Abstract: The invention provides a unique subset of GH30 subfamily 8 xylanases (GH30-8) with endo-?-1,4-xylanase activity, compositions comprising an effective amount of the GH30-8 xylanases, methods of synthesis and methods of use thereof.

Abstract: Provided herein are methods of increasing the efficiency of biomass saccharification. In particular, the methods include ways of avoiding feedback inhibition during the production of useful products.

Abstract: The present invention relates to polypeptides comprising a carbohydrate-binding module amino acid sequence and an alpha-amylase amino acid sequence as well as to the application of such polypeptides.

Abstract: Vectors expressing kanA-kanB-kanK and other kanamycin production-related genes, Streptomyces species recombinant bacteria transformed with the vectors, a method of producing kanamycin antibiotics by the bacteria, and a new kanamycin compound produced by the bacterium are provided. With the use of the recombinant bacteria of the present invention, the direct fermentative biosynthesis of amikacin and tobramycin as semi-synthetic kanamycins is possible, and the yield of kanamycin B as a precursor of the semi-synthetic kanamycin is improved.

Abstract: The present invention relates to methods for mammalian cell culture. The methods make use of independent tyrosine and cystine feed streams.

Abstract: The invention relates to a method for stabilising a biomass of microalgae containing oxidation-sensitive metabolites selected from the group consisting of carotenoids (lutein, etc.), monounsaturated and polyunsaturated fatty acids (palmitoleic acid, oleic acid, linoleic acid, etc.), chlorophyll pigments (chlorophyll A and B, etc.) and vitamins (vitamin B9 and B12, etc.) taken individually or together, more specifically carotenoids, said method comprising the fermentation of said biomass in heterotrophic conditions.

Abstract: The internally calibrated electrochemical continuous enzyme assay (ICECEA) was developed for the fast determination of enzyme activity unit. The assay uses integration of enzyme-free pre-assay calibration with the actual enzyme assay in one continuous experiment. Such integration results in a uniquely shaped amperometric trace that allows for the selective and sensitive determination of enzymes.

Abstract: An automated system for identifying in a biological sample microorganisms and their antimicrobial susceptibility (AST). The system provided an automated platform for preparing, from a single biological sample, inoculates for both ID and AST. The system loads a plate for ID testing as samples are being prepared for AST testing. The system tracks the sample and the inoculates from the samples to link the test results to the sample and the patients from whom the sample was obtained.

Abstract: Culture medium devices and systems are shown and described. In one embodiment, the device comprises a culture medium adapted for test fluid inoculation without the concerns associated with a spreading step. In particular examples, a printed grid on the outer surface of a culture device is visible on the inner surface for colony counting after a test has been developed. The result is a device that allows for detection, identification, and transportation of various microorganisms without preparation or spreading steps, and more particularly to a culture medium in which a test fluid inoculated thereto diffuses rapidly.

Abstract: Disclosed is a method for detecting spatial proximity relationships between RNA and DNA molecules in a cell. The method includes: providing a sample of RNA and DNA wherein the RNA and fDNA have ends capable of joining to other DNA and RNA, respectively; joining at least one end of the fragmented RNA to the end of at least one fragmented DNA, to create at least one joined RNA-DNA hybrid molecule, wherein the join encodes the information about the proximity of the RNA and DNA in the cell; reverse transcribing the at least one joined rRNA-DNA hybrid molecule to create least one target join DNA molecule that retains the information of the join, and determining the sequence of the target join thereby detecting spatial proximity relationships between RNA and DNA molecules in a cell.

Abstract: Systems and methods for processing sample processing devices. The system can include a sample processing device comprising a detection chamber, a motor configured to rotate the sample processing device about an axis of rotation, and an optical module operatively positioned relative to the sample processing device and configured to determine whether a selected volume of material is present in the detection chamber of the sample processing device. The method can include rotating the sample processing device about an axis of rotation, and determining whether a selected volume of material is present in the detection chamber, while rotating the sample processing device. In some embodiments, determining whether a selected volume of material is present can be performed by optically interrogating the detection chamber for an optical property of the material.

