Abstract: The present invention relates to primers for the universal amplification and detection of Archaea, which primers are designed based on a multiple sequence alignment of Archaea Type II chaperonin (thermo-some) genes. For detection of Archaea having templates with a GC content of below 60%, primers are designed so that inosine residues are found at degenerate positions. For amplification of higher GC content templates, degenerate positions are replaced with specific nucleotide bases found in the high GC organism. The primers are useful for detecting, identifying and quantifying Archaea in a sample and for determining a phylogenetic relationship of a test Archaea organism.

Abstract: Disclosed herein are modified phage comprising a fusion protein located on the surface of the phage wherein the fusion protein comprises a surface protein and a post-translationally modified protein. Also disclosed are methods of making and using modified phage comprising post-translationally modified proteins located on the surface of the phage.

Abstract: A method for preparing a stool sample without any need for complicated operations is provided which is capable of efficiently recovering a nucleic acid originating from mammalian cells, such as the cells exfoliated from the large intestine, in the stool. A solution for preparing a stool sample and a kit for stool collection are also provided. The collected stool is mixed with a solution for preparing a stool sample which has a water-soluble organic solvent as an active ingredient. A method is disclosed for recovering a nucleic acid including recovering a nucleic acid originating from indigenous enteric bacterium and a nucleic acid originating from an organism other than indigenous enteric bacterium at the same time from the stool sample prepared by the preparation method.

Abstract: The present invention provides systems for identifying genes and gene products associated with nitrogenous bisphosphonate treatment (NBP) treatment of calcium disorders. The invention also provides systems for identify and/or characterizing agents in treating calcium disorders. The invention further provides systems for diagnosing a calcium disorder and monitoring treatment of a subject.

Abstract: Described herein are techniques for assembling a polynucleotide encoding a transcription activator-like effector nucleases (TALEN). The techniques ligate and digest necessary modules for a TALEN assembly in one reactor or system. Methods and Kits for generating a TALEN are also described.

Abstract: The present disclosure provides an improvement to quantitative Nuclease Protection Assay (qNPA) and quantitative Nuclease Protection Sequencing (qNPS) methods. The disclosed methods use nuclease protection probes (NPPs) that include 5?-end and/or 3-end flanking sequences, which provide a universal hybridization and/or amplification sequence. The disclosed methods can be used to sequence or detect target nucleic acid molecules, such as those present in fixed or insoluble samples.

Abstract: Prognostic methods useful in assessing patients who have received a transplant and reagents that can be used to carry out those methods are provided. The inventions are based, in part, on our analysis of gene expression in renal allografts and clinical parameters, i.e., variables associated with the donor, the recipient and/or the graft. The genes that can be assessed include those encoding agents that mediate inflammation, immune activation, and cell death (we may refer to these genes as “inflammatory”, “immune” or “cytoprotective”). Surprisingly, the levels of gene expression could predict the occurrence of DGF, AR, and the quality of later graft function even when analyzed shortly after (e.g., after vascular anastomosis and tissue reperfusion). We also found that clinical parameters available at the time of transplantation correlate with decreased graft health and can be considered in combination with gene expression to evaluate a patient's risk for an adverse outcome.

Abstract: A method for detecting a target nucleic acid of a pathogen in a test sample, the method comprising preparing a target nucleic acid detecting reagent and contacting the target nucleic acid detecting reagent with an oligonucleotide microarray. A kit for detecting a target nucleic acid of a pathogen in a test sample is also described. The kit comprises at least one primer pair and an oligonucleotide microarray comprising at least one probe.

Abstract: The present invention provides a novel, highly sensitive and specific probe panel which detects the type of renal cortical neoplasm present in a biopsy sample. As such, the invention permits diagnosis of the predominant subtypes of renal cortical neoplasms without the use of invasive methods. The present invention further provides a molecular cytogenetic method for detecting and analyzing the type of renal cortical neoplasm present in a renal biopsy sample.

Abstract: The present invention relates to automated devices and methods for the amplification of segments of nucleic acid in a convenient and portable manner. A single-use nucleic acid amplification device for producing an amplicon includes a housing and an amplification chamber. The chamber includes an ingress with a first reversible seal, an egress with a second reversible seal, a sealable sample entry orifice, and a first wall forming a portion of the chamber. The first wall includes a thermally conductive material and includes an interior surface and an exterior surface. The exterior surface includes a heating circuit and a temperature sensor. The sample entry orifice permits a sample of nucleic acid to enter the amplification chamber. The ingress is connected to a first conduit along with a pneumatic pump and a fluid pouch. The egress is connected to a second conduit permitting egress of the amplicon from the amplification chamber.

