Abstract: The present invention provides methods for protein engineering. Specifically, the invention provides methods utilizing site evaluation libraries to design libraries that optimize two or more properties of a protein.

Abstract: Provided is a DNA molecule comprising a multicistronic transcription unit coding for i) a selectable marker polypeptide functional in a eukaryotic host cell, and for ii) a polypeptide of interest, the polypeptide of interest having a translation initiation sequence separate from that of the selectable marker polypeptide, wherein the coding sequence for the polypeptide of interest is downstream from the coding sequence for the selectable marker in the multicistronic transcription unit, and the nucleic acid sequence coding for the selectable marker polypeptide comprises a mutation that decreases the translation efficiency of the selectable marker in a eukaryotic host cell. Also provided are methods for obtaining host cells expressing a polypeptide of interest, the host cells comprising the described DNA molecules. Further provided is the production of polypeptides of interest, comprising culturing host cells comprising the DNA molecules hereof.

Abstract: Compositions and methods are provided for ligating polynucleotides having a length that is greater than 8 nucleotides on an RNA splint. The ligation reaction provides consistent results in high or low ATP concentrations. The reaction can occur rapidly and is generally at least 10 fold more efficient than T4DNA ligase under optimal conditions for T4DNA ligase and the reaction time is less than 6 hours for example, less than 1 hour.

Abstract: The invention provides for carrying out 3-dimensional similarity searching by comparing a probe molecule to each member of a 3-dimensional database. The probe molecule is overlapped with each member of a database of molecules and then the database molecule is rotated and translates until its similarity with the probe molecule is maximized. The system can contain ten different scoring functions to rate the similarity between the two molecules. Each function employs different molecular features when scoring a particular comparison. Some methods are based on the relative shape of the two molecules, and some are based on the overlap of key atoms such as oxygen, nitrogen, sulfur, and/or halogens.

Abstract: A method for identifying persons with increased risk of developing type 1 diabetes mellitus, or having type I diabetes mellitus, utilizing selected biomarkers described herein either alone or in combination. The present disclosure allows for broad based, reliable, screening of large population bases. Also provided are arrays and kits that can be used to perform such methods.

Abstract: The present invention refers to a method for identifying hetero-multimeric ubiquitins with binding capability to a ligand. Furthermore, the invention provides DNA libraries encoding for a population of said hetero-multimeric ubiquitins as well as protein libraries obtained by expression of said DNA libraries, cells and phages containing said DNA or proteins, polynucleotides encoding for said fusion proteins and vectors comprising said polynucleotides. Further new binding proteins based on hetero-multimeric ubiquitin being able to bind specifically with high affinity to selected ligands are provided.

Abstract: The present invention relates generally to a method for screening a subject for the onset, predisposition to the onset and/or progression of a colorectal neoplasm by screening for modulation in the level of expression of one or more nucleic acid markers. More particularly, the present invention provides a method for screening a subject for the onset, predisposition to the onset and/or progression of a colorectal neoplasm by screening for modulation in the level of expression of one or more gene markers in membranous microvesicles. The expression profiles of the present invention are useful in a range of applications including, but not limited to, those relating to the diagnosing and/or monitoring of colorectal neoplasms, such as colorectal adenoma and adenocarcinomas.

Abstract: Provided herein is a method for detecting the presence or absence of a cancer in a biological sample of an individual, by determining the level of mutation and methylation of one or more genes from a group of genes comprising TP53, CTNNB1, hTERT, RASSF1A, GSTP1, p16, p15 and SFRP-1. Also provided herein is an assay to detect p53 mutations suitable for DNA isolated from biological body fluid in order to screen cancer patients. Also provided is a method for detecting the presence or absence of a liver cancer in an individual by determining the level of methylation. Also provided is a suitable method for detecting the presence or absence of a liver cancer in an individual by determining the level of methylation of the promoter of the GSTP1 gene in body fluid such as urine or blood. Also provided is a suitable method for detecting the presence or absence of a liver cancer in an individual by determining the level of methylation of the promoter of the RASSF1A gene in body fluid such as urine or blood.

Abstract: The invention provides a novel cell line development method useful to screen for recombinant protein production. The method utilizes a membrane-anchored reporter or an intracellular reporter residing in the expression vector for a gene of interest to facilitate initial cell selection by FACS or MACS. A switching mechanism can be used to delete the reporter from the chromosome by providing an appropriate DNA recombinase, which turns the selected cells into production cells that secrete the protein of interest without co-expression of the reporter.

