Abstract: The present invention relates to novel bacteria and the uses thereof. The invention particularly relates to bacteria having a metabolic pathway ratio between pentose phosphate and glycolysis greater than 0.5, and their uses in the chemical, pharmaceutical and agro-chemical industries, e.g., for producing compounds of industrial interest.

Abstract: The invention relates to a method for the simultaneous integration of two or more copies of a polynucleotide of interest into the chromosome of a fungal host cell comprising at least two pairs of recognition sequences of a site-specific recombinase, each pair flanking a resident negative selection marker; transformation of the cell with a construct carrying a gene of interest also flanked by the recognition sequences to ensure double-crossover events after transient expression of the recombinase, followed by selection for excision of all negative selection markers from the cell.

Abstract: Polynucleotides and isolated polypeptides, nucleic acid constructs comprising the isolated polynucleotides, transgenic plants expressing same and methods of using same for increasing abiotic stress tolerance, yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, and/or nitrogen use efficiency of a plant are disclosed.

Abstract: Methods and means are provided to modify in a targeted manner the plant genome of transgenic plants comprising chimeric genes wherein the chimeric genes have a DNA element commonly used in plant molecular biology. Re-designed meganucleases to cleave such an element commonly used in plant molecular biology are provided.

Abstract: Methods are provided for making a citrus plant that is capable of producing fruit with increased levels of anthocyanins in the fruit when compared to a citrus fruit from a wild-type or control plant. Such methods involve increasing the expression of Ruby, an R2R3 Myb transcription factor, in a citrus plant, particularly in the fruit of a citrus plant. Further provided are citrus plants, citrus fruit, and citrus plant cells made by such methods, nucleic acid molecules and expression cassettes comprising nucleotide sequences that encode Ruby, and the Ruby proteins encoded thereby.

Abstract: The present invention relates to transgenic guayule plants that produce increased amounts of rubber uses thereof.

Abstract: This invention is in the field of plant molecular biology. More specifically, this invention pertains to isolated nucleic acid fragments encoding PAE or PAE-Like proteins in plants and seeds and the use of such fragments to modulate expression of a gene encoding PAE or PAE-Like protein activity in a transformed host cell.

Abstract: The present invention relates to the field of plant molecular biology, more particularly Jatropha microsomal co6 oleate desaturases. The present invention also relates to Jatropha plants or plants of other oil crops having seeds with altered ratios of monosaturated and polyunsaturated fats. In particular, the present invention relates to Jatropha plants or plants of other oil crops where the plants exhibit elevated levels of oleic acid.

Abstract: The present invention relates to a genetically modified plant having an increased amount of oil in its green biomass as compared to the oil in the green biomass of its non-genetically modified counterpart. The plants may be used for producing bio-fuels such as biodiesel fuel.

Abstract: Polynucleotide sequences encoding diacylglycerol acyltransferase genes and the use of these acyltransferases for increased seed storage lipid production and altered fatty acid profiles in oilseed plants are disclosed. Transgenic soybean seed having increased total fatty acid content of at least 20% and altered fatty acids when compared to the total fatty acid content of non-transgenic, null segregant soybean seed are described. Methods for increasing the total fatty acid content of a soybean seed by at least 20% include steps of transformation and selection.

Abstract: Methods of making a targeted modification in a male fertility gene in the genome of a plant are disclosed. The methods involve contacting a plant cell with an engineered double-strand-break-inducing agent capable of inducing a double-strand break in a target sequence in the male fertility gene and identifying a cell comprising an alteration in the target sequence. Also disclosed are plants, plant cells, plant parts, and seeds comprising a male fertility gene with an alteration in a male fertility gene. Nucleic acid molecules comprising male fertility genes with at least one targeted modification therein, optimized nucleic acid molecules encoding endonucleases that are engineered double-strand-break-inducing agents and expression cassettes, host cells, and plants comprising one or more of the nucleic acid molecules are further disclosed.

Abstract: The present invention provides polynucleotide vectors for high expression of heterologous genes, and methods for constructing such vectors. Some vectors further comprise novel transposons and transposases that further improve expression. Further disclosed are vectors that can be used in a gene transfer system for stably introducing nucleic acids into the DNA of a cell. The gene transfer systems can be used in methods, for example, but not limited to, gene expression, gene therapy, insertional mutagenesis, or gene discovery.

