Abstract: The invention relates to methods and compositions for increasing resistance or tolerance to a nematode plant pest in a plant or part thereof. Nucleotide sequences that confer resistance or tolerance to nematode plant pests when expressed in a plant are provided as well as compositions comprising the polypeptides encoded by the nucleotide sequences, and transgenic plants and parts thereof comprising the nucleotide sequences.

Abstract: The invention provides nucleic acids, and variants and fragments thereof, obtained from strains of Bacillus thuringiensis encoding polypeptides having pesticidal activity against insect pests, including Lepidoptera. Particular embodiments of the invention provide isolated nucleic acids encoding pesticidal proteins, pesticidal compositions, DNA constructs, and transformed microorganisms and plants comprising a nucleic acid of the embodiments. These compositions find use in methods for controlling pests, especially plant pests.

Abstract: Nucleotide sequences, amino acid sequences, and an associated promoter sequence are useful in methods of controlling male fertility in plants. Recombinant expression cassettes, vectors, plant cells, and plants comprise a disclosed nucleotide sequence and may encode a disclosed amino acid sequence. The recombinant expression cassettes are useful in controlling fertility, especially male fertility of annual crops. The promoter is useful in driving expression of an operably-linked heterologous polynucleotide. Constructs comprising homology to the promoter sequence are useful for downregulation of a polynucleotide associated with the promoter.

Abstract: A Thy1 gene promoter specifically expressed in neurons and a recombinant vector including the Thy1 gene promoter are provided. The Thy1 gene promoter may be utilized to regulate an expression of a target gene in preparation of an animal model similar to a human.

Abstract: The present invention provides novel mRNA elements capable of forming hairpin, double-stranded RNA structures independent of other non-coding RNAs. These mRNAs are stably expressed, lack polyadenylation tails, and allow minimal protein translation except when in the presence of specific proteins. Also provided, are compositions and kits comprising the mRNA element, as well as methods for its use in the regulation of protein translation. Advantageously, the disclosed elements represent a novel tool useful in regulating the expression of a wide variety of proteins of interest.

Abstract: The present invention relates nucleic acid constructs for the production of recombinant parvoviral (e.g. adeno-associated viral) vectors in insect cells, to insect cells comprising such constructs and to methods wherein the cells are used to produce recombinant parvoviral virions. The insect cells preferably comprise a first nucleotide sequence encoding the parvoviral rep proteins whereby the initiation codon for translation of the parvoviral Rep78 protein is a suboptimal initiation codon that effects partial exon skipping upon expression in insect cells. The insect cell further comprises a second nucleotide sequence comprising at least one parvoviral (AA V) inverted terminal repeat (ITR) nucleotide sequence and a third nucleotide sequence comprising a sequences coding for the parvoviral capsid proteins.

Abstract: The present invention is directed to cellulytic host cells. The host cells of the invention expressing heterologous cellulases and are able to produce ethanol from cellulose. According to the invention, host cells expressing a combination of heterologous cellulases can be used to produce ethanol from cellulose. In addition, multiple host cells expressing different heterologous cellulases can be co-cultured together and used to produce ethanol from cellulose. Furthermore, the invention demonstrates for the first time the ability of Kluyveromyces to produce ethanol from cellulose. The yeast strains and co-cultures of yeast strains of the invention can be used to produce ethanol on their own, or can also be used in combination with externally added cellulases to increase the efficiency of saccharification and fermentation processes.

Abstract: A process is defined for the continuous steam pretreatment and fractionation of low lignin lignocellulosic biomass to produce a concentrated cellulose solid stream that is sensitive to enzymatic hydrolysis. Valuable chemicals are recovered by fractionating the liquid and vapor stream composed of hydrolysis and degradation products of the hemicellulose. Cellulosic derived glucose is produced for fermentation to biofuels. A xylo-oligosaccharides rich liquids fraction is recovered that can be converted to value added products including ethanol.

Abstract: Disclosed are methods of synthesizing racemic 2-(difluoromethyl)-1-(alkoxycarbonyl)-cyclopropanecarboxylic acids and 2-(vinyl)-1-(alkoxycarbonyl)-cyclopropanecarboxylic acids and their salts, such as the dicyclohexylamine salt. Also disclosed are methods for preparing enantioenriched (1R,2R)-1-((tert-butoxycarbonyl)amino)-2-(difluoromethyl)cyclopropane-1-carboxylic acid and esters of the same. These compounds are useful intermediates in the synthesis of viral protease inhibitors.