Abstract: The invention describes the integration of polynucleotides into chromosomal DNA of S. spinosa species, which are useful for the production of insecticides, integrants thereof, and also to the use of the integrants. The invention includes the stable integration and expression of an oxygen-binding protein, VHb, which results in increased spinosyn production.

Abstract: A proteinaceous particle, for example a bacteriophage, ribosome or cell, displaying on its surface a T-cell receptor (TCR). The displayed TCR is preferably a heterodimer having a non-native disulfide bond between constant domain residues. Such display particles may be used for the creation of diverse TCR libraries for the identification of high affinity TCRs. Several high affinities are disclosed.

Abstract: Provided herein are methods and systems for characterizing a phenotype by detecting microRNAs, vesicles, or biomarkers that are indicative of disease or disease progress. The disease can be a gastrointestinal disorder, such as colorectal cancer. The microRNAs, vesicles, or biomarkers can be detected in a bodily fluid.

Abstract: Methods for the detection and screening of esophageal adenocarcinoma (EAC) patients and for the monitoring of EAC treatment using a panel or panels of small molecule metabolite biomarkers are disclosed. In other aspects, methods for detection and screening for the progression of high-risk conditions (BE and HGD) to EAC and to monitoring treatment using a panel or panels of small molecule metabolite biomarkers are disclosed. The biomarkers are sensitive and specific for the detection of EAC, and can also be used to classify Barrett's esophagus (BE) and high-grade dysplasia (HGD), which are widely regarded as precursors of EAC.

Abstract: Provided is a photoamplified fluorescence turn-off assay where a masked photosensitizer is mixed with a fluorescent molecule. This mixture is brightly fluorescent because the masked photosensitizer is not capable of quenching the fluorophore. When the photosensitizer is released and amplified, the photosensitizer quenches the emission of fluorophores very efficiently.

Abstract: The present invention provides methods for personalized therapeutic management of a disease in order to optimize therapy and/or monitor therapeutic efficacy. In particular, the present invention comprises measuring an array of one or a plurality of biomarkers at a plurality of time points over the course of therapy with a therapeutic agent to determine a mucosal healing index for selecting therapy, optimizing therapy, reducing toxicity, and/or monitoring the efficacy of therapeutic treatment. In certain instances, the therapeutic agent is a TNF? inhibitor for the treatment of a TNF?-mediated disease or disorder.

Abstract: The present invention provides methods of determination of a global DNA methylation index (GDMI) in a sample from a subject, using a variety of methods which can detect global, genome-wide, and gene-specific DNA methylation to create methylation portraits that can be used for early detection, diagnosis, and clinical management in the personalized medicine space. Further, the invention provides methods of diagnosis of cancer, including gastric cancer and hepatocellular cancer in a subject, by comparing the GDMI in a sample obtained from a subject to the methylation index of standard controls. These methods allow diagnosis of gastric carcinoma and liver cancer in patients who may be asymptomatic or have inconclusive pathology, and allowing earlier treatment of the subject.

Abstract: The present disclosure provides a cover sheet for a microarray reaction device. In one aspect, the present cover sheet or device ensures the reaction units/volumes are stable and/or consistent among assay samples and assay runs, allowing samples (e.g., reaction solutions) to be conveniently added and distributed uniformly.

Abstract: A method for treating a human subject afflicted with multiple sclerosis or a single clinical attack consistent with multiple sclerosis with a pharmaceutical composition comprising glatiramer acetate and a pharmaceutically acceptable carrier, comprising the steps of determining whether the human subject is a glatiramer acetate responder by evaluating a biomarker selected from the group consisting of IL-17 concentration, TNF-? concentration, IL-2 concentration and IFN-? concentration, or a combination thereof, in the blood of the human subject and administering the pharmaceutical composition comprising glatiramer acetate and a pharmaceutically acceptable carrier to the human subject only if the human subject is identified as a glatiramer acetate responder.

Abstract: The present invention relates generally to the fields of pathological muscle pain/fatigue conditions. More specifically, the invention concerns methods and compositions useful for diagnosing and treating pathological muscle pain/fatigue conditions.

