Abstract: The present invention comprises methods and compositions for controlling nematode parasitism in host plant. The present invention comprises novel polynucleotides and polypeptides encoded by such polynucleotides comprising one or more nucleic acid sequences disclosed herein having a nucleotide sequence comprising any one of SEQ ID NO: 1-142 or 161, a fragment or variant thereof, or a complement thereof, or a polypeptide sequence comprising any one of SEQ ID NO: 143-160, a fragment or variant thereof.

Abstract: Disclosed herein is a method for manufacturing a recombinant polypeptide of interest modified by a CTP extension in a mammalian cells culture system.

Abstract: Recombinant viral vectors, especially parvovirus vectors such as adeno-associated virus (AAV) vectors, capable of enhanced expression of heterologous sequences, and methods for their construction and use, are provided. The vectors have a structure, or are capable of rapidly adopting a structure, which involves intrastrand base pairing of at least one region in a heterologous sequence.

Abstract: The invention relates to methods of improving titer in transfection-based bioreactor culture production or transfection-based production systems using eukaryotic cells. A method of improving viral titer in a transfectionbased production system using a eukaryotic cell is provided. The method can include at least one of: harvesting a confluent population of eukaryotic cells that have progressed beyond log phase of cell growth for at least 24 hours prior to transfection; transfecting the cells by mixing the population with transfection reagents and plasmid DNA at the time of re-seeding the cells into a culture vessel, where the harvesting and transfecting steps, alone or in combination, results in an improved viral titer, by at least 2-fold, in a transfectionbased production using a eukaryotic cell.

Abstract: The embodiments disclosed herein relate to the construction of fully-deleted Adenovirus-based gene delivery vectors packaged without helper Adenovirus, and more particularly to their use in gene therapy for gene and protein expression, vaccine development, and immunosuppressive therapy for allogeneic transplantation. In an embodiment, a method for propagating an adenoviral vector includes (a) providing an Adenovirus packaging cell line; (b) transfecting a fully-deleted Adenoviral vector construct into the cell line; and optionally (c) transfecting a packaging construct into the cell line, wherein the fully-deleted Adenoviral vector construct and optionally the packaging construct can transfect the Adenovirus packaging cell line resulting in the encapsidation of a fully-deleted Adenoviral vector independent of helper Adenovirus. In an embodiment, a target cell is transduced with the encapsidated fully-deleted Adenoviral vector for treating a condition, disease or a disorder.

Abstract: Methods of multiplex genome engineering in cells using Cas9 is provided which includes a cycle of steps of introducing into the cell a first foreign nucleic acid encoding one or more RNAs complementary to the target DNA and which guide the enzyme to the target DNA, wherein the one or more RNAs and the enzyme are members of a co-localization complex for the target DNA, and introducing into the cell a second foreign nucleic acid encoding one or more donor nucleic acid sequences, and wherein the cycle is repeated a desired number of times to multiplex DNA engineering in cells.

Abstract: Disclosed herein are methods and compositions for enhancing insertion of transgene sequences encoding proteins that is aberrantly expressed in disease or disorder such as a lysosomal storage disease or a hemophilia by administering one or more topoisomerases inhibitors, one or more stabilizers of R loop formation or inhibitors of R-loop repair and/or one or more up-regulators of the TC-NER pathway to the target cell.

Abstract: The invention provides for delivery, engineering and optimization of systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are delivery systems and tissues or organ which are targeted as sites for delivery. Also provided are vectors and vector systems some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in eukaryotic cells to enable genome engineering in an organism to recapitulate the genetic complexity of disease or a condition and further interrogate gene function.

Abstract: The invention relates to a two phase fermentation process for producing an organic compound, in particular an isoprenoid and to a bioreactor comprising a two phase fermentation system for producing an organic compound.

Abstract: A system and method for converting biomass with no chemical pretreatment is disclosed. Combination of a microbial system and the use of mechanical disruption during fermentation may help achieve high conversion rate without the extra cost and undesirable by-products typically associated with the pretreatment process.

Abstract: A process for preparing 1-butanol from butane by incubating a host organism having a functional P153 enzyme under elevated butane pressure in the presence of oxygen.