Abstract: The present invention relates to an L-lysine-producing microorganism of the genus Corynebacterium and a method for producing L-lysine using the same.

Abstract: The present disclosure is directed to microorganisms that are genetically modified to express at least one exogenous enzyme involved in N-acetylglucosamine uptake and metabolism. Methods for the production of an exopolysaccharide are also disclosed. The exopolysaccharide comprises N-acetylglucosamine and D-glucose and may be used as a bioresorbable implant for soft tissue repair, replacement, or augmentation.

Abstract: The present disclosure is directed to microorganisms that are genetically modified to express at least one exogenous enzyme involved in D-glucosamine uptake and metabolism. Methods for the production of an exopolysaccharide are also disclosed. The exopolysaccharide comprises N-acetylglucosamine and D-glucose and may be used as a bioresorbable implant for soft tissue repair, replacement, or augmentation.

Abstract: The present invention provides methods and compositions for improving the efficiency of nucleic acid amplification reactions. The invention encompasses hybrid polymerases that show increased processivity over wild type polymerases as well as decreased exonucleases activity. The invention also encompasses methods, compositions and kits for conducting nucleic acid synthesis and amplification reactions in which non-specific amplification of primers is reduced.

Abstract: The present invention relates to a method for producing a glycosylated synthon or a monomer. Said method includes at least one step of placing at least one glycan-saccharase in the presence of at least one hydroxylated synthon and at least one saccharose. The invention also relates to a method for producing a glyco(co)polymer, including polymerizing at least two monomers separately obtained from the enzymatic glycosylation method according to the invention, and to a method for producing a glyco(co)polymer, preferably a block glyco(co)polymer, including coupling at least two monomers separately obtained from the enzymatic glycosylation method according to the invention.

Abstract: The present disclosure relates to a recombinant gram-negative bacterial cell comprising: a) a mutant spr gene encoding a spr protein having a mutation at one or more amino acids selected from D133, H145, H157, N31, R62, I70, Q73, C94, S95, V98, Q99, R100, L108, Y115, V135, L136, G140, R144 and G147 and b) a gene capable of expressing or overexpressing one or more proteins capable of facilitating protein folding, such as FkpA, Skp, SurA, PPiA and PPiD, wherein the cell has reduced Tsp protein activity compared to a wild-type cell, methods employing the cells, use of the cells in the expression of proteins in particular antibodies, such as anti FcRn antibodies and proteins made by the methods described herein.

Abstract: The present disclosure provides a method of detecting a target bacterium. The method includes forming a primary enrichment culture that includes a test sample, a primary enrichment medium and a redox dye; incubating the primary enrichment culture for a first period of time equal to eight hours or less; assessing the primary enrichment culture during the first period of time to detect whether the redox dye changes from a first state to a second state; if the second state is detected in the primary enrichment culture during the first period of time, mixing a portion of the primary enrichment culture with a secondary enrichment medium to form a secondary enrichment culture and incubating the secondary enrichment culture for a second period of time; and performing a test to detect the target bacterium using a portion of the second enrichment culture.

Abstract: A nitrate sensing biosensor and bacteria and applications relating to the use of same are described. The nitrate biosensor comprises a two component sensor system (TCS) comprising: a nitrate-sensing sensor kinase (SK) gene comprising a ligand binding domain operably coupled to a kinase domain, and, a cognate response regulator (RR) gene comprising a receiver domain operably coupled to an DNA binding domain (DBD), as well as an output promoter that binds said DBD that is operably coupled to a heterologous reporter gene.

Abstract: Orally administered physiologically acceptable anti-biofilm compositions comprising enzymes and if desired additional components such as antimicrobials, antibiotics, antifungals, herbals, chelating agents, lactoferrin and related compounds, minerals, surfactants, binders, and fillers useful for the inhibition and treatment of gastrointestinal biofilms in humans. Physiologically acceptable anti-biofilm compositions containing these enzymes are useful in the inhibition, reduction and/or treatment of gastrointestinal biofilm infections, and associated systemic symptoms caused by biofilms associated microorganisms within the gastrointestinal tract. Methods of identification, preparation and use of such physiologically acceptable anti-biofilm compositions are also provided.