Abstract: The present invention relates to combinations of fluorescent dyes used in molecular biology, particularly in multiplex PCR. In particular, the present invention relates to a combination of dyes for amplification reactions, wherein at least four different dyes are used, wherein the first dye is 5-FAM or 6-FAM or a blend thereof, the second dye is selected from the group consisting of DY-530, HEX, CAL Fluor Orange 560 and ATTO 532, the third dye is selected from the group consisting of ATTO 550, DY-555 and DY-556, the fourth dye is selected from the group consisting of ROX, DY-510XL and ATTO 565, and optionally a fifth dye is selected from the group consisting of DY 632 and DY-520XL.

Abstract: The present invention provides a method for identifying a tumor as likely to metastasize, or likely to have metastasized, comprising obtaining a sample of the tumor and quantitating alternatively spliced mRNA isoforms of a cell motility gene, a cell adhesion gene and/or an actin cytoskeletal remodeling gene in the sample, or any specified genes or the level of RNA binding proteins compared to a predetermined non-metastasizing control.

Abstract: The present invention provides a method for detecting or enriching for a target deoxyribonucleic acid (DNA) present in a nucleic acid sample, said method comprising: (a) fragmenting a nucleic acid sample to generate nucleic acid fragments including a target fragment containing said target DNA and non-specifically ligating an adaptor sequence to an end of said fragments; (b) rendering said fragments at least partially single-stranded; (c) contacting the at least partially single-stranded fragments of step (b) with oligonucleotides A and B of a single target-specific nucleic acid probe; (d) ligating oligonucleotide B of said probe to the part of the single-stranded portion of said target fragment which is hybridised to oligonucleotide A of said probe to produce a probe-target fragment hybrid; and (e) detecting or enriching for said probe-target fragment hybrid.

Abstract: Methods of characterizing a nucleic acid library by digital assay.

Abstract: The present invention provides antibody-based arrays for detecting the activation state and/or total amount of a plurality of signal transduction molecules in rare circulating cells and methods of use thereof for facilitating cancer prognosis and diagnosis and the design of personalized, targeted therapies.

Abstract: Methods for the detection and screening of esophageal adenocarcinoma (EAC) patients and for the monitoring of EAC treatment using a panel or panels of small molecule metabolite biomarkers are disclosed. In other aspects, methods for detection and screening for the progression of high-risk conditions (BE and HGD) to EAC and to monitoring treatment using a panel or panels of small molecule metabolite biomarkers are disclosed. The biomarkers are sensitive and specific for the detection of EAC, and can also be used to classify Barrett's esophagus (BE) and high-grade dysplasia (HGD), which are widely regarded as precursors of EAC.

Abstract: Fluid analyte sensors include a photoelectrocatalytic element that is configured to be exposed to the fluid, if present, and to respond to photoelectrocatalysis of at least one analyte in the fluid that occurs in response to impingement of optical radiation upon the photoelectrocatalytic element. A semiconductor light emitting source is also provided that is configured to impinge the optical radiation upon the photoelectrocatalytic element. Related solid state devices and sensing methods are also described.

Abstract: The invention provides methods and compositions for detecting dicarboxylic acids using a transcription factor biosensor.

Abstract: The present invention provides methods for protein engineering. Specifically, the invention provides methods utilizing site evaluation libraries to design libraries that optimize two or more properties of a protein.

Abstract: Provided are methods of detecting cancer or pre-cancerous conditions in patients comprising assaying a patient sample for an elevated level of target molecules representative of expression of nucleosome assembly protein 1-like 1 (NAP1L1), wherein elevated levels of expression of NAP1L1 are indicative of a cancer of the colon, or a precancerous condition of the colon. Also provided are similar methods using panels of biomarkers such as HMGB1; PHB; RPL6; NAP1L1 and CK18. The invention also provides a method for assessing effectiveness of a therapy or putative therapy, methods of staging cancer and assessing progression of a cancer and methods of determining an appropriate cancer treatment regimen.

Abstract: Provided are methods, nucleic acids, and arrays for assessing the susceptibility of a subject to the development of ototoxicity in response to receiving one or more platinum-coordinating compounds, the method including determining the presence or absence of one or more polymorphisms, wherein the presence or absence of one or more such polymorphisms is indicative of susceptibility to the development of ototoxicity.