Abstract: A method of generating a particle is disclosed, the particle being for delivery of a polynucleotide to a target cell. The method comprises (a) contacting the polynucleotide with a composition comprising cationic molecules, wherein the cationic molecules condense the polynucleotide by electrostatic interactions to generate a complex, wherein the cationic molecules are not comprised in a liposome; and (b) covalently binding the complex to a targeting moiety at a pH equal to or below about 4.5, thereby generating the particle for delivery of the polynucleotide agent to the target cell. Use of the particles and compositions comprising same are also disclosed.

Abstract: Methods and compositions for treatment of a genetic disease are provided.

Abstract: The disclosure provides a process for producing a fermentation product from a lignocellulosic feedstock. The process describes soaking a lignocellulosic feedstock in an aqueous solution to produce a soaked feedstock. The soaked feedstock is at least partially dewatered and the at least partially dewatered feedstock is subjected to pretreating in the presence of sulfur dioxide, sulfurous acid or a combination thereof to produce a pretreated feedstock composition. The pretreated feedstock composition is fed to an enzymatic hydrolysis in which the concentration of dissolved solids fed to the enzymatic hydrolysis is at least 50% (w/w) of the concentration of dissolved solids in the pretreated feedstock composition. The cellulose in the pretreated feedstock composition is hydrolyzed with cellulase enzymes in the presence of the dissolved solids to produce glucose. The glucose is fermented to produce the fermentation product.

Abstract: The present application provides a method for producing organic acid, such as acetic acid, propionic acid, butyric acid, or another high-quality raw material designed for methane fermentation and obtained by converting waste paper and other forms of cellulose-based biomass to organic acid, wherein said method comprising a step for reacting rumen fluid collected from a ruminant animal with cellulose-containing waste matter. This method provides the effective use of cellulose-containing waste matter, which is a high-quality fermentation resource.

Abstract: The present disclosure relates to a novel strain capable of saccharifying and fermenting biomass-derived cellulose and a recombinant strain thereof with improved biomass saccharification capability. The present disclosure also relates to a method for producing a material useful as a bioenergy source material such as ethanol, acetic acid, formic acid, etc. using the strain or the recombinant strain. The strain or the recombinant strain may be usefully used in bioenergy industry.

Abstract: The invention relates to a process for producing one or more polyunsaturated fatty acids by means of heterologous gene expression comprising the steps of providing a production organism which comprises a heterologous gene cluster encoding a polyunsaturated fatty acid biosynthetic pathway encompassing a subsequence ER encoding an enoylreductase and a subsequence AT encoding an acyltransferase, growing the production organism in the presence of a fermentable carbon source whereby one or more polyunsaturated fatty acids are produced, and optionally recovering the one or more polyunsaturated fatty acids.

Abstract: The present invention describes a method for producing a useful metabolite using a bacterium of the family Enterobacteriaceae, particularly a bacterium belonging to the genus Escherichia, which has been modified to contain a gene(s) expression system including elements of the LysR-type protein-regulated transcriptional machinery modified in such a way that auto-inducible positive feedback regulation of the system is mediated by a coinducer. The method is suitable for producing branched-chain L-amino acids, particularly L-valine, L-isoleucine and L-leucine; and D-pantothenic acid.

Abstract: Immune function of an animal can be modulated by administration of a composition that includes algae meal or beta glucan. The algae meal can be made by growing Euglena using particular methods and conditions, including certain continuous, semi-continuous, fed-batch, and repeat batch methods in sterile fermenters. Euglena provides a form of beta glucan that is different from other organisms, where the beta glucan is predominantly unbranched beta-1,3-glucan. Use of algae meal and beta glucan produced by the disclosed processes can improve the wellbeing of an animal or human, and may augment or even replace the use of antibiotics in certain circumstances.

Abstract: A method for the secretory production of a glycoprotein having a human-type sugar chain, comprising a step of introducing a gene of an enzyme capable of performing a transfer reaction of a galactose residue to a non-reducing terminal acetylglucosamine residue, and a gene of heterologous glycoprotein, to obtain a transformed plant cell, a step of culturing the plant cell, and a step of recovering the culture medium of the plant cell. The method further includes isolating the glycoprotein from the culture medium and contacting the isolated glycoprotein with a sialic acid transferase to add a sialic acid residue attached to the galactose residue in the N-glycan.

Abstract: A sampling device for a specimen container having a closure sealing the interior of the specimen container from the environment includes a needle, a body coupled to the needle and defining a chamber in fluid communication with the needle, the body further comprising a port forming an opening in the body, the port in fluid communication with the chamber. A multitude of the sampling devices may be stored in a cassette. The sampling devices may include a second chamber for separation and concentration of a microbial agent present in a sample. In this configuration second chamber is connected to the first chamber via a valve or the like.

