that are capable of binding to and identifying target molecules based on the probes' label codes. Methods of making and using such probes are also provided. The probes can be used in diagnostic, prognostic, quality control and screening applications.

Abstract: The present invention relates to a purified molecules, including antibodies, that bind specifically to murine ?-catenin phosphorylated at amino acid position Serine552 and to orthologs thereof, such as mammalian orthologs, including human orthologs. Methods of making and using such purified molecules are also provided. Kits containing such purified molecules are further provided.

Abstract: The present invention relates generally to methods for identifying organ-specific secreted proteins and for identifying organ-specific molecular blood fingerprints therefrom. As such, the present invention provides compositions comprising such proteins, detection reagents for detecting such proteins, and panels, and arrays for determining organ-specific molecular blood fingerprints.

Abstract: The present invention relates generally to methods for identifying drug side effects by detecting perturbations in organ-specific molecular blood fingerprints. The invention further relates to methods for identifying drug-specific organ-specific molecular blood fingerprints. As such, the present invention provides compositions comprising organ-specific proteins, detection reagents for detecting such proteins, and panels and arrays for determining organ-specific molecular blood fingerprints.

Abstract: The present invention relates generally to methods for identifying organ-specific secreted proteins and for identifying organ-specific molecular blood fingerprints therefrom. As such, the present invention provides compositions comprising such proteins, detection reagents for detecting such proteins, and panels, and arrays for determining organ-specific molecular blood fingerprints.

Abstract: Enhanced yields of photosynthetically fixed carbon produced by hypersaline photosynthetic algae are provided by co-culturing with a halophilic archaea. Further, methods are provided to control harvesting of desired metabolic products from hypersaline photosynthetic algae by controlling caspase activity.

Abstract: The invention provides methods for identifying polypeptides. The method can include the steps of simultaneously determining the mass of a subset of parent polypeptides from a population of polypeptides and the mass of fragments of the subset of parent polypeptides; comparing the determined masses to an annotated polypeptide index; and identifying one or more polypeptides of the annotated polypeptide index having the determined masses. The method can further include the steps of determining one or more additional characteristics associated with one or more of the parent polypeptides; comparing the determined characteristics to the annotated polypeptide index; and optionally repeating the steps one or more times, wherein a set of characteristics is determined that identifies a parent polypeptide as a single polypeptide in the annotated polypeptide index. The method can additionally include the step of quantitating the amount of the identified polypeptide in a sample containing the polypeptide.

Abstract: The invention is directed to an improved method to manufacture virus for use in vaccine by culturing infected cells that have been modified to overexpress miR-144. The invention is also directed to manipulating the activity or level of miR-144 in subjects in order to modulate the antiviral and immune response systems.

Abstract: Methods of using halogenated peptides as internal standards for liquid chromatography-mass spectrometry, and novel halogenated peptides useful for the same, are disclosed. In particular, methods of using halogenated peptides as internal standards in proteomic analyzes, as well as methods of using halogenated peptides to conduct quality control assessments of and/or to calibrate liquid chromatography-mass spectrometry systems are disclosed.

Abstract: The invention provides an efficient multiplex method for identifying binding partners of small molecules and proteins. The small molecules and proteins are tagged with a nucleic acid barcode that can be used to identify the protein or small molecule, and thereby its partner.

Abstract: Methods, compositions, and devices are disclosed which use microRNA to detect, predict, treat, and monitor physiological conditions such as disease or injury. microRNA are isolated and their differential expression is measured to provide diagnostic information. This information may then be utilized for evaluation and/or treatment purposes.

Abstract: New markers in the form of miRNA levels in plasma are provided for indicating the presence of CLL in a subject as well as suggesting routes of therapeutic treatment.