Abstract: Region shuffling methods for efficiently introducing diversity and exploring sequence space are described. Libraries produced directly from these methods contain high fractions of protein variants harboring multiple beneficial mutations. Typically, the methods produce these variants efficiently without the need for sequencing beneficial mutants identified at intermediate stages of the process.

Abstract: Methods for diagnosing the presence of a disorder, such as prostate cancer, in a subject are provided, such methods including detecting the relative frequency of expression of RNA biomarkers in a biological sample obtained from the subject using RNA-seq technology and comparing the relative levels of expression with predetermined threshold levels. Levels of expression of at least two of the RNA biomarkers that are above the predetermined threshold levels are indicative of the presence of prostate cancer in the subject.

Abstract: The invention provides compounds of general formulae (I)-(IV) or pharmaceutically acceptable salts thereof: The invention also provides methods of preparing the compounds, pharmaceutical compositions comprising the compounds and use of the compounds for the preparation of medicaments intended to modulate the activity of one or more members of the G-protein coupled receptor (GPCR) class. Compounds of the invention may be used to create a compound library for use in screening for agents which modulate signalling through GPCRs.

Abstract: The disclosure provides bisindole suitable for inhibiting lipoxygenases or A?-formation, and treating associated diseases, such as Alzheimer's disease. The bisindoles are indolo[2,3-b]carbazole derivatives, and may be administered to a patient as part of a pharmaceutical formulation.

Abstract: In alternative embodiments, the invention provides nucleic acid sequences that are genetic polymorphic variations of the human TMEM216 gene, and TMEM216 polypeptide encoded by these variant alleles. In alternative embodiments, the invention provides methods of determining or predicting a predisposition to, or the presence of, a ciliopathy (or any genetic disorder of a cellular cilia or cilia anchoring structure, basal body or ciliary function) in an individual, such as a Joubert Syndrome (JS), a Joubert Syndrome Related Disorder (JSRD) or a Meckel Syndrome (MKS). In alternative embodiments, the invention provides compositions and methods for the identification of genetic polymorphic variations in the human TMEM216 gene, and methods of using the identified genetic polymorphisms and the proteins they encode, e.g., to screen for compounds that can modulate the human TMEM216 gene product, and possibly treat JS, JSRD or MKS.

Abstract: According to various embodiments, a method is provided that comprises washing an array of DNA-coated beads on a substrate, with a wash solution to remove stacked beads from the substrate. The wash solution can include inert solid beads in a carrier. The DNA-coated beads can have an average diameter and the solid beads in the wash solution can have an average diameter that is at least twice the diameter of the DNA-coated beads. The washing can form dislodged DNA-coated beads and a monolayer of DNA-coated beads. In some embodiments, first beads for forming an array are contacted with a poly(ethylene glycol) (PEG) solution comprising a PEG having a molecular weight of about 350 Da or less. In some embodiments, slides for forming bead arrays are provided as are systems for imaging the same.

Abstract: Electrochemical experiments are performed on a collection of samples by suspending a drop of electrolyte solution between an electrochemical experiment probe and one of the samples that serves as a test sample. During the electrochemical experiment, the electrolyte solution is added to the drop and an output solution is removed from the drop. The probe and collection of samples can be moved relative to one another so the probe can be scanned across the samples.

Abstract: The invention relates to the surprising find that low density lipoprotein receptor-deficient mice (LDLr?/?) mice when fed with high energy diets produce controllable and consistent diabetic complications, especially renal damage, similar to the human pathophysiology and biological response. The invention thus comprises a method for discovering a preventive or therapeutic regimen for the prevention or treatment of diabetic micro- or macrovascular complications, comprising the steps of: a. feeding LDLr?/? mice, which have not been treated with streptozotocin, with a high energy diet; b. before, during and/or after this diet treating the mice with the preventive or therapeutic regimen; c. checking whether any change in the micro- or macrovascular system of the animal occurs. Specifically in such a method renal damage is assessed. Also use of said mice fed with a high energy diet for studying the diabetic micro- and macrovascular complications is part of the invention.

Abstract: Methods for diagnosis of Kawasaki disease (KD) are disclosed. In particular, the invention relates to the use of biomarkers for aiding diagnosis, prognosis, and treatment of KD, and more specifically to biomarkers that can be used to distinguish KD from other inflammatory diseases, including infectious illness and acute febrile illness.

