Abstract: This invention relates to methods, assays, devices and systems for identifying patients having a myelodysplastic syndrome for treatment with ezatiostat or a salt thereof, or evaluating the patient's response possibility to the treatment by measuring and evaluating the patient's gene expression profile. This invention also relates to methods of treating myelodysplastic syndromes.

Abstract: Disclosed are methods of identifying and diagnosing certain types of cancers and pre-stages thereof in a patient by identifying alternatively spliced isoforms of wild type KLF6 (KLF6wt), in particular any one of the isoforms selected from the group consisting of: KLF6 splice variant-1 (KLF6SV1), KLF6 splice variant-2 (KLF6SV2), and KLF6 splice variant-3 (KLF6SV3). Also disclosed are methods for diagnosing cancer using the polypeptides and polynucleotides identified herein, as well as methods of treating certain types of cancers by inhibiting polynucleotides and polypeptides identified herein.

Abstract: A method of identifying alleles of polymorphic sites in a plurality of nucleic acid samples including the steps of determining a source tag sharing number “d” for each of the alleles; performing a first reaction in a plurality of pools of the alleles to be identified to produce reaction products including a source tag identifying said each pool; pooling the pools to provide pooled pools; for each of the alleles to be identified, performing a second reaction using said reaction products to produce allele-specific second reaction products comprising a marker tag and a derived source tag; identifying said allele-specific second reaction products to identify the alleles. If “d” is equal to or larger than a maximum pool size, the first reaction may not be performed. Alleles may be binned together. A microparticle comprising one or more capture probes each comprising an oligonucleotide complementary to a subsequence of a target polynucleotide.

Abstract: Material transfer/interrogation devices (e.g. liquid handling workstations) have been designed in the past for transferring material from a source to a destination location or for interrogating a material at a location, where the locations remain fixed. The invention provides methods and apparatuses for transferring or interrogating materials by one or more carrier devices to one or more receiving devices, where the carrier and receiving devices move independently and simultaneously on multiple axes. In some embodiments, one or more of the carrier and receiving devices can move along an X, Z, Y, and Theta axis, which allows the source and destination locations to rotate and translate relative to each other. Due to this rotation and translation, containers can be positioned to minimize the distance traveled between a pick location from the source and a place location on the destination, greatly increasing the speed at which material transfer can occur.

Abstract: A method for monitoring breast conditions in a subject is disclosed. The method comprises determining a Paired Box 2 gene-to-beta defensin-1 gene (PAX2-to-DEFB1) expression ratio (the “Donald Predictive Factor” or “DPF”) in cells obtained from the breast of the subject, wherein the PAX2-to-DEFB1 expression ratio is correlated with breast conditions. Also disclosed is a kit for monitoring breast conditions and determining drug resistance.

Abstract: The present invention relates to polypeptide fragments comprising an amino-terminal fragment of the PA subunit of a viral RNA-dependent RNA polymerase possessing endonuclease activity, wherein said PA subunit is from Influenza A 2009 pan-demic H1N1 virus or is a variant thereof. This invention also relates to (i) crystals of the polypeptide fragments which are suitable for structure determination of said polypeptide fragments using X-ray crystallography and (ii) computational methods using the structural coordinates of said polypeptide to screen for and design compounds that modulate, preferably inhibit the endonucleolytically active site within the polypeptide fragment. In addition, this invention relates to methods identifying compounds that bind to the PA polypeptide fragments possessing endonuclease activity and preferably inhibit said endonucleolytic activity, preferably in a high throughput setting.

Abstract: A method for monitoring breast conditions in a subject is disclosed. The method comprises determining a Paired Box 2 gene-to-beta defensin-1 gene (PAX2-to-DEFB1) expression ratio (the “Donald Predictive Factor” or “DPF”) in cells obtained from the breast of the subject, wherein the PAX2-to-DEFB1 expression ratio is correlated with breast conditions. Also disclosed is a kit for monitoring breast conditions and determining drug resistance.

Abstract: Transposon nucleic acids comprising a transposon end sequence and a calibration sequence for DNA sequencing in the transposon end sequence. In one embodiment, the transposon end sequence is a Mu transposon end. A method for the generation of DNA fragmentation library based on a transposition reaction in the presence of a transposon end with the calibration sequence providing facilitated downstream handling of the produced DNA fragments, e.g., in the generation of sequencing templates.