Abstract: Capillary electrophoresis fractionation of an environmental microbiota segregates high abundance microbes from lower abundance species, and results in a three-fold increase in the number of 16s rRNA OTUs that map to known species. However, most of the bacteria are found in a few wells, although reasonably large numbers of OTUs were found in over half the wells.

Abstract: Provided herein is technology relating to the biological process of protein ubiquitination and particularly, but not exclusively, to compositions and methods for studying protein ubiquitination and developing therapeutics to modulate protein ubiquitination.

Abstract: The present disclosure relates methods of chromogen layering, wherein a first chromogen and a first stain (color) are produced on a sample, specific for a first analyte, followed by a second chromogen and a second stain (color) being produced on the same sample, specific for a second analyte. In addition, if desired, by overlaying the second stain on top of the first stain, a unique third color is produced that is specific for a third analyte. Therefore, the distribution of different colors throughout the sample could be used to identify at least two or more analytes simultaneously within a single sample.

Abstract: The instant invention provides workflows for the design and characterization of mechanism-based sirtuin modulating compounds, including new or improved sirtuin activating compounds. Workflows for the design of mechanism-based sirtuin activating compounds are provided, based on conditions that must be satisfied by activators if they are to exploit the common catalytic mechanism of all sirtuin enzymes and hence increase catalytic efficiency for any sirtuin and any substrate.

Abstract: Disclosed are devices that can perform multiple independent digital PCRs with real time monitoring capability. The device comprises multiple PCR mini-reactors thermally coupled with its own temperature control element, a detection unit, and a motorized platform for holding and moving the PCR mini-reactors. The real time digital PCR device can simultaneously perform multiple digital PCRs, generate amplification curves of thousands and millions of individual PCR processes, evaluate binary readouts based on the amplification curves, and identify different target sequences based on the amplification curves. Methods of using the real time digital PCR device to detect target nucleic acid and count circulating tumor cells are also disclosed.

Abstract: This disclosure provides microwell capsule array devices. The microwell capsule array devices are generally capable of performing one or more sample preparation operations. Such sample preparation operations may be used as a prelude to one more or more analysis operations. For example, a device of this disclosure can achieve physical partitioning and discrete mixing of samples with unique molecular identifiers within a single unit in preparation for various analysis operations. The device may be useful in a variety of applications and most notably nucleic-acid-based sequencing, detection and quantification of gene expression and single-cell analysis.

Abstract: Provided herein are media, methods, kits, primers and oligonucleotide probes for use in the molecular detection of pathogens. These may be used in combination for the rapid, high-throughput screening PCR-based techniques to simultaneously detect multiple pathogens. The multiplex-detection methods have improved sensitivity and specificity for the detection of multiple pathogens simultaneously. Real-time PCR assaying techniques using such primers include microarrays and multiplex arrays, the latter optionally simultaneously with oligonucleotide TaqMan probes.

Abstract: Imaging systems including an objective lens and a line generation module are described herein. The objective lens may focus a first light beam emitted by the line generation module and a second light beam emitted by the line generation module at a focal point external to a sample so as to adjust line width. Line width may be increased to lower overall power density of a light beam on a surface of the sample such that the power density of the light beam on the surface of the sample is below a photosaturation threshold of a dye on the sample.

Abstract: Provided herein is technology relating to the detection of analytes and particularly, but not exclusively, to methods, systems, compositions, and kits for detecting analytes such as nucleic acids, proteins, small molecules, and other molecules using a technology based on the transient binding of detection probes.

Abstract: A method of diagnosing bacterial vaginosis in a woman, which involves determining an amount of each of more than one BV-associated bacterium in a vaginal sample obtained from the female and assessing a BV status of the female based on the amount of each of the more than one BV-associated bacterium in the sample

Abstract: Fluorescence quenching nitrodiarylethene analogs are useful in oligonucleotide conjugates and probes. These analogs, whose absorption spectra are substantially blue-shifted relatively to emission spectra of common fluorophores (such as fluorescein), do not need to rely on spectral overlap of quencher absorbance and fluorophore's emission for their quenching abilities. The oligonucleotide-quencher conjugates may be used in detection methods for nucleic acid targets.