Abstract: The invention is directed to droplet actuator devices and assay methods. The invention includes assay methods of conducting an assay comprising combining a sample with an umbelliferyl derivative, wherein the sample potentially comprises an enzyme capable of cleaving the umbelliferyl derivative and where the umbelliferyl derivative comprises an umbelliferyl core modified with one or more modifying moieties.

Abstract: The invention relates to methods for the determination of vitamin B6 in samples as well as to reagent compositions for assaying a sample for vitamin B6 and to a test kit suitable for carrying out the methods according to the present invention. Further, the invention relates to the use of such methods for the application to different analyzing devices such as micro-titer plate readers and fully automated clinical chemistry analyzers (autoanalyzers).

Abstract: Provided is a compound comprising the structure: (SIG)-(SI-MOD)m. In this compound, SIG is a signaling molecule, SI is a self-immolative structure bound to SIG such that SIG has a reduced signal relative to the signal of SIG without SI, MOD is a moiety bound to SI that is subject to modification by an activator, and m is an integer from 1 to about 10. With this compound, when MOD is modified by an activator, SI is destabilized and self-cleaved from SIG such that SIG generates an increased signal. Also provided is a method of determining whether a sample comprises an activator, using the above-described compound. Additionally provided is a method of determining whether a cell comprises a nitroreductase using the above-described compound where nitroreductase is the activator. Further provided is a method of determining whether a mammalian cell is hypoxic using the above-described compound where nitroreductase is the activator.

Abstract: The invention provides compounds, compositions, methods, substrates, and kits useful for analyzing the metabolic activity in cells, tissue, and animals and for screening test compounds for their effect on cytochrome P450 activity. In particular, a one-step and two-step methods using luminogenic molecules, e.g. luciferins or coelenterazines, that are cytochrome P450 substrates and that are also bioluminescent enzyme, e.g., luciferase, pro-substrates are provided. The present method further provides a method for stabilizing and prolonging the luminescent signal in a luciferase-based assay using luciferase stabilizing agents such as reversible luciferase inhibitors.

Abstract: Secreted luciferases which are different from those known heretofore have been desired. The present invention provides a luciferase mutant comprising an amino acid sequence in which at least one amino acid selected from amino acids at the positions of 1 to 4 is deleted in the amino acid sequence of SEQ ID NO: 2.

Abstract: The invention relates to the preparation of a biological sample for performing verifications and examinations, wherein the aim of the invention is the creation of a method for preparing a biological sample having an improved PCR sensitivity compared to the reference standard having standard PCR without having to raise the cost thereof.

Abstract: Provided herein is a method of using transposition to improve methods of sequencing RNA molecules. Provided herein is a method of tagging nucleic acid duplexes, such as DNA:RNA duplexes or DNA:DNA duplexes. The method includes the steps of providing a transposase and a transposon composition, providing one or more nucleic acid duplexes immobilized on a support, and contacting the transposase and transposon composition with the one or more nucleic acid duplexes under conditions wherein the one or more nucleic acid duplexes and transposon composition undergo a transposition reaction to produce one or more tagged nucleic acid duplexes, wherein the transposon composition comprises a double stranded nucleic acid molecule comprising a transferred strand and a non-transferred strand.

Abstract: A method for detecting variation of gene based on fluorescence quenching quantification comprises: performing single base extension at a specific site of a gene to be detected with marked probes and marked dideoxyribonucleotide triphosphate; detecting fluorescence quenching values, and determining SNP of the gene to be detected. The present invention also provides an oligonucleotide probe for the method.

Abstract: The present invention provides a new and improved oligonucleotide detection method based on the nanopore technology with a probe containing a complementary sequence to the target oligonucleotide and a terminal extension at the probe's 3? terminus, 5? terminus, or both termini. The improved nanopore sensor with the probe enables sensitive, selective, and direct detection, differentiation and quantification of target oligonucleotides such as miRNAs. The inventive detection method may also be employed as a non-invasive and cost-effective diagnostic method for cancer detection based on miRNA levels in the patient's blood sample.

Abstract: Methods and systems for detecting allelic imbalance using nucleic acid sequencing are provided.

