Abstract: The present disclosure is in the field of plant transformation. The disclosure provides methods for increasing the rate of site-directed integration of a sequence of interest in plants. The disclosure also provides methods for increasing the efficiency of Rhizobiales-mediated plant transformation.

Abstract: Disclosed herein are viral vectors based on modifications of the Citrus Tristeza virus useful for transfecting citrus trees for beneficial purposes. Included in the disclosure are viral vectors including one or more gene cassettes that encode heterologous polypeptide s. The gene cassettes are positioned at desirable locations on the viral genome so as to enable expression while preserving functionality of the virus. Also disclosed are methods of transfecting plants and plants transfected with viral vector embodiments.

Abstract: Methods and compositions for improved bacterial-mediated plant transformation are provided. The methods generally allow plant transformation with reduced vector backbone integration and a high frequency of low-copy transformation events. Vectors for achieving these results are described, as are methods for their use.

Abstract: The present disclosure provides methods for the stable transformation of meristem explants from cowpeas (Vigna unguiculata) and dry beans (Phaseolus vulgaris).

Abstract: The present invention provides a method and means to change fatty acid and ultimately triacylglycerol production in plants and algae. Methods of the invention comprise the step of altering the activity levels of the committed step for de novo fatty acid biosynthesis, acetyl-CoA carboxylases (ACCase). More specifically, methods of the invention directly enhance the activity of ACCase by overexpression of ?-CT or a catalytic portion thereof.

Abstract: Materials and methods are provided for making plants (e.g., Solanum varieties) with resistance to black-spot bruising, specifically, by making TALE-nuclease-induced mutations in genes encoding tuber specific expressed polyphenol oxidase.

Abstract: The invention relates to a new gene that produces a protein which is capable of inferring oomycete resistance, more preferably resistance to Phytophthora infestans when expressed in a plant, wherein said nucleotide sequence encodes a protein that is encoded by the protein produced by the nucleotide sequence of FIG. 10 or the protein depicted in FIG. 11 or a nucleotide sequence that codes for a protein that has an identity of at least 95% with said protein produced by the nucleotide sequence of FIG. 10 or the protein depicted in FIG. 11. The invention also relates to a method for providing at least partial resistance or increasing resistance in a plant against an oomycete infection comprising providing a plant or a part thereof with a nucleotide sequence as indicated above or a functional fragment thereof, preferably wherein said plant is a plant from the Solanaceae family, more preferably Solanum tuberosum.

Abstract: Tomato plants exhibiting resistance to Fusarium oxysporum f. sp. lycopersici (Fol) are provided, together with methods of producing, identifying, or selecting plants or germplasm with a Fol resistance phenotype and lacking undesirable soft fruit traits. Such plants include tomato plants comprising introgressed genomic regions conferring disease resistance. Compositions, including novel polymorphic markers for detecting plants comprising introgressed disease resistance alleles, are further provided.

Abstract: Compositions and methods for controlling pests are provided. The methods involve transforming organisms with a nucleic acid sequence encoding an insecticidal protein. In particular, the nucleic acid sequences are useful for preparing plants and microorganisms that possess insecticidal activity. Thus, transformed bacteria, plants, plant cells, plant tissues and seeds are provided. Compositions are insecticidal nucleic acids and proteins of bacterial species. The sequences find use in the construction of expression vectors for subsequent transformation into organisms of interest including plants, as probes for the isolation of other homologous (or partially homologous) genes. The pesticidal proteins find use in controlling, inhibiting growth or killing Lepidopteran, Coleopteran, Dipteran, fungal, Hemipteran and nematode pest populations and for producing compositions with insecticidal activity.

Abstract: The present invention relates to nucleic acid molecules for use in inducing apomixis in a plant, transgenic cells, in particular transgenic plant cells, comprising said nucleic acid molecule, transgenic plants, in particular plant seeds, comprising said nucleic acid molecule, methods for inducing apomixis in a plant, methods for the production of apomictic plants and uses thereof.

Abstract: A nuclear maize gene is mutated to result in dominant male sterility. Two mutants are provided which impact signal peptide processing. Restoration constructs and methods are provided for use of the dominant male-sterile mutants in producing hybrid seed for male-sterile hybrid plants. Other signal-peptide modifications are provided. Orthologs of the wild type or mutated gene in various species are provided.

Abstract: This invention comprises: compositions comprising a derivative, plasmids, a reagent kit and methods of making these compositions a derivative, vaccine- and non-vaccine-compositions of above for causing death of cancer cells that form part of a tumour and virus infected Dengue, Measles and other diseased cells; the derivative comprising replicating as well as non-replicating derivatives of an attenuated negative stranded RNA virus belonging to family paramyxoviridae, including Measles Virus, comprising a single additional transcriptional unit carrying either only one or two or more non-viral genes, and the non-replicating derivatives being free from contaminating replicating Measles Virus (b) a Measles Virus packaging cell line for making above compositions, expressing the M, F and H proteins of MV stably. And (c) a reagent kit for producing the Measles Virus derivatives described above.