Abstract: Methods, systems, and reagents for real-time single molecule sequencing of nucleic acids, particularly long DNA molecules, is described. Preferably, such methods and systems combine FRET (Förster Resonance Energy Transfer)-based proximity sensing of labeled nucleotides in or near a DNA polymerase's active site with FRET-based monitoring of the conformational changes in the polymerase that occur during nucleotide incorporation.

Abstract: The present invention provides a method for detecting the presence or absence of a target analyte in a test sample, comprising the steps: i) providing a plurality of detector nanoparticles comprising a first detector nanoparticle functionalised with a first probe specific for a first region of a target analyte and a second detector nanoparticle functionalised with a second probe specific for a second region of said target analyte; and ii) contacting said detector nanoparticles with a test sample under conditions suitable for the binding of the specific probes to the target analyte, wherein target analyte-induced agglomeration of the detector nanoparticles permits the release of a detectable signal means from a signal reservoir. Also provided are related devices and systems for performing the method of the invention.

Abstract: Disclosed are methods for polynucleotide sequencing that detect the location of selected nucleobases with greater precision. The methods can be used to determine the location and nature of modified bases in a polynucleotide, that is, non-canonical bases, or to improve accuracy of sequencing of “problem” regions of DNA sequencing such as homopolymers, GC rich areas, etc. The sequencing method exemplified is nanopore sequencing. Nanopore sequencing is used to generate a unique signal at a point in a polynucleotide sequence where an abasic site (AP site, or apurinic or apyrimidinic site) exists. As part of the method, an abasic site is specifically created enzymatically using a DNA glycosylase that recognizes a pre-determined nucleobase species and cleaves the N-glycosidic bond to release only that base, leaving an AP site in its place.

Abstract: The present invention relates to a method for genotyping single nucleotide polymorphisms (SNPs) using a lateral flow test device. The invention also relates to a kit comprising said lateral flow test device and also to the use thereof for genotyping single nucleotide polymorphisms (SNPs).

Abstract: Disclosed are compositions, methods and kits for determining the presence, absence, amount, copy number, or other characteristics of one or more polynucleotide sequences in two or more samples and use thereof in genotyping, evaluation of copy number variation, expression analysis, determination of splice variants and fusion genes, and other genetic analyses.

Abstract: Methods and kits for depleting amplicons that correspond to undesired RNA species present in a sample are provided. The disclosed methods and kits employ a blocker that anneals with at least a portion of the undesired RNA, resulting in a duplex that is not a suitable substrate for ligating an adapter to the end of the undesired RNA.

Abstract: The present invention relates to differentiating signals of interest for target nucleic acid sequences. The present invention permits to obtain an individual signal value (i.e., variable) contained in a total signal detected at detection temperatures by using mathematical equations. The present invention based on equation-solving approach enables to obtain the individual signal value in a systematical manner, thereby providing analysis results in much more accurate and convenient manner.

Abstract: The present invention relates to quality assurance methods for use in amplification techniques, such as Next Generation Sequencing (NGS).

Abstract: Apparatus and methods to identify nucleotides of a DNA strand. The method includes exposing the DNA strand to a first dye or peptide, attaching the first dye or peptide to a first type of nucleotide (A,T,C,G) of the DNA strand, the first dye or peptide changing a conductance of the first type of nucleotide to which the first dye or peptide is attached, and measuring a tunneling current signal for all nucleotides of the DNA strand, the changed conductance of the first type of nucleotide providing amplified tunneling current discrimination of the nucleotides of the DNA strand.

Abstract: The present invention provides novel compositions, methods and apparatus for DNA sequencing that can be performed, e.g., in a two-electrode chamber. The present invention also provides a method for sequencing a nucleic acid comprising immobilizing a plurality of complexes comprising a target nucleic acid, a primer nucleic acid, and a polymerase onto a surface, contacting the surface with a plurality of charged particles comprising a nucleotide phosphate by applying an electric field, reversing the electric field to transport unbound charged particles away from the surface, and detecting the incorporation of a nucleotide phosphate into a single molecule of the primer nucleic acid.

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 invention provides microRNA markers and methods for determining the risk a subject has for developing mild traumatic brain injuries (mTBI). In some aspects, the methods further include determine the fitness of a subject for participating in an activity with increased chances of receiving a head impact. Certain embodiments are directed to kits designed for these purposes.