Abstract: The present method relates to methods of quantifying nucleic acids, and in particular to the use of a universal reference nucleic acid to generate a calibration curve from which the level of a target nucleic acid in a sample can be calculated.

Abstract: Provided are methods and compositions for characterization of bacterial compositions for the maintenance or restoration of a healthy microbiota in the gastrointestinal tract of a mammalian subject, and the resulting characterized compositions. Provided are methods of characterizing bacterial compositions including subjecting the compositions to various detecting processes.

Abstract: Systems and methods to assess the health of various microbiomes and to identity species therein are disclosed. Described assessments and identifications can inform treatment decisions if a microbiome is determined to have a less than optimal balance of bacterial species within it; the presence of one or more negative species; and/or the absence of one or more positive species.

Abstract: Embodiments of the invention provide a method of genotyping a C. gattii sample, which can include forming a plurality of mixtures for nucleic amplification. The method can include amplification of specific sequences within the C. gattii genome that can provide definitive genotype information to distinguish between one or more types or subtypes of C. gattii.

Abstract: Disclosed are methods for isolating a target nucleic molecule of interest from a sample. The methods include contacting a sample comprising a target nucleic molecule of interest with at least one single stranded nucleic acid targeting probe comprising a nucleic acid sequence between about 30 nucleotide and the length of the target nucleic acid length that hybridizes to the target nucleic molecule of interest under highly stringent hybridization conditions. The probe comprises a capture moiety covalently linked to one or more nucleotide bases in the probe. The targeting probes can be captured with a specific binding agent that specifically binds the capture moiety, thereby isolating the target nucleic molecule of interest. In some embodiments, the sample is further contacted with a crosslinking agent before contacting the sample with a targeting probe. Thus, complexes formed with the target nucleic acid can also be isolated.

Abstract: Methods and compositions for the detection and quantification of nucleic acids are provided. In certain embodiments, methods involve the use of cleavable probes that comprise a ribonucleotide position that is susceptible to endoribonuclease (e.g., RNase H) cleavage in the presence of target nucleic acid molecules. Probes of the embodiments may also comprise non-natural nucleotide linked to a reporter and/or quenching moiety.

Abstract: Methods for detecting the amplifications of sequences in the BRCA1 locus, which sequences have ends consisting of or are framed with sequence stretches present at least twice in the BRCA1 locus, and which amplification results in at least two or at least three, especially three, tandem copies of the amplified sequence; methods for determining a predisposition to diseases or disorders associated with these amplifications, including predisposition to ovarian cancer or breast cancer and methods for detecting amplifications with similar features in other loci and/or for predicting breakpoints of such amplifications.

Abstract: A method of obtaining cut-off expression values should be selected so as to maximise the separation of the respective survival curves of the two groups of patients. Pairs of genes are statistically significant genes are generated by generating a plurality of models, each of which represents a way of partitioning a set of subjects based on the optimal cut-off expression values of the pair of genes. Those gene pairs are identified for which one of the models has a high prognostic significance. Novel survival significant gene sets forming functional modules which could be used to develop specific prognostic and predictive tests are derived.

Abstract: Systems and methods are provided for calibrating emission data or other information signals collected during a polymerase chain reaction (PCR), amplification reaction, assay, process, or other reaction. Calibration of multiple detectable materials can be achieved during a single cycle or run, or during a plurality of runs of the reaction. A reading from every well, container, or other support region of a sample support does not have to be taken. Interpolation can be used to determine values for emission data or other information signals that were not taken, or are unknown, using detected emission data, or other detected information signals. By calibrating the detected emission data and the interpolated data, a more accurate reading of emission data or information signal can be obtained.

Abstract: A method for determining the sequence of nucleotide bases in a polynucleotide analyte is provided. It is characterised by the steps of (1) generating a stream of single nucleotide bases from the analyte; (2) producing captured molecules by reacting each single nucleotide base with a capture system; (3) amplifying at least part of the captured molecule to produce a plurality of amplicons characteristic of the single nucleotide base; (4) labelling the amplicons with a corresponding probe having a characteristic detectable element and (5) detecting a property characteristic of the detectable element.

