Abstract: Methods for obtaining a product comprising a substituted or unsubstituted C3 to C10 alcohol from a substituted or unsubstituted C3 to C10 carboxylic acid. The method comprises contacting a substituted or unsubstituted C3 to C10 carboxylic acid with a gaseous composition and a Chlostridia species to produce a substituted or unsubstituted C3 to C10 alcohol under an anaerobic environment.

Abstract: The invention relates to a method comprising the steps a) providing isobutyric acid, b) bringing isobutyric acid into contact with the combination of isobutyrate kinase and phosphotransisobutyrylase and/or isobutyryl-coenzyme A synthetase/ligase and/or isobutyrate-coenzyme A transferase, c) bringing the product from step a) into contact with isobutyryl-coenzyme A dehydrogenase, d) bringing the product from step b) into contact with methacrylyl-coenzyme A hydratase, and e) hydrolyzing the product from step d) to form 3-hydroxyisobutyric acid, where at least one of the enzymes is used in the form of a cell which, compared to its wildtype, comprises a reduced activity of a 3-hydroxyisobutyric acid dehydrogenase or a variant thereof, a cell which has at least one enzyme from the group comprising isobutyryl-coenzyme A synthetase/ligase, isobutyrate-coenzyme A transferase, isobutyrate kinase, phosphotransisobutyrylase, isobutyryl-coenzyme A dehydrogenase, methacrylyl-coenzyme A hydratase and 3-hydroxyisobutyryl-coe

Abstract: The present invention relates to a cell which has been modified in comparison with its wild type in such a way that it is capable of forming more, by comparison with its wild, 3-hydroxyisobutyric acid or polyhydroxyalkanoates based on 3-hydroxyisobutyric acid via methylmalonate-semialdehyde or 3-hydroxybutyryl-coenzyme A as precursors. The invention also relates to a method of generating a genetically modified cell, to the genetically modified cell obtainable by these methods, to a method of producing 3-hydroxyisobutyric acid or polyhydroxyalkanoates based on 3-hydroxyisobutyric acid, to a method of producing methacrylic acid or methacrylic esters, and to a method of producing polymethacrylic acid or polymethacrylic esters. The present invention furthermore relates to an isolated DNA, to a vector, to the use of this vector for transforming a cell, to a transformed cell, and to a polypeptide.

Abstract: A process for producing an optically active 2-alkyl-1,1,3-trialkoxycarbonylpropane (2), comprising a step of asymmetric hydrolysis of 2-alkyl-1,1,3-trialokoxycarbonylpropane (1) by using an enzyme capable of selectively hydrolyzing an ester moiety of either one enantiomer of 2-alkyl-1,1,3-trialkoxycarbonylpropane (1), or by using a culture of a microorganism capable of producing the enzyme or a treated object thereof.

Abstract: Disclosed are compositions and methods related to eukaryotic microorganisms that can produce unsaturated fatty acids which can be purified and used.

Abstract: Disclosed herein are methods of manufacturing renewable chemicals through the manufacture of novel triglyceride oils followed by chemical modification of the oils. Methods such as transesterification, hydrogenation, hydrocracking, deoxygenation, isomerization, interesterification, hydroxylation, hydrolysis and saponification are disclosed. Novel oils containing fatty acid chain lengths of C8, C10, C12 or C14 are also disclosed and are useful as feedstocks in the methods of the invention.

Abstract: A method for producing an L-amino acid using a fatty acid as the carbon source is provided. An L-amino acid is produced by culturing a bacterium belonging to the family Enterobacteriaceae and having an L-amino acid-producing ability, which has been introduced with the lcfA gene, in a medium containing a fatty acid, and collecting the L-amino acid from the medium.

Abstract: A fungal alpha amylase is provided from Aspergillus clavatus (AcAmyl). AcAmyl has an optimal pH of 4.5 and is operable at 30-75 C, allowing the enzyme to be used in combination with a glucoamylase and a pullulanase in a saccharification reaction. This obviates the necessity of running a saccharification reaction as a batch process, where the pH and temperature must be readjusted for optimal use of the alpha amylase or glucoamylase. AcAmyl also catalyzes the saccharification of starch substrates to an oligosaccharide composition significantly enriched in DP2 and (DP1+DP2) compared to the products of saccharification catalyzed by an alpha amylase from Aspergillus kawachii. This facilitates the utilization of the oligosaccharide composition by a fermenting organism in a simultaneous saccharification and fermentation process, for example.