Abstract: Disclosed here is a method for the detection of a naturally occurring mutation in a target sequence in one or more members of a population, comprising: providing a plurality of pools of amplification products each comprising the target sequence amplified from genomic DNA of a subset of the one or more members of the population, wherein each pool of the amplification products shares a unique pool identifier; determining the nucleotide sequence of the amplification products using high throughput sequencing; and identifying mutations by clustering/aligning the sequences of the amplified products without the use of an enzyme which recognizes and cuts single nucleotide sequence mismatches and without performing heteroduplex analysis, and identifying the one or more members carrying the mutation using the pool identifier.

Abstract: Methods for identifying and/or distinguishing a homogeneous population of cells based on their replication domain timing profile using high resolution genomic arrays or sequencing procedures are provided. These methods may be used to compare the replication timing profile for a population of cells to another replication timing profile(s), a replication timing fingerprint, and/or one or more informative segments of a replication timing fingerprint, which may be simultaneously or previously determined and/or contained in a database, to determine whether there is a match between them. Based on such information, the identity of the population of cells may be determined, or the identity of the population of cells may be distinguished from other populations of cells or cell types. Methods for determining a replication timing fingerprint for particular cell types are also provided.

Abstract: Devices and methods for controlling reversible chemical reactions at solid-liquid interfaces are disclosed. In particular, the invention relates to a method of increasing reaction rates by concentrating a target molecule in a liquid phase in the region of a reactant or ligand immobilized on a solid followed by removal of the liquid phase and replacement with an immiscible phase, such as an immiscible gas or liquid to impede the reverse reaction. Devices for performing this method to increase the rates and degree of completion of kinetically limited ligand binding or nucleic acid hybridization reactions in affinity chromatography and microarray applications are also disclosed.

Abstract: The present invention relates to a method for the detection of nucleic acid synthesis and/or amplification, characterized in that the method includes adding at least one colorimetric metal indicator and at least one bland magnesium chelator to a reaction mixture for nucleic acid amplification. The present invention further relates to a kit for carrying out such a method and to the use thereof in the health, food and agricultural or veterinary fields.

Abstract: The present invention provides methods and compositions for analyzing nucleic acid sequences. In some aspects, the methods utilize clonal objects, such as DNA balls, that have been captured on beads. Using the methods described here, compositions are fabricated wherein a bead and one clonal object are affinity bound or hybridized to each other through an affinity binding patch or hybridization patch on the surface of the bead. The invention also provides a population of beads having affinity bound or hybridized clonal objects at a ratio of 1:1. The invention additionally provides methods for amplifying a target nucleic acid molecule utilizing the compositions described herein.

Abstract: A method for sequencing includes steps of (a) providing first and second nucleic acid templates, wherein the two templates have different sequences; (b) extending a first primer bound to the first template using a first polymerase species and a first set of nucleotide analogs; (c) extending a second primer bound to the second template using a second polymerase species and a second set of nucleotide analogs, wherein the first polymerase species is different from the second polymerase species and wherein the first set of nucleotide analog is different from the second set of nucleotide analog, (d) detecting the first and second primer extension products; and (e) repeating steps (b) through (d), thereby determining the different sequences of the first and second templates.

Abstract: Provided herein is a method of sample analysis. In certain embodiments, the method comprises: a) cross-linking protein of a cell using a first compound to produce a first cross-linked product comprising cross-linked protein, and RNA; b) contacting the first cross-linked product and a second compound under conditions by which an oligonucleotide portion of the second compound hybridizes to the RNA; c) activating a reaction the first and second compound, thereby covalently crosslinking the oligonucleotide to the cross-linked protein to produce a second cross-linked product; d) isolating the second cross-linked product using an affinity tag; and e) analyzing the isolated second cross-linked product. Compounds for performing the method are also provided.

Abstract: Disclosed are methods for differentiating fertile and sterile plant lines by detecting markers in chloroplast DNA from plants that have not yet flowered as well as from plant seeds. The method may be applied in selecting a seed lot based on the level of contamination of normal fertile plant line seeds being below a predetermined threshold, e.g., below 1% or 0.1%.

Abstract: Gene expression profiling is a powerful tool that has varied utility. It enables classification of multiple myeloma into subtypes and identifying genes directly involved in disease pathogensis and clinical manifestation. The present invention used gene expression profiling in large uniformly treated population of patients with myeloma to identify genes associated with poor prognosis. It also demonstrated that over-expression of CKS1B gene, mainly due to gene amplification that was determined by Fluorescent in-situ hybridization to impart a poor prognosis in multiple myeloma. It is further contemplated that therapeutic strategies that directly target CKS1B or related pathways may represent novel, and more specific means of treating high risk myeloma and may prevent its secondary evolution.