Abstract: Provided herein is technology relating to genetically modified organisms and particularly, but not exclusively, to compositions comprising one or more genetically modified microorganisms, and related methods and systems, for producing liquid fuels from alkanes such as methane.

Abstract: The present invention relates to an improved biocatalytic process for producing vanillin from ferulic acid based on a genetically engineered Pseudomonas strains, as well as to said Pseudemonas strains.

Abstract: Provided herein are recombinant yeast cells having an active 3-Hydroxypropionic Acid (3-HP) pathway and further comprising a heterologous polynucleotide encoding an aspartate 1-decarboxylase (ADC) of the Class Insecta, Bivalvia, Branchioporia, Gastropoda, or Leptocardii. Also described are methods of using the recombinant yeast cells to produce 3-HP and acrylic acid.

Abstract: A method of producing a chemical product includes cultivating microorganisms or culture cells in a fermentation tank; transferring a culture liquid from the fermentation tank to a membrane separation tank to filter the culture liquid through a separation membrane; and collecting a fermentation product from a filtration liquid as the chemical product while refluxing an unfiltered culture liquid that has not been filtered to be joined to the culture liquid on an upstream side of the membrane separation tank, wherein one portion of the culture liquid to be transferred from the fermentation tank is allowed to bypass the membrane separation tank depending on a pressure at a culture liquid flow-in side of the membrane separation tank.

Abstract: The invention relates to a method for the enzyme-catalysed hydrolysis of polyacrylic acid esters. According to the method, at least one polyacrylic acid ester is provided and incubated with at least one enzyme selected from enzymes (EC 3.1) acting on ester bindings, until the ester groups contained in the polyacrylic acid ester are partially or fully hydrolytically split, and optionally the modified polymer obtained thereby is isolated. The invention also relates to the enzymes used and mutants thereof, nucleic acids coding for the enzymes, vectors comprising the nucleic acids, micro-organisms comprising the vectors, and the use of the enzymes, the vectors or the micro-organisms for carrying out a method for the enzyme-catalysed hydrolysis of polyacrylic acid esters. The present application also relates to polymer reaction products that can be obtained by the method, and methods for producing esterases.

Abstract: A method of producing bi-functional fatty acids comprising introducing into a host cell or organism, which comprises one or more ?- or ?-1 functionalized acyl-CoAs, and expressing therein a KASIII, which can use one or more of the ?- or ?-1 functionalized acyl-CoAs as a substrate; a method of producing a ?-1 hydroxy branched fatty acid, a ?-1 branched fatty acid, or a combination thereof by culturing a mutant E. coli, which does not express a functional KASIII from the endogenous fabH gene and expresses a phaA and a phaB and a functional exogenous KASIII; and a mutant E. coli, a method of making the mutant, a culture comprising the mutant, and a composition comprising ?-1 hydroxy branched fatty acids, a ?-1 branched fatty acids, or a combination thereof obtained from the culture.

Abstract: The invention provides novel methods for making or modifying oils, e.g., plant animal or microbial oils, such as vegetable oils or related compounds, that are low in a particular fatty acid(s), for example, low linoleic oils, linolenic oils, low palmitic oils, low stearic oils or oils low in a combination thereof.

Abstract: Provided are a novel modified ornithine decarboxylase protein having improved putrescine productivity and a use thereof.

Abstract: The present invention relates to a process for producing a syrup comprising liquefying an aqueous granular starch slurry with an alpha-amylase variant comprising an alteration at one or more positions corresponding to any of positions 1, 2, 68, 71, 126, 133, 142, 144, 156, 158, 176, 185, 201, 205, 213, 239, 279, 316, 318, 360, 416, 437 and 450 of SEQ ID NO: 1 to provide liquefied starch-containing material; saccharifying the liquefied starch-containing material in the presence of a glucoamylase, and a pullulanase derived from Bacillus deramificans, Bacillus subtilis, Bacillus amyloderamicans, or Bacillus acidopullulyticus to provide a dextrose syrup, and optionally isomerizing to provide a fructose syrup.