Abstract: Disclosed is an acetyl-CoA-producing microorganism, which is obtained by imparting malate thiokinase and malyl-CoA lyase enzymatic activities to a microorganism having none of the following (a), (b), (c) or (d), without imparting any of (a), (b), (c) or (d), or, even when one or more of (a), (b), (c) or (d) are imparted, not allowing the functions thereof to be exerted: (a) a carbon dioxide fixation cycle having an enzymatic reaction from malonyl-CoA to malonate semialdehyde or 3-hydroxypropionate, (b) a carbon dioxide fixation cycle having an enzymatic reaction from acetyl-CoA and CO2 to pyruvate, (c) a carbon dioxide fixation cycle having an enzymatic reaction from crotonyl-CoA and CO2 to ethylmalonyl-CoA or glutaconyl-CoA or (d) a carbon dioxide fixation cycle having an enzymatic reaction from CO2 to formate.

Abstract: Methods and compositions are provided for increasing the ligation yields of polynucleotides in vitro.

Abstract: Methods for efficient and high throughput emulsion-based nucleic amplification are provided. In some aspects, emulsion mixtures are provided that require extremely low input energy (e.g., the energy generated by pipetting) to form emulsions that are effective for nucleic acid amplification. Efficient formulations for breaking emulsions are likewise provided.

Abstract: This invention relates to a method for producing a protein of interest, comprising introducing a protein expression vector which comprises a gene fragment a gene fragment comprising a DNA encoding a protein of interest and a selectable marker gene and transposon sequences at both terminals of the gene fragment, into a suspension mammalian cell; integrating the gene fragment inserted between a pair of the transposon sequences, into a chromosome of the mammalian cell to obtain a mammalian cell capable of expressing the protein of interest; and suspension-culturing the mammalian cell; and a suspension mammalian cell capable of expressing the protein of interest.

Abstract: The instant disclosure describes a novel genotype and phenotype assay to elucidate and/or evaluate new potential HIV integrase inhibitors, but also currently approved and experimental compounds that target protease, reverse transcriptase, and RNaseH. This assay allows studying linked mutations and mutational patterns that occur under HAART and experimental therapies.

Abstract: A system for detecting microbial cells in a sample includes an apparatus configured to image at least one cell in the sample, and a cooling device. The apparatus includes a holder having an internal portion and an external portion which are configured so as to secure a membrane between the portions, and an imaging device disposed above the external portion and configured to permit examination of the at least one cell. The apparatus further includes a stage attachable to a stage platform configured to connect to a motor, and a projecting member projecting from an upper surface of the stage and configured to receive and exchange solution. The cooling device includes a thermoelectric cooling element and/or at least one tube configured to circulate a cooling medium beneath the stage so as to cool the sample.

Abstract: An apparatus includes a housing and an actuator. The housing, which defines a reagent volume that can receive a reagent container, can be removably coupled to a reaction chamber. The housing includes a puncturer that defines a transfer pathway in fluid communication with the reagent volume. A delivery portion of the housing defines a delivery pathway between the transfer pathway and the reaction chamber when the housing is coupled to the reaction chamber. The actuator has a plunger portion disposed within the reagent volume. An engagement portion of the actuator can be manipulated to move the plunger portion within the reagent volume to deform the reagent container. The puncturer can pierce a frangible portion of the reagent container to convey a reagent from the reagent container into the reaction chamber via the transfer pathway and/or the delivery pathway.

Abstract: The present invention encompasses methods and compositions for detecting pathogenic bacteria. Additionally, the present invention encompasses methods and compositions for catalyzing the dismutation of superoxide radicals. Further, the present invention encompasses methods for determining the antibiotic susceptibility of pathogenic bacteria.

Abstract: The present disclosure provides systems for the rapid and sensitive detection of organisms and molecules in samples. Reactants that produce Raman-active products are used in combination with Raman light scattering. Such compounds may comprise phosphates permitting the detection of phosphatases. The present disclosure can also be used to measure enzyme-kinetics.

Abstract: Disclosed herein are methods and systems for rapid detection of microorganisms in a sample, without culturing for enrichment of the microorganism. A modified bacteriophage is also disclosed which comprises a non-native indicator gene in the late gene region. The indicator product is not a fusion protein. The specificity of infectious agents allows a specific microorganism to be targeted, and an indicator signal may be amplified to optimize assay sensitivity.

