Abstract: Methods and systems for detecting chemical and biological agents using oligonucleotide aptamers. A sensor includes a detection complex between an aptamer that has a binding domain for the chemical or biological agent, and a first oligonucleotide with a sequence complementary to a region of the aptamer. In the absence of the agent, the aptamer and the first oligonucleotide form an intermediate combination. In the presence of the agent, the intermediate combination dissociates. The sensor further includes a second oligonucleotide with a sequence that interacts with a region of the first oligonucleotide to form a duplex structure only when the first oligonucleotide is dissociated from the aptamer. When the duplex structure is formed, it can interact with a reporter molecule which in turn initiates a signal reporting detection of the chemical or biological agent.

Abstract: The present invention generally relates to bacterial polypeptide display systems, libraries using these bacterial display systems, and methods of making and using these systems, including methods for improved display of polypeptides on the extracellular surface of bacteria using circularly permuted transmembrane bacterial polypeptides that have been modified to increase resistance to protease degradation and to enhance polypeptide display characteristics.

Abstract: The present invention relates to a device for determining or studying the state of stimulation of the natural defenses of plants or plant portions, which plants advantageously belong to the Rosaceae family. The corresponding device includes means for determining the expression level, in a sample of plants or plant portions, of at least one target gene in each of the following groups (a) to (i): (a) PR-1, PR-2, PR-4 PR-5, PR-8, PR-14, PR-15; (b) PAL, CHS, DFR, ANS, PPO; (c) HMGR, FPPS, Far; (d) CSL; (e) APOX, GST, POX; (f) CalS, Pect, CAD; (g EDS1, WRKY; (h) LOX2, JAR; and (i) ACCO, EIN3. Said device preferably consists of a kit which contains a determination means in the form of pairs of primers, for implementing a quantitative PCR technique.

Abstract: The present invention describes a spatial addressing technique that uses a very high-density micro-pore array for high-throughput screening of biological interactions. The therapeutic, diagnostic and drug-discovery implications of being able to identify, select and characterize specific protein-protein, protein-DNA and/or protein-carbohydrate interactions from heterogeneous populations of millions (to billions) of cells is discussed. Importantly, this technique possesses the screening and selection capacity of current display-based screening systems (i.e., millions-billions) but with greater efficiency and shorter time.

Abstract: The present invention relates generally to cinnamate crosslinkers. Specifically, the present invention relates to gels, biochips, and functionalized surfaces useful as probes, in assays, in gels, and for drug delivery, and methods of making the same using a newly-discovered crosslinking configuration.

Abstract: The invention provides methods for determining the interactions between phage-displayed proteins and test molecules. The phage-displayed proteins are contacted with a reference moiety in the presence and absence of a test molecule; the behavior of the phage-displayed proteins as a function of concentration of the test molecule permits calculation of the binding affinity of the phage-displayed protein for the test molecule.

Abstract: The present invention provides compositions including peptide display scaffolds that present at least one candidate peptide and at least one detectable moiety in at least one of the N-terminal and C-terminal candidate peptide presenting domains that when expressed in a cell are accessible at a surface of the cell outermembrane. In addition, the present invention also provides kits and methods for screening a library of cells presenting the candidate peptides in peptide display scaffolds to identify a ligand for an enzyme.

Abstract: Methods for making a combinatorial antibody library from human germline segments are provided. Also provided are libraries of nucleic acid molecules compiled from germline segments encoding VL chains and libraries of nucleic acid molecules encoding VH chains, and resulting antibody libraries. The libraries are provided as addressable libraries. Methods for screening antibody libraries against a target protein antigen, and the identified or selected antibodies are provided.

Abstract: Methods of assembling modified adenoviruses, libraries of adenoviral gene modules and compositions thereof are provided herein.

Abstract: The invention provides methods and compositions, including kits, for directional nucleic acid amplification and sequencing. The invention further provides methods and compositions for the construction of directional cDNA libraries.

Abstract: The invention provides a method of screening a library of candidate agents by contacting the library with a target in a reaction mixture under a condition of high stringency, wherein the target includes a tag that responds to a controllable force applied to the tag, and passing the members of the library through a microfluidic device in a manner that exposes the library members to the controllable force, thereby displacing members of the library that are bound to the target relative to their unbound counterparts. Kits and systems for use with the methods of the invention are also provided.