Abstract: Disclosed herein are recombinant CMV vectors which may comprise a heterologous antigen that can repeatedly infect an organism while inducing a CD8+ T cell response to immunodominant epitopes of the heterologous antigen. The CMV vector may comprise a deleterious mutation in the US11 glycoprotein or a homolog thereof.

Abstract: A synthetic lentiviral vector construct comprises a genomic RNA packaging enhancer (GRPE) element and lentiviral nucleic acid sequences sufficient for reverse transcription and packaging in a host cell.

Abstract: A cell for producing retroviral vectors comprising nucleic acid sequences encoding: i) gag-pol; ii) env; iii) the RNA genome of the retroviral vector; and iv) optionally rev, or a functional substitute thereof, wherein at least two nucleic acid sequences are located at the same genetic locus; and wherein the at least two nucleic acid sequences are in reverse and/or alternating orientations.

Abstract: RNA virus vectors comprising a gene encoding the DNA-dependent activator of interferon-regulatory factors (DAI) protein, and optionally further comprising a gene encoding the receptor-interacting serine/threonine-protein kinase 3 (RIPK3) may be used therapeutically to induce cell death, as well as an inflammatory immune response, against tumors and virally-infected cells.

Abstract: The present invention relates to the industrialization of the production of recombinant lentiviral vectors in order to manufacture sufficient materials for therapeutic applications such as gene therapy and/or DNA vaccination, for use in clinical trials and/or commercial use.

Abstract: This invention relates generally to pharmaceutical compositions and preparations of curons and uses thereof.

Abstract: The present application provides materials and methods for treating a patient with one or more conditions associated with DMPK whether ex vivo or in vivo. In addition, the present application provides materials and methods for editing and/or modulating the expression of DMPK gene in a cell by genome editing.

Abstract: A plant activator composition increases the concentration of terpenes and terpinoids in aromatic plant oils, and hence resulting in an increased concentration of terpene and terpinoids in the harvested dried plant or fruit. The composition contains one of more bio-active compounds that are optionally extracted from plants selected from one or more of the group consisting of mango, citrus (including grapefruit), Catharanthus roseus and Pelargonium odoratissimum, but alternatively may include one or more synthetic compounds selected from the group consisting of geranyl acetate, geraniol, beta-sitosterol, alpha-amyrin, beta amyrin, carotenoid, geranyl acetate, alpha-humulene, mevalonate kinase and geranyl. Depending on the type of plant being treated, the formulation is added during watering and feeding in optimum doses during the vegetative growth, flowering, and fruit set and/or swell stages.

Abstract: Compositions and methods for synthesizing a citrus terpenoid using a recombinant host cell that produces isopentenyl pyrophosphate and dimethylallyl pyrophosphate, and expresses one or more enzymes that convert the IPP and DMAPP to a citrus terpenoid are described.

Abstract: A dry grind biochemical production process and system with front end milling method is provided for improving biochemical and/or by-product yields, such as oil and/or protein yields. In one example, the process includes grinding corn kernels into particles then mixing the corn particles with a liquid to produce a slurry including oil, protein, starch, fiber, germ, and grit. Thereafter, the slurry is subjected to a front end milling method, which includes separating the slurry into a solids portion, including fiber, grit, and germ, and a liquid portion, including oil, protein, and starch, then milling the separated solids portion to reduce the size of the germ and grit and release bound starch, oil, and protein from the solids portion. The starch is converted to sugar, and a biochemical is produced therefrom then recovered. Also, the fiber can be separated and recovered. Oil and protein may be separated and recovered as well.

Abstract: The invention is intended to metabolize acetic acid in a medium at the time of culture, such as ethanol fermentation by yeast, and to reduce acetic acid concentration. Specifically, the invention relates to a recombinant yeast resulting from introduction of the acetaldehyde dehydrogenase gene (EC 1.2.1.10) and regulation of an enzyme involved with trehalose accumulation.

Abstract: The present invention provides methods for catalyzing the conversion of an olefin to any compound containing one or more cyclopropane functional groups using heme enzymes. In certain aspects, the present invention provides a method for producing a cyclopropanation product comprising providing an olefinic substrate, a diazo reagent, and a heme enzyme; and admixing the components in a reaction for a time sufficient to produce a cyclopropanation product. In other aspects, the present invention provides heme enzymes including variants and fragments thereof that are capable of carrying out in vivo and in vitro olefin cyclopropanation reactions. Expression vectors and host cells expressing the heme enzymes are also provided by the present invention.

Abstract: The present disclosure relates to cap analogs, which can result in high levels of capping efficiency and transcription and improved translation efficiencies. The present disclosure also relates to methods useful for preparing cap analogs and using mRNA species containing such analogs, as well as kits containing the novel cap analogs.

Abstract: The present invention relates to recombinant cells and microorganisms of the phylum Labyrinthulomycota and their use in heterologous protein production. Novel promoter, terminator, and signal sequences for efficient production and, optionally, secretion of polypeptides from recombinant host cells and microorganisms are also encompassed by the present invention.