Abstract: The invention concerns methods for detecting a nucleic acid of interest in a solution comprising (a) contacting a solution suspected of containing the nucleic acid of interest with a PNA capture probe and a PNA reporter probe; wherein (i) the PNA capture probe comprises at least two trans-cyclopentanes; (ii) the PNA reporter probe comprises at least six biotin groups; (iii) the PNA capture probe bound to a surface; and (iv) the PNA capture probe and the PNA reporter probe each comprise a nucleobase sequence that is complementary to different non-overlapping portions of the nucleic acid of interest; (b) detecting the presence of the PNA capture probe and the PNA reporter probe bound to the surface; wherein the nucleic acid of interest is detected when 1-1000 molecules of the nucleic acid of interest are present in the solution being tested.

Abstract: The invention relates to a light measurement apparatus for a reaction vessel, and a light measurement method, whereby the optical state on the inside of a reaction vessel can be measured efficiently and reliably.

Abstract: The present invention generally relates to devices and methods for immobilizing nucleic acids on a substrate. In certain embodiments, devices of the invention include a voltage source, and a substrate coupled to the voltage source, in which hydrophobicity of the substrate changes in response to an applied electric field and a surface of the substrate is coated with a substance that retains nucleic acids.

Abstract: The invention is directed to a method of using DNA oligonucleotides as baits to capture and selectively remove highly abundant RNAs from a heterogeneous RNA sample for improved enrichment of other RNAs that are unrelated to the highly abundant RNAs.

Abstract: A method for detecting food poisoning bacteria includes allowing a plurality of types of food poisoning bacteria including at least Staphylococcus aureus to grow at the same time using a culture medium that includes a peptone, a yeast extract, and magnesium sulfate, extracting DNA from the plurality of types of food poisoning bacteria that have been allowed to grow, adding a primer for specifically amplifying an amplification target region of the DNA of each of the plurality of types of food poisoning bacteria to a PCR solution, amplifying the amplification target region by PCR, and detecting the resulting amplified product.

Abstract: The present invention relates to methods for the rapid detection of the presence or absence of Staphylococcus aureus in a biological or nonbiological sample, The present invention includes methods of detection comprising performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, the present invention relates to primers, probes, and kits that are designed for the detection of Staphylococcus aureus.

Abstract: The present invention relates to methods for the rapid detection of the presence or absence of Staphylococcus aureus in a biological or nonbiological sample. The present invention includes methods of detection comprising performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, the present invention relates to primers, probes, and kits that are designed for the detection of Staphylococcus aureus.

Abstract: The present invention relates to methods for the rapid detection of the presence or absence of Staphylococcus aureus in a biological or nonbiological sample. The present invention includes methods of detection comprising performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, the present invention relates to primers, probes, and kits that are designed for the detection of Staphylococcus aureus.

Abstract: This invention includes methods for analyzing single-stranded nucleic acid sequences, either RNA sequences or DNA sequences (ssDNA) utilizing dyes that fluoresce when associated with double strands, so-called DNA binding dyes or dsDNA-dyes. Methods according to this invention utilize a dsDNA-dye in combination with one or more hybridization probes that hybridize to a target nucleic acid sequence and that are labeled with a non-fluorescent quencher moiety, for example, a Black Hole quencher.

Abstract: Here provided is a method for multiplex nucleic acid analysis. The method includes steps of hybridizing sets of probes to target nucleic acids in a sample, ligating the hybridized probes, amplifying the ligated probes, and assaying the amplification products to determining the presence, absence, or quantity of the target nucleic acids in the sample. The multiplexity is made available in part by adding detectable moieties and inserting stuffer sequences in primers so that amplification products may be identified on the basis of the detectable moieties and fragment sizes. Also provided is a sensitive method of detecting small copy number changes by measuring the copy number of a plurality of target sites in the nucleic acid in a test sample in comparison to a control sample and then determining the copy number of the nucleic acid based on the measured copy number of the plurality of target sites. Further provided is a kit for multiplex nucleic acid analysis and for small copy number change determination.

Abstract: The present invention provides methods of detecting and mapping chromosomal or genetic abnormalities associated with various diseases or with predisposition to various diseases, or to detecting the phenomena of large scale copy number variants. In particular, the present invention provides advanced methods of performing array-based comparative hybridization that allow reproducibility between samples and enhanced sensitivity by using the same detectable label for both test sample and reference sample nucleic acids. Invention methods are useful for the detection or diagnosis of particular disease conditions such as cancer, and detecting predisposition to cancer based on detection of chromosomal or genetic abnormalities and gene expression level. Invention methods are also useful for the detection or diagnosis of hereditary genetic disorders or predisposition thereto, especially in prenatal samples.