Abstract: Described herein are methods and compositions for the diagnosis, prognosis and treatment of ovarian cancer. Also described are methods of identifying anti-cancer agents.

Abstract: It has been discovered that amplifications in the gene coactivator activator (CoAA) blocks stem cell differentiation and induces cancer stem cells. One embodiment provides compositions and methods for treating or alleviating one or more symptoms associated with cancer due to gene amplifications in CoAA. Another embodiment provides methods and compositions for detecting cancer due to gene amplifications in CoAA. Still another embodiment provides methods for identifying compounds, antibodies and nucleic acid molecules that are useful for treating cancer due to gene amplifications in CoAA. Preferably the disclosed compositions antagonize or interfere with the CoAA amplicons and the biological activity of CoAA and or splice variants thereof.

Abstract: Whole exome sequencing of 12 tumor-normal DNA pairs, RNAseq analysis and targeted deep sequencing identified new genetic alterations in PTCL transformation. These analyses identified highly recurrent epigenetic factor mutations in TET2, DN-MT3A and IDH2 as well as a new highly prevalent RHOA p.Gly17Val (NM_001664) mutation present in 22/35 (67%) of angioimmunoblastic T-cell lymphomas (AITL) and in 8/44 (18%) not otherwise specified PTCL (PTCL NOS) samples. Mechanistically, the RHOA Gly17Val protein interferes with RHOA signaling in biochemical and cellular assays, an effect potentially mediated by the sequestration of activated Guanine Exchange Factor (GEF) proteins. In addition, new and recurrent, genetic defects are described including mutations in FYN, ATM, B2M and CD58 implicating SRC signaling, impaired DNA damage response and escape from immune surveillance mechanisms in the pathogenesis of PTCL.

Abstract: The invention relates to a method for detection of a methicillin resistant coagulase positive Staphylococcus aureus (MRSA) strain by means of a sequence specific amplification reaction.

Abstract: The invention provides compositions of oligonucleotides targeted at influenza genes and at host animal genes involved in response to influenza infection. In some embodiments, the oligonucleotides are modified. In some embodiments, the compositions contain one, or more than one, oligonucleotide. The invention also provides methods and kits using the compositions of the invention for the treatment and prevention of influenza.

Abstract: The present invention provides methods for universally detecting citrus viroids in plant material such as germplasm. In particular embodiments, the invention enables the determination of citrus viroid infection and plant resistance. Accordingly, the present method provides methods for improved universal detection of any citrus viroid.

Abstract: Devices and methods are provided for electrically lysing cells and releasing macromolecules from the cells. A microfluidic device is provided that includes a planar channel having a thickness on a submillimeter scale, and including electrodes on its upper and lower inner surfaces. After filling the channel with a liquid, such that the channel contains cells within the liquid, a series of voltage pulses of alternating polarity are applied between the channel electrodes, where the amplitude of the voltage pulses and a pulsewidth of the voltage pulses are effective for causing irreversible electroporation of the cells. The channel is configured to possess thermal properties such that the application of the voltage produces a rapid temperature rise as a result of Joule heating for releasing the macromolecules from the electroplated cells. The channel may also include an internal filter for capturing and concentrating the cells prior to electrical processing.

Abstract: An improved two roll sugarcane crushing mill with a semi closed frame having a plurality of improved two roll mill modules in tandem. Each improved two roll mill modules has a bottom roll and top roll, the bottom roll being rotatingly mounted in a pair of main frames at the two ends and the top roll is rotatingly mounted in a pair of top beams. One end of each of the top beams being pivotedly attached near the upper end of the main frame towards feed side for swinging the top beams along with the top roll. A hydraulic loader is provided which is pivotally attached between the end of the top beam and the base of the main frame. The semi closed frame fitted at the bottom end to the base of the Head Stock is designed to bear the forces of heavy and fluctuating loads.

Abstract: In a method and a device for operating a smelting reduction process, at least part of an export gas from a blast furnace or a reduction unit is thermally utilized in a gas turbine and the exhaust gas of this gas turbine is used in a waste heat steam generator to generate steam. The remaining part of the export gas is fed to a CO2 separation apparatus, the tail gas thereby obtained being fed to a waste heat steam generator and burned for additional steam generation. The combustible components of the tail gas are sent for thermal utilization in a steam generator, so that the overall energy balance of the thermal use of the export gas is improved. In addition, a further part of the export gas is qualitatively improved by the CO2 separation apparatus, so as to generate a high-quality reduction gas which can be supplied for metallurgical use.