Abstract: Disclosed is a method of preparing pure or substantially pure D-myo-inositol-3-phosphate from glucose-6-phosphate and/or fructose-6-phosphate. The method may also be applied to protected and/or derivative forms of glucose-6-phosphate and/or fructose-6-phosphate so as to form protected/derivative forms of D-myo-inositol-3-phosphate, for use in further chemical reactions. The enzyme D-myo-inositol-3-phosphate synthase (INO1) is contacted with the glucose-6-phosphate and/or fructose-6-phosphate to generate labeled or unlabeled, protected or unprotected D-myo-inositol-3-phosphate, which may be further reacted and/or purified.

Abstract: The present invention relates to a method of preparing galactooligosaccharides having % a galactosyllactose content of 40 wt % or more.

Abstract: The present disclosure provides compositions and methods related to the degradation of cellulose and cellulose-containing materials. CDH-heme domain polypeptides and GH61 polypeptides and related polynucleotides and compositions are provided herein.

Abstract: This document describes biochemical pathways that include the production of 3-oxopent-4-enoyl-CoA by condensation of acryloyl-CoA and acetyl-CoA using a ?-ketothiolase with a SER-HIS-HIS catalytic triad. These pathways described herein rely on enzymes such as, inter alia, dehydrogenases, dehydratases and ?-ketothiolases.

Abstract: The invention provides improved methods for synthesizing polynucleotides, such as DNA and RNA, using enzymes and specially designed nucleotide analogs. Using the methods of the invention, specific sequences of polynucleotides can be synthesized de novo, base by base, in an aqueous environment, without the use of a nucleic acid template. Because the nucleotide analogs have an unmodified 3? OH, i.e., as found in “natural” deoxyribose and ribose molecules, the analogs result in natural polynucleotides suitable for incorporation into biological systems.

Abstract: This disclosure relates to the field of the microbial production of specific types of glycolipids that are potentially useful as replacements for petroleum-based detergents and emulsifiers. This disclosure, more specifically, discloses the usage of yeasts having a dysfunctional acetyltransferase for producing high amounts of bolaamphiphilic glycolipids when using conventional and cheap substrates. Furthermore, the disclosure relates to yeasts having a dysfunctional acetyltransferase optionally combined with a dysfunctional lactonase and/or second glucosyltransferase. The latter microorganisms are capable of producing high amounts of bolaamphiphilic sophorolipids.

Abstract: The present invention relates to a biosensor capable of measuring the total concentration of one or a plurality of amino acids with the use of a reagentless system comprising an electrode modified by hydrogel that comprises at least one enzyme that oxidizes at least one substrate that is at least one amino acid. In some embodiments, the biosensor comprises a hydrogel comprising alginate. In some embodiments, the biosensor comprises use of a thermophilic bacterial metabolic enzyme immobilized or attached to the hydrogel.

Abstract: Disclosed herein are methods for screening clinical or biological samples to determine the presence of L-form bacteria within the sample. Methods include contacting a sample to a liquid growth medium and incubating the liquid growth medium at a temperature lower than 37 degrees C. The liquid growth medium is monitored for L-form bacterial growth. An amount of the liquid growth medium is transferred as an inoculant to a solid growth medium, and the solid growth medium is incubated under conditions that maintain a hydrated state of the inoculant to enable the L-form bacteria to efficiently interface with the solid growth medium and continue to grow.

Abstract: Compositions and methods for detecting pathogens are provided. In one aspect, a method for detecting a pathogen on or within an object comprises: providing a detection agent configured to generate a visible indication when exposed to the pathogen; contacting the detection agent with the object; and visually detecting the presence or absence of the visible indication, wherein the presence of the visible indication indicates that the pathogen is present on or within the object.

Abstract: A method for producing raw materials and finished products intended for food and pharmaceutical industries which are devoid of any toxicity toward probiotic bacteria is described. A probiotic bacteria-based toxicity test method is also described.

Abstract: A sampling probe, system and analysis method is disclosed. The sampling probe in one embodiment is constructed of a silicon substrate having a first channel, a second channel, a first tapered tip with an opening, and a second tapered tip with an opening, wherein the first channel extends from the first tapered tip opening to the second tapered tip opening, and wherein the second channel extends from an inlet port to a junction with the first channel.

Abstract: Provided is a method for diagnosing cancer through a difference with a control group in view of the ratio of a deglycosylated peptide fragment and a non-glycosylated peptide fragment in a protein including an N-linked glycosylation motif. Further provided is a method for diagnosing cancer through the detection of the glycosylation ratio in the protein according to the subject matter enables the diagnosis of cancer with high specificity and sensitivity using at least one existing marker, and can be useful in discovering new markers for diagnosing cancer.