Abstract: Provided a target particle determining method of detecting a non-light emitting particle, including the steps of: (a) combining a non-light emitting observation particles, a solid phase carriers and a target particles in a first solution; (b) forming a complex of the target particle bound with a non-light emitting observation particle and a solid phase carrier; (c) removing the observation particles that are not bound to the target particles; (d) separating observation particles from solid phase carriers; (e) dispersing the separated observation particles in a second sample solution; (f) detecting the separated observation particles; and (g) determining the target particles that correspond to each of the detected observation particles in step (f).

Abstract: The invention relates to methods using constructs comprising a helicase and an additional polynucleotide binding moiety. The helicase is attached to the polynucleotide binding moiety and the construct has the ability to control the movement of a polynucleotide. The constructs can be used to control the movement of polynucleotides and are particularly useful for sequencing polynucleotides.

Abstract: In some embodiments, an analyte detection system is provided that includes a nanochannel, an electrode arrangement, and a plurality of nanoFET devices disposed in the nanochannel. A plurality of nucleic acid base detection components can be used that include a plurality of nanopores, a plurality of nanochannels, a plurality of hybridization probes, combinations thereof, and the like. According to other embodiments of the present teachings, different coded molecules are hybridized to a target DNA molecule and used to detect the presence of various sequences along the target molecule. A kit including mixtures of coded molecules is also provided. In some embodiments, devices including nanochannels, nanopores, and the like, are used for manipulating movement of DNA molecules, for example, in preparation for a DNA sequencing detection. Nanopore structures and methods of making the same are also provided as are methods of nucleic acid sequencing using the nanopore structures.

Abstract: Methods and kits for selectively enriching non-random polynucleotide sequences are provided. Methods and kits for generating libraries of sequences are provided. Methods of using selectively enriched non-random polynucleotide sequences for detection of fetal aneuploidy are provided.

Abstract: This invention relates to improved methods for sequencing and genotyping nucleic acid in a single molecule configuration. The method involves single molecule detection of fluorescent labeled PPi moieties released from NTPs as a polymerase extension product is created.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

Abstract: The present invention discloses uses of a HLA-B*1301 allele, comprising: 1) a use of a substance for detecting whether a person has the HLA-B*1301 allele in preparation of a product for evaluating a risk of adverse drug reactions in response to dapsone in the person; 2) a method for detecting or evaluating a risk of adverse drug reaction in response to dapsone in a person, comprising detecting whether the person has the HLA-B*1301 allele, wherein, a person with LA-B*1301 allele suffers a higher risk of adverse drug reaction upon being administered dapsone, as compared with a person without HLA-B*1301 allele, and a person with LA-B*1301 alleles at both chromosomes of a pair of homologous chromosomes suffers a higher risk of adverse drug reaction upon being administered dapsone, as compared with a person with HLA-B*1301 allele at only one of a pair of homologous chromosomes.

Abstract: A method for obtaining useful data for the determination of an individual's risk of suffering from severe sensorineural hearing loss, preferably in Ménière's disease, primers useful in the determination and kit comprising same.

Abstract: The present invention relates to an isolated polynucleotide encoding at least a part of calmodulin and an isolated polypeptide comprising at least a part of a calmodulin protein, wherein the polynucleotide and the polypeptide comprise at least one mutation associated with a cardiac disorder. The present invention also relates to a method for determining whether an individual has an increased risk of contracting a cardiac disorder, a method for diagnosing a cardiac disorder, method for treatment of an individual having a cardiac disorder, method for identifying a compound, capable of enhancing the binding of calmodulin to ryanodine receptor 2 and use of such compound in a treatment of an individual having a cardiac disorder. The invention further provides a kit that can be used to detect specific mutations in calmodulin encoding genes.

Abstract: This application is directed to the use of biomarkers for predicting the sensitivity to treatment with an FGF-18 compound in a patient having a cartilage disorder, such as osteoarthritis, cartilage injury, fractures affecting joint cartilage or surgical procedures with impact on joint cartilage (e.g., microfracture), in order to reduce the risk of adverse events and increase the overall benefit after therapy.

Abstract: Embodiments of the invention relate generally to methods for assessing the immune response related to a specific antigen or antigens. In several embodiments, the methods described herein are used to enable a recommendation for a particular type of therapy against a particular antigen, such as a foreign infectious agent or cancer cell. In several embodiments, the methods disclosed herein enable the ongoing monitoring of a subject's immune function.

Abstract: The present invention relates generally to the identification of subjects with a predisposition to recurrent depression, predicting a subject's responsiveness to therapy, and determining whether a subject has remitted from depression following therapy. In particular, provided herein are biomarkers, methods, and kits for such uses.