Abstract: The problem to be solved by the present invention is to provide a highly-efficient transformation technology, specifically, a highly-efficient promoter used for transforming algae, a vector comprising the promoter, and a method for transforming algae by using the vector. The promoter according to the present invention is characterized in comprising a polynucleotide constituting a non-coding region located upstream of a gene encoding a structural protein of a ClorDNA virus, and the like.

Abstract: The present invention relates to methods, compositions and systems for detecting perchlorate in a sample. Compositions useful for detecting perchlorate in a sample include those comprising a perchlorate reductase, a reductant and an electron shuttle. In an exemplary embodiment, the composition comprises perchlorate reductase from Dechloromonas agitata, reduced nicotinamide adenine dinucleotide and N-methylphenazinium methylsulfate. The present invention also provides for methods of using the compositions disclosed herein, as well as systems thereof. In some exemplary embodiments, the methods comprise a concentration step, in which, for example, the sample is contacted with a cationic solid phase extraction column. Employing this step provides certain advantages such as a lowered detection limit and the removal of contaminants.

Abstract: A system and method of quantitating the concentration of a molecule of interest in one embodiment includes establishing a plurality of test environments at a plurality of test sites, each of the plurality of test environments associated with one of a plurality of response curves, each of the plurality of response curves different from the other of the plurality of response curves, storing a combined response curve resulting from a summation of the plurality of response curves, exposing the plurality of test sites to a sample having a concentration of a molecule of interest, obtaining a plurality of quantitation signals, each of the plurality of quantitation signals associated with one of the plurality of test sites, associating a summation of the plurality of quantitation signals with the stored combined response curve, and generating a signal related to the concentration of the molecule of interest based upon the association.

Abstract: The invention provides compositions and methods for the differential detection of high risk forms of HPV from a urine sample provided by a patient. Specifically, the invention provides primers and probes that specifically recognize and bind sequences within the E1 gene of HPV. Detection of high risk forms of HPV identify individuals at risk of developing or in the early stages of cervical carcinoma.

Abstract: The present invention provides expression vectors and helper display vectors which can be used in various combinations as vector sets for display of polypeptides on the outer surface of eukaryotic host cells. The expression vector of the invention can be used alone for soluble expression without having to change or reengineer the display vectors. The display systems of the invention are particularly useful for displaying a genetically diverse repertoire or library of polypeptides on the surface of yeast cells, and mammalian cells.

Abstract: A biosensor for use in detecting the presence of diseases, the biosensor comprising a detector for detecting a presence of at least one marker indicative of a specific disease. A method of determining efficacy of a pharmaceutical for treating a disease or staging disease by administering a pharmaceutical to a sample containing markers for a disease, detecting the amount of at least one marker of the disease in the sample, and analyzing the amount of the marker in the sample, whereby the amount of marker correlates to pharmaceutical efficacy or disease stage. Markers for gynecological disease selected from the list in Table 8. An immuno-imaging agent comprising labeled antibodies, whereby the labeled antibodies are isolated and reactive to proteins overexpressed in vivo. Informatics software for analyzing the arrays of claim 17, the software including analyzing means for analyzing the arrays.

Abstract: The invention relates to methods of affinity maturing antibodies.

Abstract: A method for assessment of the suitability of and/or effectiveness of a target therapy for a gastrointestinal-related disorder, such as Crohn's disease, in a subject evaluates the presence, absence, and/or magnitude of expression of one or more genes in a 10-member gene panel in a sample. The method enables identification of the effectiveness of target therapies prior to or after starting a patient on such therapies.

Abstract: Disclosed are methods of selecting phage encoding a target binding protein. The methods can include forming a mixture comprising a plurality of diverse display phage, a target, and a support, and forming phage immobilized to the support, each of which comprises a phage which binds the target and the target immobilized to the support. Phage that do not bind to the target are separated. Host cells are contacted with the phage immobilized to the support via binding to the target so that the host cells are infected by the phage immobilized to the support. Replicate phage are produced from the infected cells in the presence of the target immobilized to the support, thereby forming replicate phage immobilized to the support via binding to the support. Replicate phage that do not bind to the target are separated. Host cells are contacted with the replicate phage immobilized to the support.

Abstract: Described are methods and means for enhancing enzyme activity toward insoluble substrates. This is achieved by means of in vitro compartmentalization in which an insoluble microparticle functions both as the enzyme substrate and as a structure for negative selection. Enhanced enzymes expressed from a microparticle-linked polynucleotide library preferentially degrade the microparticle releasing specific gene variants into solution. Gene variants encoding less active enzyme variants remain linked to the microparticle and may be removed through centrifugation, thus enriching the polynucleotide library for more active enzyme variants. These methods may be used to enhance cellulase and ligninase activity toward insoluble cellulosic biomass.