Abstract: The present invention is based, at least in part, on the identification of molecules involved in the differentiation and/or activity of osteoblasts and osteoclasts. Accordingly, the present invention provides methods of identifying modulators of bone formation, mineralization, and/or osteoclastogenesis and methods for treating disorders that would benefit from modulation of bone formation, mineralization, and/or osteoclastogenesis using agents identified as described herein.

Abstract: Disclosed is a composition comprising the nucleic acid and a chemical compound, said composition forming a star structure defining 3 or more stems extending from a reaction center. The stems are formed by a nucleic acid duplex and the chemical compound has been formed in the reaction center as the reaction product of 3 or more chemical groups. The advantage of the composition is that a close proximity is provided between the chemical groups in the reaction center, thereby promoting a reaction. The invention also relates to a method for preparation of the composition. The advantage of the method is that it does not require the pre-synthesis of a large number of templates and that it is not dependent upon codon/anti-codon recognition for an encoded molecule to be formed.

Abstract: Various highly sensitive detection methods, particularly improved PNA-LNA-PCR clamp methods, are provided as methods for detecting the presence or absence of a mutated gene contained in a gene pool rapidly, in a simple manner, with high accuracy, and with high sensitivity. As a step before the main step for detection, a pre-amplification step comprising allowing (1) a clamp primer consisting of PNA which hybridizes with all or part of a target site having a sequence of a wild-type gene or a sequence complementary to the wild-type gene, (2) a primer capable of amplifying a region comprising a target site having a sequence of the mutated gene, and (3) the gene pool to coexist in a reaction solution for gene amplification, and selectively amplifying the region comprising a target site of the mutated gene by a gene amplification method.

Abstract: Described herein are methods for predicting recurrence, progression, and metastatic potential of a prostate cancer in a subject. In certain embodiments, the methods comprise analyzing a sample from a subject for aberrant expression patters of one or more biomarkers disclosed herein. An increase or decrease in one or more biomarkers as compared to a standard indicates a recurrent, progressive, or metastatic prostate cancer.

Abstract: The invention encompasses microfluidic microarray assemblies (MMA) and subassemblies and methods for their manufacture and use. In one embodiment, first and second channel plates are provided and are sealingly connected to a test chip in consecutive steps. Each plate includes microfluidic channels configured in a predetermined reagent distribution pattern. The test chip comprises a plurality of discrete test positions, each test position being located at the intersection between a first predetermined reagent pattern and a second predetermined reagent pattern, wherein at least one of said patterns is non-linear. The first channel plate allows the distribution of a first reagent on said test chip, wherein said first reagent is immobilized at said test positions. The second channel plate allows the distribution of a second reagent on said test chip, wherein said second reagent comprises a plurality of different test samples.

Abstract: The present invention relates to a method for assessing a hypoxia phenotype of a tumour of a subject in which the gene expression of between 3 and 50 hypoxia-related genes of a sample obtained from said tumour of the subject is determined, thereby obtaining a sample expression profile of said hypoxia-related genes. The sample gene expression profile is then compared with a reference expression profile of said hypoxia-related genes. The hypoxia-related genes comprise at least SLC2A1, VEGFA and PGAM1. Probes, arrays and kits for use in the method are also disclosed.

Abstract: Methods for the determination of tissue-specific genetic variation are provided. For example, in certain aspects methods for using iPS cell-derived specific cell types for differential molecular analysis of tissue-specific genetic variation are described.

Abstract: The increasing use of nanotechnology in consumer products and medical applications underlies the importance of understanding its potential toxic effects to people and the environment. Herein are described methods and assays to predict and evaluate the cellular effects of nanomaterial exposure. Exposing cells to nanomaterials at cytotoxic doses induces cell cycle arrest and increases apoptosis/necrosis, activates genes involved in cellular transport, metabolism, cell cycle regulation, and stress response. Certain nanomaterials induce genes indicative of a strong immune and inflammatory response within skin fibroblasts. Furthermore, the described multiwall carbon nanoonions (MWCNOs) can be used as a therapeutic in the treatment of cancer due to its cytotoxicity.