Abstract: The present invention discloses methods, kits, and apparatus as well as reagents and compositions associated therewith for deriving an indicator for use in diagnosing the presence, absence or degree of at least one condition in a biological subject or in prognosing at least one condition in a biological subject. Also disclosed is a biomarker signature for use in diagnosing the presence, absence or degree of at least one condition in a biological subject or in prognosing at least one condition in a biological subject. The present invention further discloses methods, kits and apparatus, as well as reagents and compositions associated therewith, for identifying biomarkers for use in a biomarker signature.

Abstract: Described are methods for predicting a clinical response to B-lymphocyte inhibiting or depleting therapies (BCIDT) using expression levels of genes of the Type I INF pathway. In another aspect, disclosed is a method for evaluating a pharmacological effect of a treatment with B-lymphocyte inhibiting or depleting therapy. More particularly, it relates to methods for prognosticating the clinical response of a patient to treatment with a soluble BCID or TCID agent, the method including obtaining at least two samples from the patient wherein a first sample has not been exposed to a soluble BCID or TCID agent and wherein at least a second sample has been exposed to a soluble BCID or TCID agent, determining the level of an IFN (preferably type I) response in the at least two samples, comparing the level of the IFN (preferably type I) response in the first sample with the level of the IFN (e.g., type I) response in the at least second sample and prognosticating the clinical response from the comparison.

Abstract: The invention provides a primer group for detecting CpO island methylation of p16 gene using methylation specific fluorescence technique. The primer group comprises a pair of oligonucleotide primers and a fluorescence-labeled probe. Said oligonucleotide primer pair has base sequence represented by SEQ ID NO.1 and SEQ ID NO.2. Said fluorescence-labeled probe has base sequence represented by SEQ ID NO.3 or SEQ NO.4.

Abstract: The present disclosure provides for and relates to the identification of novel biomarkers for diagnosis and prognosis of kidney cancer. The biomarkers of the invention show altered methylation levels of certain CpG loci relative to normal kidney tissue, as set forth.

Abstract: The invention discloses high levels of receptors for Clostridium perfringens enterotoxin (CPE) have been found in ovarian cancer and uterine cancer tissue samples. In addition, successful in vivo treatment of a mouse model of ovarian cancer with intraperitoneal injection of CPE is disclosed. High levels of Ep-CAM protein is also disclosed in ovarian cancer tissue samples. Thus, the invention provides a method of treating ovarian cancer and uterine cancer by administering CPE. The invention also provides a method of treating cancer in a mammal involving intraperitoneal administration of CPE, where at least some cancerous cells are located in or adjacent to the peritoneal cavity of the mammal. The invention also provides a method of treating ovarian cancer involving administering an anti-Ep-CAM antibody. The invention also provides a method of treating cancers expressing claudin-3 or claudin-4 by administering an antibody against claudin-3 and/or an antibody against claudin-4.

Abstract: The invention relates to methods and related products for treatment and determining modes of treatment for cancer or prognosis of cancer. Preferably the methods are related to the induction of CD80 in p53 responsive cancer cells.

Abstract: The present invention relates to prostate cancer signatures which are useful for providing a clinical assessment of prostate cancer from a biological sample of a subject. By performing initial gene expression studies on urine samples from prostate cancer and non-prostate cancer subjects, and using the PCA3/PSA prostate cancer test as a performance benchmark, the present inventors have surprisingly discovered multiple signatures that are informative in urine-based prostate cancer tests, as well as in tissue-based tests. The signatures relate to combinations of at least two prostate cancer markers whose expression pattern in urine has been validated as being associated (either positively or negatively) with a clinical assessment of prostate cancer. The prostate cancer markers can be used in conjunction with bioinformatics approaches to generate a prostate cancer score, which correlates with a clinical assessment of prostate cancer.

Abstract: The present invention provides methods for the treatment of esophageal cancer patients as well as the identification and selection of esophageal cancer patients for treatment with an anti-EGFR agent treatment including anti-EGFR antibody treatment, e.g., cetuximab treatment. In some embodiments, the drug is against a heterodimer formed by EGFR and another member of the ErbB receptor family such as EfbB2/Her2/neu.

Abstract: The present invention relates to methods for diagnosing breast cancer; methods for assigning risk of reoccurrence of breast cancer; methods for assigning risk of mortality due to breast cancer, methods of monitoring breast cancer; methods of staging breast cancer; and various devices and kits adapted to perform such methods. These methods comprise measurement gene expression from one or more protein fatty acyl transferase genes in a tissue sample, and preferably in a tumor sample, from the patient.