Abstract: This present technology relates to the use of inflammation-enabling polypeptides (or their coding sequences) to screen for agents useful for the prevention, treatment and/or alleviations of symptoms associated with an inflammatory disorder, to identify individuals susceptible of developing an exacerbated inflammatory response as well as to determine if a therapeutic regimen is capable of preventing, treating or alleviating the symptoms associated to an inflammatory disorder in an individual. The present technology also provides methods for preventing, treating and/or alleviating the symptoms associated to an inflammatory condition based on the inhibition of expression or activity of the inflammation-enabling targets.

Abstract: The present invention provides a detection probe and a method for using and producing the same. The detection probe of the invention comprises boranephosphonate moiety and a target selective moiety. The present invention also provides a method for using the metal ion reducing properties of boranephosphonates (BPs) to determine the presence, the concentration or the location of a target molecule in a sample.

Abstract: The invention provides a method for identifying or detecting small RNA (sRNA) predictors of a disease or a condition. The method comprises identifying one or more sRNA sequences that are present in one or more samples of an experimental cohort, and which are not present across a comparator cohort; and optionally identifying one or more sRNA sequences that are present in one or more samples of a comparator cohort, and which are not present across an experimental cohort. In contrast to identifying dysregulated non-coding RNAs (such as miRs that are up- or down-regulated), the invention identifies sRNAs that are binary predictors, that is, present in one cohort (e.g., an experimental cohort) and not another (e.g., a comparator cohort). Further, by quantifying reads for individual sequences (e.g., iso-miRs), without consolidating reads to annotated reference sequences, the invention unlocks the diagnostic utility of miRs and other sRNAs.

Abstract: The present invention concerns particular biomarkers for diagnosing and/or prognosticating colorectal cancer, in particular in a non-invasive manner. The methods and compositions concern analysis of methylation patterns of one or more genes from a set of 29 genes identified as described herein. In certain embodiments, the gene set includes at least P15.INK4b, SST, GAS7, CNRIP1, and PIK3CG.

Abstract: This invention provides methods of using phagocytic cells in the diagnosis, prognosis, or monitoring of diseases or conditions. The invention also provides methods of using phagocytic cells to identify markers of diseases or conditions.

Abstract: The invention provides compositions, methods, and systems for using cell-free RNA for improved detection of rare cells and/or species that are useful for diagnosing and/or monitoring cancer. The invention also provides for compositions, methods, and systems for early detection of cells that are resistant and/or developing resistance to cancer therapies.

Abstract: A diagnostic test for ovarian cysts is based on the detection of mutations characteristic of the most common neoplasms giving rise to these lesions. With this test, tumor-specific mutations were detected in the cyst fluids of 19 of 24 (79%) borderline tumors and 28 of 31 (90%) malignant ovarian cancers. In contrast, we detected no mutations in the cyst fluids from 10 non-neoplastic cysts and 12 benign tumors. When categorized by the need for exploratory surgery (i.e., presence of a borderline tumor or malignant cancer), the sensitivity of this test was 85% and the specificity was 100%. These tests could inform the diagnosis of ovarian cysts and improve the clinical management of the large number of women with these lesions.

Abstract: The invention provides methods of detecting cancer biomarkers, such as one or more SWI/SNF complex mutations, in order to determine a cancer subject's amenability to therapeutic treatment with a BRM inhibitor. Kits, methods of screening for candidate FIRM inhibitors, and associated methods of treatment are also provided.

Abstract: A method for diagnosing a lymphoid proliferative disorder (such as lymphoma, T-cell lymphoma or leukemia) in a subject or determining the risk of a subject for a lymphoid proliferative disorder recurrence after transient remission, which includes high throughput T-Cell Receptor ? (TCR?) sequencing tests to identify dominant oncogenic clones in the subject suffering from the lymphoid proliferative disorder. Oligonucleotides primer compositions and kits associated with the above-described methods are also provided herein. Said subject includes living organisms, such as mammals (e.g., dogs, cats, pigs, cows, horses, goats, rabbits, humans), non-mammalian vertebrates, such as birds (e.g., chicken, ducks), fish (e.g., sharks), or frogs, and transgenic species thereof.