Abstract: Embodiments of the present invention provide a system and method for analyzing a plurality of samples comprising obtaining with an autosampler a plurality of samples from a first plate having a plurality of sample wells wherein the autosampler has a plurality of probes for sampling a set of samples and wherein each probe of the plurality of probes is in communication with a separate flow cytometer via a separate conduit. The plurality of samples comprising particles is moved into a fluid flow stream for each separate conduit. Adjacent ones of the plurality of samples are separated from each other in the fluid flow stream by a separation gas, thereby forming a gas-separated fluid flow stream. The gas-separated fluid flow stream is independently guided to and through each separate flow cytometer.

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 present invention provides a method of determining bacterial metastructure by integrating multiple genome-scale information yielded by high-throughput technologies. The metastructure constructs a universal metabolic engineering platform enabling a rational design of bacterial strains through optimization of gene and protein expression.

Abstract: The present invention embraces methods and kits for facilitating the propogation of PrPSc, and use of the same in increasing the sensitivity diagnostic assays and in identifying compounds that modulate the conversion of PrPc to PrPSc.

Abstract: A selective targeting method is disclosed comprising contacting a library of ligands, particularly a peptide library, with an anti-target to allow the ligands to bind to the anti-target; separating the non-binding ligands from the anti-target bound ligands, contacting the non-binding anti-target ligands with a target allowing the unbound ligands to bind with the target to form a target-bound ligand complex; separating the target-bound ligand complex from ligands which do not bind to the target, and identifying the target-bound ligands on the target-bound ligand complex wherein the target-bound ligands have a KD in the range of about 10?7 to 10?10 M. Additionally claimed are the ligands identified according to the method.

Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.

Abstract: The present invention relates to a system and method for controlling peptide display valency on virus-like particles (VLPs), especially including MS2 VLPs. In this method, large amounts of wild-type and low quantities of single-chain dimer coat proteins may be produced from a single RNA. Valency is controlled in immunogen (vaccine) production by providing a system that allows the production of large amounts of wild-type and low quantities of single-chain dimer coating proteins from a single RNA, allowing facile adjustment of display valency levels on VLPs, especially MS2 VLPS over a wide range, from few than one-on average—to as many as ninety per particle. This facilitates the production of immunogens and vaccines, including VLPs exhibiting low valency.

Abstract: A culturing method includes culturing a sample having one or more species of target pathogens of a detection assay and competing microorganisms under oxygen-poor condition in a growth medium. The growth medium can be a non-selective medium. The oxygen-poor condition is effective to prevent competing microorganisms from suppressing growth of the target pathogens. This method can be used in combination with a sample preparation method for large volume particulate samples using highly porous filter material and porous spherical filter aid.

Abstract: Based on the observation of the cooperation of osteopontin (OPN) and matrixmetalloproteinase-9 (MMP-9) in the promotion of the metastatic phenotype, therapies and diagnostic assays are disclosed for the treatment of a tumor that overexpresses OPN, such as hepatocellular carcinoma (HCC), for example metastatic HCC. In one example, methods of treating a tumor include administration of an agent that reduces cellular invasion resulting from the interaction between a fragment of OPN (OPN-5kD) generated by MMP-9 cleavage and CD44 receptor. Examples of such agents include fragments of OPN-5kD and antibodies specific for OPN-5kD. Therapeutic compositions are also provided that include such agents. Also provided are methods of diagnosing or prognosing a tumor, for example by detecting expression of OPN-5kD peptide or OPN-c mRNA in a biological sample obtained from the subject. Also provided are antibodies that specifically bind OPN-5kD.

Abstract: The present invention relates to methods for generating functional biomolecules. In one exemplary aspect of the invention, generation of functional biomolecules may be performed against multiple targets simultaneously within a single system. In general, a plurality of targets may be disposed within in a single reaction volume and a library of biomolecules, such as a nucleic acid library, may be applied to the reaction volume. The members of the library that do not bind to any of the plurality of targets under given conditions may then be partitioned. The remaining members of the library may then be marked and/or tagged, such as to identify the particular target or targets to which the member of the library binds. The binding members of the library may then be isolated and, by virtue of the marking or tagging, be matched to a particular target or targets.

Abstract: Methods of assessing the risk of recurrence of endometrial cancer on the basis of the presence or absence of mutations in FGFR2 are disclosed.