Abstract: A method for determining the sequence of nucleotide bases in a polynucleotide analyte is provided. It is characterised by the steps of (1) generating a stream of single nucleotide bases from the analyte by pyrophosphorolysis; (2) producing captured molecules by reacting each single nucleotide base with a capture system labelled with detectable elements in an undetectable state; (3) releasing the detectable elements from each captured molecule in a detectable state and (4) detecting the detectable elements so released and determining the sequence of nucleotide bases therefrom. The method can be used advantageously in sequencers involving the use of microdroplets.

Abstract: Some embodiments of the present application relate to novel modified nucleotide linkers for increasing the efficiency of nucleotide incorporation in Sequencing by Synthesis applications. Methods of preparing these modified nucleotide linkers are also provided herewith.

Abstract: An array of transportable particle sets is used in a microfluidic device for performing chemical reactions in the microfluidic device. The microfluidic device comprises a main channel and intersecting side channels, the main channel and side channels forming a plurality of intersections. The array of particle sets is disposed in the main channel, and the side channels are coupled to reagents. As the particle sets are transported through the intersections of the main channel and the side channels, reagents are flowed through the side channels into contact with each array member (or selected array members), thereby providing a plurality of chemical reactions in the microfluidic system.

Abstract: The present invention relates to a method of sequencing a target polynucleotide by enzymatic and/or chemical means. The sequencing method includes a method for characterizing multiple alleles in a sample, a method of calculating confidence levels in ascertained sequences, a method for comparing polynucleotide sequences and a method of resolving ambiguities in a polynucleotide sequence. It also provides methods for appropriately preparing samples, for immobilising template molecules, for organising the template molecules and to conduct the sequencing of many molecules in parallel. The method involves analysing molecules as members of an array. Many target polynucleotides or many segments of a single target polynucleotide can be sequenced simultaneously. In a preferred embodiment the method involves analysing individual molecules within an array and base calls are based on the signals from two or more molecules. A method to prevent non-specific signal in sequencing is also provided.

Abstract: The disclosure relates to methods for determining the sequence of a genomic region of interest comprising a target nucleotide sequence comprising: providing a DNA comprising a genomic region of interest, fragmenting the DNA, separating the DNA fragments, fragmenting and ligating the DNA fragments to provide for ligated fragments of the DNA fragments (or ligated DNA subfragments), and determining at least part of the sequences of at least part of the ligated DNA subfragments that comprise the target nucleotide sequence.

Abstract: The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.

Abstract: Improved solid supports and methods for analyzing target nucleotide sequences are provided herein. Certain improvements are directed to efficiently preparing nucleic acids that comprise nucleotide sequences identical to or substantially identical to one or more target nucleotide sequences, or complement thereof. The prepared nucleic acids include a reference sequence that facilitates sequence analysis. The solid supports and methods provided herein minimize the number of steps required by published sequence analysis methodologies, and thereby offer improved sequence analysis efficiency.

Abstract: The present invention recognizes that diagnosis and prognosis of many conditions can depend on the enrichment of rare cells, especially tumor cells, from a complex fluid sample such as a blood sample. In particular, the present invention is directed to methods and compositions for detecting a non-hematopoietic cell, e.g., a non-hematopoietic tumor cell, in a blood sample via, inter alia, removing red blood cells (RBCs) from a blood sample using a non-centrifugation procedure, removing white blood cells (WBCs) from said blood sample to enrich a non-hematopoietic cell, if any, from said blood sample; and assessing the presence, absence and/or amount of said enriched non-hematopoietic cell.

Abstract: The present invention relates to methods, monitors and systems, useful, for example, for advanced detection of sepsis in a subject.

Abstract: The invention provides a non-invasive technique for the detection and quantification of the immune repertoire, in a biological sample containing a plurality of distinct cell populations. Methods are conducted using sequencing technology to detect and enumerate immune repertoire within a heterogeneous biological sample.

Abstract: Methods for inducing cell apoptosis by cellular comparison of genetic copy number variants of ultra-conserved elements.