Abstract: The present invention is comprised of a novel assay and related kit for analyzing the L-glutamine content in samples such as cell cultures and blood serum, plasma, urine, cell, tissue samples. This enzymatic reaction is highly specific to L-glutamine and the enzyme converts L-glutamine to the blue compound indigoidine which is visible and can be accurately measured using a spectrophotometer at 600 nm. This single-enzyme assay provides a quick and accurate assay for determination of the L-glutamine concentration. A kit is designed and described based on this L-glutamine assay.

Abstract: Methods and composition related to the engineering of a novel protein with methionine-?-lyase enzyme activity are described. For example, in certain aspects there may be disclosed a modified cystathionine-?-lyase (CGL) comprising one or more amino acid substitutions and capable of degrading methionine. Furthermore, certain aspects of the invention provide compositions and methods for the treatment of cancer with methionine depletion using the disclosed proteins or nucleic acids.

Abstract: Provided are methods of labeling and analyzing features along at least one macromolecule such as a linear biopolymer, including methods of mapping the distribution and frequency of specific sequence motifs or the chemical or proteomic modification state of such sequence motifs along individual unfolded nucleic acid molecules. The present invention also provides methods of identifying signature patterns of sequence or epigenetic variations along such labeled macromolecules for direct massive parallel single molecule level analysis. The present invention also provides systems suitable for high throughput analysis of such labeled macromolecules.

Abstract: The present invention relates to a newly developed immediate chromatin immunoprecipitation procedure (“ZipChIP”). ZipChIP significantly reduces the time and increases sensitivity allowing for rapid screening of multiple loci. ZipChIP enables the detection of histone modifications (e.g., H3K4 mono- and trimethylation) and at least two yeast histone demethylases, Jhd2 and Rph1, which were previously found difficult to detect using standard methods. ZipChIP further relates to the enrichment of the histone deacetylase Sir2 at heterochromatin in yeast and enrichment of the chromatin remodeler, PICKLE, in Arabidopsis thaliana.

Abstract: A method of analysing a sample includes providing a first part of the sample and a second part of the sample. A first analysis is conducted on the first part of the sample and the results of the first analysis are considered. A second analysis is conducted on the second part of the sample, the second analysis being conducted according to a procedure using a value for each of one or more characteristics of the procedure. The consideration of the results of the first analysis is used to determine whether the value for one or more of the characteristics of the procedure is changed to a different value. The second analysis is started before the results of the first analysis are obtained.

Abstract: A cartridge for assay of a target nucleic acid sequence in a liquid sample. The cartridge comprises: a fluidic portion through which the sample flows and in which nucleic acid amplification and detection takes place; a pneumatic portion which controls flow through the fluidic portion; and at least two electrodes which provide a potential difference for the detection of an amplified nucleic acid of interest.

Abstract: Primers and probes specific to genes encoding carbapenem-resistant Enterobacteriaceae (CREs) that include KPC (Klebsiella pneumoniae carbapenemase), NDM-1 (New Delhi Metallo-beta-lactamase), VIM (Verona Integron-Mediated Metallo-?-lactamase), IMP-type carbapenemase and OXA 48 (oxacillinase), that cause resistance in Enterobacteriaceae bacteria, are described herein, with methods and kits for using these primers and probes to detect target nucleic acids. In the methods described, nucleic acids present in a clinical or test sample obtained from a biological sample or tissue suspected of containing the the NDM1, KPC, IMP, VIM and OXA genes are amplified and corresponding sequences for the NDM1, KPC, IMP, VIM and OXA genes are detected. The amplified nucleic acid can be detected by a variety of state of the art methods, including fluorescence resonance energy transfer (FRET), radiolabels, enzyme labels, and the like.

Abstract: A case for containing a plurality of biological samples contains a base, a substrate and a cover. The substrate is attached to the base and comprises a plurality of reaction regions configured to receive one or more biological samples. The cover comprises an inner surface and is configured to be attached to the base such that the base and cover together provide a cavity containing the substrate. The inner surface includes a central area and a recessed area disposed about the central area. The central area is configured to cover the reaction regions, while the recessed area is offset from the central area in a direction normal to the inner surface.