Abstract: The disclosure provides compositions and methods for determining the likely tumor recurrence in breast cancer patients by screening IGFR1 polymorphism in samples isolated from the patient.

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 method of sample analysis is provided. In certain embodiments the method comprises: a) obtaining from a diploid individual a chromosomal sample that comprises maternally-derived chromosomes and homologous paternally-derived chromosomes; b) determining the parent of origin of a first chromosome of the sample by detecting a parent-specific copy number variation relative to a second chromosome that is homologous to the first chromosome; c) isolating the first chromosome; and d) genotyping the first chromosome.

Abstract: Methods are provided for isolating and identifying novel pesticide-encoding nucleic acid molecules from bacterial strains identified as having a pesticidal polypeptide. The methods involve selecting a bacterial strain having or suspected of having at least one pesticide-encoding plasmid, curing the at least one pesticide-encoding plasmid from the bacterial strain and performing a subtractive hybridization to obtain plasmid mRNA encoding the pesticidal polypeptide. The plasmid mRNA can be used to make a cDNA library from which the pesticidal polypeptide can be isolated and subsequently identified.

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: A method of preparing a protein chip by gelation of a sol composition. In the method, a mixture of specific silicate monomers, such as SolB1, SolB2 and SolB3, SolBH, and a mixture of SolBS, distilled water and a detector protein are mixed sequentially, so that the gelation rate of the sol composition can be delayed, thus inducing the stable gelation of the composition. Also, the biochip can be fabricated in a simple and easy manner by dispensing the sol composition by hand using an arrayer or a tool such as a pipette. In addition, a uniform biochip can be prepared by dispensing the sol composition, solution I (SolBH) and solution II (a mixture of buffer, SolBS, distilled water and a detector protein) sequentially onto a substrate without needing a conventional pretreatment process such as mixing.

Abstract: There is provided herein adipokine biomarkers for prostate cancer and methods and uses thereof.

Abstract: A method for detecting analytes in a sample liquid is provided in which the sample liquid is subjected to a mixing treatment on a surface of a support having in particular immobilized reactants, wherein an in particular trough-like vessel with an essentially flat bottom as a support surface for the immobilized reactants is used as the vessel for the sample liquid. The sample liquid is moved relative to the immobilized reactants by an oscillating movement of the vessel during the mixing treatment in one direction, typically along a line or a curve. In addition, a device is provided for carrying out the method according to the present disclosure.

Abstract: The present invention relates to a method and a kit for identifying a subjects macronutrient sensitivity. The method involves assaying a genetic sample from the subject to determine a polymorphism profile, analysing the polymorphism profile to identify risk alleles and determining the macronutrient sensitivity based on the number of risk alleles present. This information can be used for determining an appropriate diet to induce satiety, formulating a diet for inducing satiety, or for treating a range of medical complaints associated with metabolism.

Abstract: The invention relates generally to the field of industrial microbiology and butanol production. More specifically, the invention relates methods of reducing 2,3-dihydroxy-2-methyl butyrate (DHMB) in butanol production. DHMB can be reduced by inhibiting the reduction of acetolactate to DHMB, for example, by knocking out enzymes that catalyze the reduction or by removing DHMB during or after fermentation. Yeast strains, compositions, and methods for reducing DHMB and increasing butanol yield are provided.

Abstract: The present invention relates to methods of dividing cancer into subgroups based upon Akt pathway gene expression. In one embodiment, the present invention provides a method of diagnosing glioblastoma multiforme (GBM) subtype in an individual by determining the presence of an abnormal expression of an Akt pathway gene cluster and diagnosing the cancer subtype in the individual.

Abstract: The present invention provides methods and systems for sequencing long nucleic acid fragments.

Abstract: The present invention relates to the use of the level of certain cytokines in a patient's blood as an objective measure for the purpose of assessing disease progression in patients suffering from Alzheimer's disease and for the purpose of determining therapeutic effectiveness of a treatment regimen. Methods for treating Alzheimer's disease and monitoring therapeutic effectiveness are provided.