Abstract: Methods and systems to characterize multiple sclerosis in a subject, e.g., in a subject a progressive form of MS are disclosed.

Abstract: Disclosed herein are single nucleotide polymorphisms (SNPs) characteristic of functional subgroups of KIR3DL1. Also disclosed herein are methods for classifying KIR3DL1 alleles by using a series of oligonucleotide primers and PCR reaction conditions uniquely designed to identify group-specific SNPs from genomic DNA. The compositions and methods disclosed herein are useful in clinical settings and research laboratories, and enable prospective assessment of prognoses of various diseases and selection of most appropriate donors for HCT.

Abstract: Congenital abnormalities of the kidney or the urinary tract (CAKUT) are the most common cause of pediatric kidney failure. These disorders are highly heterogenous, and their etiology is poorly understood. Dual serine/threonine and tyrosine protein kinase (DSTYK) mutations were detected in 2.2% of patients with congenital abnormalities of the kidney and urinary tract, suggesting that DSTYK is a major determinant of human urinary development, downstream of fibroblast growth factor (FGF) signaling. Methods and kits are provided for identifying and treating subjects at greater risk of developing CAKUT based on the presence of DSTYK mutations. Techniques include obtaining a biological sample from a subject and determining if the biological sample indicates a mutation of a gene for DSTYK. If it is determined that the biological sample indicates the mutation of the gene for DSTYK, then it is determined that the subject has or is at risk of developing CAKUT.

Abstract: Methods and compositions for the effect of Cholesteryl ester transfer protein (CETP) polymorphisms on mRNA splicing, statin treatment outcome, response to CETP inhibitor drugs, and myocardial infarction risk are described.

Abstract: Provided herein are methods of determining a treatment regimen for a subject with a mood disorder and methods of identifying a patient with a mood disorder as amenable to treatment with a calcium channel blocker (CCB). In exemplary embodiments, the methods comprise (a) analyzing a sample obtained from a subject with a mood disorder for the presence of allele [A] of CACNA1C, wherein allele [A] comprises the sequence of the polymorphic marker rs1006737.

Abstract: The invention pertains to a method of determining a statin dosage for an individual in need of treatment with a statin, comprising determining a SLCO1B1 genotype from a nucleic acid sample of the individual, said genotype comprising the presence or absence of the SLCO1B1-056 polymorphism, and determining an ApoE genotype or phenotype identifying an ApoE polymorphism selected from the group consisting of ApoE2, ApoE3, ApoE4, and any combination thereof, wherein the combination of a SLCO1B1 genotype identifying the presence of the SLCO1B1-056 C polymorphism and the ApoE genotype or phenotype identifying one of the ApoE3/4 or ApoE4/4 genotypes indicates the statin dosage.

Abstract: This disclosure relates to amplification and detection of a rare variant or variants of a DNA sequence in an abundant variant of the sequence, such as detection of a low-level somatic mutations and minority alleles in an excess of normal nucleic acid target sequences.

Abstract: Provided in the present invention are a method using in vitro measurement of the content of methylation or demethylation of GFRal CpG islands to estimate a risk of tumorigenesis and of tumor metastasis, or postoperative life expectancy, and a nucleotide sequence used.

Abstract: The present invention relates to the novel use of syndecan-2 (SDC2; NM_002998) gene as a gastric polyp- and gastric cancer-specific methylation biomarker, and more particularly, to the use of the syndecan-2 gene as a biomarker that enables gastric polyp and gastric cancer to be diagnosed in an early stage by measuring the methylation level thereof. The present invention has an effect in that the methylation of the CpG island of the gastric polyp- and gastric cancer-specific marker gene can be detected to thereby provide information for diagnosing gastric cancer. The use of the methylation detection method according to the present invention or the diagnostic composition, kit or nucleic acid chip according to the present invention makes it possible to diagnose gastric cancer at an early transformation stage, thus enabling the early diagnosis of gastric cancer.