Abstract: Compositions and methods useful for the diagnosis and treatment of juvenile idiopathic arthritis are disclosed.

Abstract: A method and system for amplifying non-coding RNA, microRNA, and small polynucleotide sequences through the generation of a pool of signature sequences to the target sequences. The target sequences can be amplified through DNA synthesis, RNA synthesis, or the combination of DNA and RNA synthesis. The amplification of signature sequences provides an efficient and reproducible mechanism to determine the presence or absence of the miRNAs, to analyze the quantities of the target miRNAs, and for miRNA profiling. The method may also be used for screening for unknown non-coding RNAs, including novel miRNAs.

Abstract: Peptides against neuropeptide Y (NPY), a biomarker associated with human performance and cognition, and methods of using the peptides to detect NPY.

Abstract: The present invention relates to transgenic animals comprising a mutation or deletion to the ANF-RGC protein, particularly to its ARM and/or its ATS-ST region. Such animals may be used to study the effects on pathways associated with ANF-RGC activation, including, but not limited to, hypertension. Such animals may also be used in drug screen assays, to establish toxicity profiles, or other similar methods discussed herein known in the art.

Abstract: A microarray formed in a planar surface of a moldable slab, the microarray including a plurality of microwell sets comprising a plurality of microwells formed in the planar surface of the moldable slab, each microwell being sized to contain at least a single cell, and a plurality of microchannels formed in the planar surface of the moldable slab, the plurality of microchannels being configured to permit liquid from a first region of the microarray to transit to a second region of the microarray.

Abstract: The disclosure includes the identification and use of gene expression profiles, or patterns, with clinical relevance to extended treatment and cancer-free survival in a patient. In particular, the disclosure includes the identities of genes that are expressed in correlation with benefit in a switch in endocrine therapy used to treat a patient. The levels of gene expression are disclosed as a molecular index for predicting clinical outcome, and so prognosis, for the patient. The disclosure further includes methods for predicting cancer recurrence, and/or predicting occurrence of metastatic cancer, after initial treatment with an anti-estrogen agent. The disclosure further includes methods for determining or selecting the treatment of a subject based upon the likelihood of life expectancy, cancer recurrence, and/or cancer metastasis.

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.

Abstract: A method is selects membrane-translocating peptides (MTPs) from a peptide display library that are capable of crossing or penetrating a lipid membrane. A plurality of nucleic acid constructs that encode displayed peptides are expressed, resulting in the formation of a plurality of nucleic acid-peptide complexes, each complex comprising at least one displayed peptide associated with the corresponding nucleic acid construct encoding the displayed peptide; the complexes are exposed to a population of membrane-encapsulated compartments, allowing a translocating reaction to occur; complexes that remain unassociated with the membrane are removed; optionally complexes that are associated with the membrane are removed; and internalized nucleic acid-peptide complexes are recovered. The membrane-encapsulated compartments may be artificial vesicles such as liposomes, or populations of one or more cell types.

Abstract: Methods and formulations for treating a sarcoma in humans using an epimetabolic shifter, such as Coenzyme Q10, a building block of CoQ10, a derivative of CoQ10, an analog of CoQ10, a metabolite of CoQ10, or an intermediate of the coenzyme biosynthesis pathway, are described. Methods for assessing the efficacy of treatment of, diagnosing, and prognosing sarcoma are also provided.

Abstract: An indicator device, and a biological test method, for determining the toxic fingerprint and degree of toxicity, comprising at least 3, preferably at least 11, different microorganisms freeze-dried on an inert support material, wherein the microorganisms are being selected to form a high diversity of microorganisms, on the support material, with regards to the taxonomical tree and high diversity regarding responses to toxic chemicals. Further, a kit and a process for producing the indicator device is also disclosed.

Abstract: A method of generating a hyperpigmentation condition gene expression signature for use in identifying connections between perturbagens and genes associated with a skin pigmentation condition. The method includes providing a gene expression profile for a reference sample of human skin cells not affected with a pigmentation condition; generating a gene expression profile for a sample of human skin cells from a subject exhibiting the hyperpigmentation condition; comparing the expression profiles to determine a gene expression signature that includes a set of differentially expressed genes; assigning an identifier to each gene constituting the gene expression signature and ordering the identifiers according to the direction of differential expression to create one or more gene expression signature lists; and storing the one or more gene expression signature lists on at least one computer readable medium.