Abstract: The present invention relates to predicting the risk of developing hypertriglyceridemia in a subject by quantitating the amount of enterobacteria, e.g., E. coli, in the subject's gastrointestinal system. The invention also relates to treating a subject with hypertriglyceridemia or at risk of having the condition.

Abstract: Primers and probes specific to the genes encoding extended spectrum beta-lactamase that involves CTX-M groups 1 and 9 that cause extended beta-lactamase resistance in bacteria are described herein, with methods and kits for using these primers and probes to detect CTX-M groups 1 and 9 nucleic acids. In the methods described, nucleic acids present in a clinical or test sample obtained from a biological sample or tissue suspected of containing the CTX-M groups 1 and 9 gene are amplified and corresponding sequences for CTX-M groups 1 and 9 are detected. The amplified nucleic acid can be detected by a variety of state of the art methods, including fluorescence resonance energy transfer (FRET), radiolabels, enzyme labels, and the like.

Abstract: The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences.

Abstract: The invention provides methods and compositions for enhancing the speed and sensitivity of helicase-dependent amplification through the use of an endonuclease.

Abstract: The present invention is directed to a method for performing RT-PCR for amplifying a target RNA comprising the steps of a) lysis of a cellular sample which is supposed to contain the target RNA with a lysis buffer comprising between 0.2 M and 1 M Guanidine Thiocyanate, b) diluting the sample to an extend such that Guanidine Thiocyanate is present in a concentration of about 30 to 50 mM, e) reverse transcribing in the presence of a mixture of first strand cDNA synthesis primers, the mixture consisting of oligo dT primers and random primers, and d) subjecting the sample to multiple cycles of thermocycling protocol and monitoring amplification of the first strand cDNA in real time, characterized in that steps a) to c) are done in the same vessel.

Abstract: This disclosure describes, in one aspect, methods for DNA sequencing and performing epigenomic analyses. Generally, the methods include immobilizing a plurality of copies of a DNA molecule on a surface, stretching at least a portion of the immobilized DNA molecules, and sequencing at least a portion of the immobilized, stretched DNA molecules.

Abstract: A system for determining nucleic acid sequences, including (a) an array of nucleic acid features; (b) a fluidic apparatus configured to deliver sequencing reagents, including polymerases and nucleotides, to the array; (c) a detector configured to obtain pre-equilibrium kinetic measurements from the array at a resolution that distinguishes individual nucleic acid features; (d) a control module having instructions for (i) directing the fluidic apparatus to deliver the sequencing reagents to the array, and (ii) directing the detection apparatus to obtain the kinetic measurements; and (e) an analysis module having instructions for (i) processing the kinetic measurements to determine binding of the polymerase molecules to the nucleic acid features at several pre-equilibrium time points, thereby determining a transient state of the polymerase molecules at the nucleic acid features, and (ii) identifying nucleic acid features that correctly incorporate the nucleotide molecules based on the transient state of the poly

Abstract: In one implementation, a method is described. The method includes determining an operational characteristic of sensors of a sensor array. The method further includes selecting a group of sensors in the array based on the operational characteristic of sensors in the group. The method further includes enabling readout of the sensors in the selected group. The method further includes receiving output signals from the enabled sensors, the output signals indicating chemical reactions occurring proximate to the sensors of the sensor array.

Abstract: The invention is directed to apparatus and chips comprising a large scale chemical field effect transistor arrays that include an array of sample-retaining regions capable of retaining a chemical or biological sample from a sample fluid for analysis. In one aspect such transistor arrays have a pitch of 10 ?m or less and each sample-retaining region is positioned on at least one chemical field effect transistor which is configured to generate at least one output signal related to a characteristic of a chemical or biological sample in such sample-retaining region.

Abstract: The invention generally relates to nucleotide analogs and methods of their use in sequencing-by-synthesis reactions. In certain embodiments, the invention provides a nucleotide analog including a detectable label attached to a nitrogenous base portion of a nucleotide analog by a cleavable linker, in which contact of the analog with at least one activating agent results in cleavage of the label and elimination of the linker, thereby producing a natural nucleotide, a 9-deaza-G, 9-deaza-A, or ?-uridine.