Abstract: The present invention describes a method for detecting NEPC in a patient afflicted with prostate cancer comprising (a) performing a direct analysis comprising immunofluorescent staining and morphological characterization of nucleated cells in a blood sample obtained from the patient to detect circulating tumor cells (CTC), and (b) determining presence or absence of a CTC subpopulation associated with NEPC comprising detecting a measurable feature of each biomarker in a panel of morphological and protein biomarkers, wherein the presence of the CTC subpopulation associated with NEPC is indicative of NEPC. In other embodiments, the biomarkers for the CTC subpopulation associated with NEPC comprise small size, absence of Androgen Receptor (AR?), and presence of nucleoli (nucleoli+). In additional embodiments, the methods of the invention further comprise molecular analysis of the CTCs.

Abstract: Provided herein is technology relating to detecting neoplasia and particularly, but not exclusively, to methods, compositions, and related uses for detecting premalignant and malignant neoplasms such as pancreatic and colorectal cancer. Accordingly, provided herein is technology for pancreatic cancer screening markers and other gastrointestinal cancer screening markers that provide a high signalto-noise ratio and a low background level when detected from samples taken from a subject (e.g., stool sample). As described herein, the technology provides a number of methylated DNA markers and subsets thereof (e.g., sets of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more markers) with high discrimination for G1 neoplasms overall and/or at individual tumor sites.

Abstract: This study describes a method to determine the likelihood of the development of metastasis in a subject suffering from cancer, in addition to a method to design a customized therapy in a subject suffering from cancer, in particular breast, colon, lung, kidney and thyroid cancer, based on the determination of the expression level of one or more genes whose expression is modulated by an increase in c-MAF expression. It also describes a method for the identification of marker genes with a propensity for metastatic cancer based on inducing the modulation of the c-MAF expression Finally, the use of PTHLH and PODXL inhibitors and RERG activators in the treatment and/or prevention of the cancer, in particular breast, colon, lung, kidney and thyroid cancer.

Abstract: A method to verify single data points by substituting multiple data points that predict the original value measured is described. This is applied to determining gene expression levels.

Abstract: Methods for detecting the amplifications of sequences in the BRCA1 locus, which sequences have ends consisting of or are framed with sequence stretches present at least twice in the BRCA1 locus, and which amplification results in at least two or at least three, especially three, tandem copies of the amplified sequence; methods for determining a predisposition to diseases or disorders associated with these amplifications, including predisposition to ovarian cancer or breast cancer and methods for detecting amplifications with similar features in other loci.

Abstract: The present invention relates to the field of cancer. More specifically, the present invention provides methods and compositions related to certain promoter mutations in cancer. In one embodiment, a method for treating a subject having thyroid cancer comprises the steps of (a) obtaining a biological sample from the subject; (b) performing an assay on the sample obtained from the subject to identify a mutation at 1 295 228 C>T (C228T) and 1 295 250 C>T (C250T), corresponding to ?124 C>T and ?146 C>T from the translation start site in the promoter of the telomerase reverse transcriptase (TERT) gene; (c) identifying the subject as having or likely to develop aggressive thyroid cancer if the C228T and/or C250T mutation is identified; and (d) treating the subject with one or more treatment modalities appropriate for a subject having or likely to develop aggressive thyroid cancer.

Abstract: The instant application provides biomarkers for the identification of chemosensitivity in patient having cancer, in a particular embodiment the invention provides MST for the identification of chemosensitivity in breast cancer patient, wherein a reduced expression of XIST in the breast cancer cells of the patient indicates that the breast cancer stem cells in the patient may be successfully treated with HDAC inhibitor.

Abstract: The invention is directed to methods, reagents, and kits for the detection of MAPK/ERK pathway mutations in a patient diagnosed for cancer. In one embodiment, the invention comprises a sensitive and selective method to identify mutations to the BRAF, KRAS, and NRAS genes in a single reaction. In another aspect of this embodiment, the invention comprises primers and C probes for the detection of the BRAF, KRAS, and NRAS mutations using a single nucleotide primer extension assay. In another embodiment the invention is used to identify and select patients amenable for treatment with an ERK inhibitor.