Abstract: The prognosis of a cancer patient can be determined by analyzing the modulation of expression of specified genes in the tumor tissue. Genes uniquely up-regulated in adult stem cells that can reconstitute the tissue of the tumor are analyzed for up-regulation in the patient's tumor. Up-regulation of a plurality of such genes in the tumor is an indication of good prognosis. Genes uniquely up-regulated in fetal stem cells are analyzed for up-regulation in the patient's tumor. Up-regulation of a plurality of such genes in the tumor are an indication of a poor prognosis. Specific genes are disclosed, the modulation of which, in a patient's prostate cancer tumor, will serve as an indication of prognosis. Patients with a good prognosis are subjected to watchful waiting. Patients with a poor prognosis are aggressively treated. Kits are provided containing a set of affinity reagents that specifically detect expression of the various genes.

Abstract: Panels of mammalian cell samples, kits and methods of use thereof. The panels comprise samples or sets of samples of immortalized primary cells, obtained from different tissues and organs of healthy and/or diseased donors. The cell panels are useful in assays for testing effects of drug candidates, e.g. for activity and toxicity.

Abstract: The invention provides barcode libraries and methods of making and using them including obtaining a plurality of nucleic acid constructs in which each construct comprises a unique N-mer and a functional N-mer and segregating the constructs into a fluid compartments such that each compartment contains one or more copies of a unique construct. The invention further provides methods for digital PCR and for use of barcode libraries in digital PCR.

Abstract: A label-free RF MEMS-based biosensor is described for detecting biomarkers in a given environment. The biosensor is capable of sensing the presence of biomarkers by exploiting both its mechanical and electrical characteristics. In addition, the method employed for detecting mechanical deflections due to antigen-antibody binding uses a simple electrical circuitry which allows the sensor to be used at any location and time. Such a sensor, when placed in a matrix like structure allows for the detection of multiple biomarkers simultaneously.

Abstract: Provided is a high throughput methylation detection method, particularly a combined sequence capture and bisulfite sequencing method. The method accurately and effectively analyzes the methylation status of the target area in several samples simultaneously, lowers the difficulty of probe design, enhances operation and application feasibility, and enables high throughput methylation detection of high accuracy on interested target sequences and areas in a complete genome. The method is targeted and conserves energy and time.

Abstract: The present invention provides systems and methods for identification of genes related to cancer cell growth. In particular, the present invention provides functional genomic profiling of primary patient cells for identification of targeted and efficacious patient and cell-specific treatment modalities by employing a cancer biochip system (CBCS) which demonstrates improved plating efficiency, improved transfection efficiency and improved silencing efficiency. The present invention also provides a method of classifying a cancer patient based on response of cancer cells of the patient to a plurality of active agents for prediction of efficacious treatment of the cancer patient.

Abstract: The present invention relates to a method for generating a second-generation library. In a first step, a library of encoded molecules associated with an identifier nucleic acid comprising codons identifying chemical entities that have participated in the formation of the encoded molecule is provided. In a second step, the library is partitioned and encoded molecules having a certain property are selected. Codons of identifiers of selected encoded molecules are subsequently identified, and a second-generation library is prepared using at least some of the chemical entities coded for by the identified codons. The new focussed library may be used for another partition step to select encoded molecules with a certain property.

Abstract: The invention provides methods, apparatuses, and compositions for high-throughput amplification sequencing of specific target sequences in one or more samples. In some aspects, barcode-tagged polynucleotides are sequenced simultaneously and sample sources are identified on the basis of barcode sequences. In some aspects, sequencing data are used to determine one or more genotypes at one or more loci comprising a causal genetic variant. In some aspects, systems and methods of detecting genetic variation are provided.

Abstract: A two-tiered classification system that can be integrated with the current algorithm used by pathologists for identification of the site of origin for ‘malignancy with unknown primary’ is presented. In use, morphology, immunohistochemical (IHC) studies, and microarray-based top tier gene expression classifiers first subclassify cytokeratin positive carcinomas into adenocarcinoma, squamous cell carcinoma, neuroendocrine carcinoma and urothelial carcinoma. Subsequently, organ-specific IHC-markers, if available, are used in conjunction with microarray-based second tier gene expression classifiers to assign the primary site of origin to the sample. This new hybrid approach combines IHC with a hierarchy of quantitative gene expression based classifiers into an algorithmic method that can assist pathologists to further refine and support their decision making process.