Abstract: There is provided a method of therapy of atherosclerosis, by providing microRNA let-7g, an analogue thereof or modified let-7g to organisms to inhibit the expression of lectin-like oxidized low density lipoprotein receptor-1 (LOX-1), and the binding of LOX-1 and oxidized low-density lipoprotein (oxLDL), so as to block the pathogenesis of atherosclerosis. Also, a method of diagnosis of atherosclerosis comprises determining the levels of microRNA let-7g in serum or plasma samples of organisms, in which the levels of microRNA let-7g is estimated in individuals with atherosclerosis as compared to individuals without atherosclerosis.

Abstract: This disclosure provides a biomarker profile, which is linked to cancer cell chemo-resistance. The disclosure further provides methods of diagnosis and theranosis, and screening of new therapeutic agents using these biomarkers in the profile, and kits for employing these methods and compositions.

Abstract: A method for identifying a contaminant in an environment includes providing a sensor array, the sensor array including a plurality of sensing platforms, each of the sensing platforms including a corrodible metal. A reaction is detected on the corrodible metal on one or more of the sensing platforms to identify a reaction pattern, and the reaction pattern is compared to known reaction characteristics of the corrodible metals. Based on this comparison, the contaminant, such as a corrosive gas, can be identified. The sensing platform may include a quartz crystal microbalance or a nanostructure. In some features, at least one of the corrodible metals includes gold, and a detected reaction of the gold corrodible metal indicates the presence of adverse temperature or humidity conditions in the environment.

Abstract: Provided are robust, passive, membrane-based debubblers that are readily incorporated into microfluidic devices for rapid degassing. Also provided are methods of degassing fluid disposed within fluidic systems.

Abstract: Compounds which inhibit microbial growth or attenuate the virulence of pathogen microorganisms. Compounds of the invention inhibit UDP-galactopyranose mutase (UGM) and have activity as inhibitors of microbial growth of microorganisms which contain this enzyme and particularly those microorganisms in which this enzyme is responsible for the incorporation of galactofuranose residues, particularly for uridine 5?-diphosphate (UDP) galactopyranose mutase. Compounds of the invention inhibit UDP-galactopyranose mutase (UGM) and have activity to attenuate virulence of pathogenic microorganisms, including mycobacteria.

Abstract: A method for detecting an early-onset of colorectal cancer in a human subject is disclosed herein. The method comprises the steps of: (i) identifying the human subject suspected of suffering from a colorectal cancer, (ii) obtaining one or more biological samples from the human subject; (iii) determining a LINE-1 methylation level for the one or more biological samples; and (iv) comparing the LINE-1 methylation level to a LINE-1 methylation control level, wherein a higher degree of the LINE-1 methylation level is indicative of an early-onset colorectal cancer.

Abstract: A method for predicting therapeutic effect of combination therapy with peginterferon and ribavirin in chronic hepatitis C therapy, comprising: a drug-sensitivity marker detection step of detecting a drug-sensitivity marker in a biological sample; and a drug-sensitivity evaluation step of evaluating drug sensitivity of the biological sample on the basis of an expression level of the drug-sensitivity marker, wherein the biological sample is a cell or tissue derived from liver, and the drug-sensitivity marker comprises at least one microRNA selected from the group consisting of microRNAs shown in SEQ ID NOs: 1 to 37.

Abstract: The c-Jun NH2-terminal kinase (JNK) group of MAP kinases are activated by exposure of cells to environmental stress. The role of JNK in the brain was examined by targeted disruption of the gene that encodes the neuronal isoform JNK3. It was found that JNK3 is required for the normal response to seizure activity. Methods of screening for molecules and compounds that decrease JNK3 expression or activity are described. Such molecules or compounds are useful for treating disorders involving excitotoxicity such as seizure disorders, Alzheimer's disease, Huntington disease, Parkinson's disease, and ischaemia.

Abstract: A method of determining gynaecologic tumor disease in a subject by providing a sample of peripheral blood of the subject, measuring the PPIC expression of cells in the sample, and comparing this to a reference value, the PPIC overexpression being indicative of a gynecologic tumor disease and/or disease progression, including metastatic potential in a gynecologic cancer patient.

Abstract: Provided are high-throughput detection systems. The systems include a magnetic sensor device, a magnetic field source and a reservoir plate that includes a plurality of fluid reservoirs. The magnetic sensor device includes a support with two or more elongated regions each having a magnetic sensor array disposed at a distal end. Also provided are methods in which the subject high-throughput detection systems find use.