Abstract: A method to label as defective a measure of an optical-trap force, that is exerted on a trapped particle located inside a living, dispersive, viscoelastic medium, including operations of: (i) determining a calibration constant between the optical trap forces and the sensed voltages; (ii) determining a first calibration function of the frequency of the particle oscillation with the active-passive procedure; (iii) computing a second calibration function of the frequency as the quotient between the calibration constant and the first calibration function; (iv) computing an energy function of the frequency as the product of the thermal energy of the trapped particle and the second calibration function; (v) checking whether the energy function converges to the thermal energy of the trapped particle as the frequency increases; (vi) if there is no such convergence, then label as defective the measure of the optical-trap force.

Abstract: Disclosed is the use of genetic means or a related inhibitor to inhibit and down-regulate the amount of PI4KIII? protein, RBO/EFR3/EFR3A/EFR3B membrane proteins, TTC7 protein and membrane protein complexes formed by said proteins, or related enzyme activity to promote A? secretion by neuronal cells, reduce A? accumulation within neurons, and thereby reduce AD model fruit fly and mouse nerve dysfunction.

Abstract: Provided are an organoid having a metastatic property when transplanted into an immunocompetent non-human animal of the same species, a cell strain having a metastatic property when transplanted into an immunocompetent non-human animal of the same species, and a non-human animal including the organoid or the cell strain.

Abstract: A chemically-enhanced primer is provided comprising a negatively charged moiety (NCM), an oligonucleotide sequence having a) non-nuclease resistant inter-nucleotide linkages or b) at least one nuclease resistance inter-nucleotide linkage. The chemically-enhanced primer can be used for sequencing and fragment analysis. Methods for synthesizing the chemically-enhanced primer as well as a method of preparing DNA for sequencing, a method of sequencing DNA, and kits containing the chemically-enhanced primer are also provided. The method of sequencing DNA can comprise contacting amplification reaction products with the composition wherein excess amplification primer is degraded by the nuclease and the chemically-enhanced primer is essentially non-degraded.

Abstract: A bottleneck in the Next Generation Sequencing (NGS) workflow is the quantification of libraries for accurate pooling and loading of the sequencing instrument flow cell or chip. Disclosed herein are methods that improve performance and reduce time compared to existing methods.

Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.

Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.

Abstract: Methods for the rapid detection of the presence or absence of a single-base deletion in the tcdC gene of Clostridium difficile in a biological or nonbiological sample are described. The methods can include performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, primers, probes, and kits are provided that are designed for the detection of the single-base deletion.

Abstract: Methods, compositions, and systems are provided for detecting one or more a cognition health issues by characterizing the microbiome of an individual, monitoring such effects, and/or determining, displaying, or promoting a therapy for the cognition health issue. Methods, compositions, and systems are also provided for generating and comparing microbiome composition and/or functional diversity datasets. Methods, compositions, and systems are also provided for generating a characterization model and/or therapy model for insomnia issues, light sleep issues, headache issues, sinusitis issues, and poor concentration issues.

Abstract: The invention is directed to methods, kits, and compositions, for amplifying and detecting Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Trichomonas vaginalis (TV), and Mycoplasma genitalium (MG) in a sample, which comprises a variety of combinations of forward oligonucleotide primers, reverse oligonucleotide primers, and oligonucleotide probes.

Abstract: Provided are methods for detecting biomarkers in an analyte. In some embodiments, the detection is accomplished using a competition reaction between a primer and a biomarker for binding to a salimer. The salimer, in some aspects of the invention, is hybridized to the primer, but because the salimer has a greater affinity for a biomarker than for the primer, the salimer dissociates from the primer in the presence of the target biomarker. The unbound primer generates a signal that indicates the presence of the biomarker.

Abstract: An in vitro method enables determination of the antibiotic resistance of Helicobacter pylorifor in a biological sample isolated from an individual. The method includes amplifying at least one portion of at least one gene of Helicobacter pylori. The at least one gene includes at least one mutation site responsible for resistance to an antibiotic. A kit can be used for performing the method.

Abstract: A method of screening for the presence and/or extent of a pathology in a subject, the pathology characterized by an abnormal chromosomal component in a cell of the subject, comprising the steps of: contacting a biological sample comprising cell nuclei from said subject with, one or more distinguishable labeled probes directed to at least one chromosomal sequence that characterizes the abnormality under conditions that promote hybridization of the one or more probes to the at least one sequence, automatically obtaining a representation of the one or more distinguishable labels hybridized to the chromosomal sequences, automatically analyzing the distribution and intensity of binding of the one or more labels in the representation to determine the presence and/or extent of an abnormal chromosomal component; and automatically reporting results of the analysis; wherein the steps are carried out without intervention by a human.

Abstract: A method of sample analysis is provided. In certain embodiments, the method may comprise: (a) filtering a liquid sample containing rolling circle amplification (RCA) products using a porous capillary membrane, thereby producing an array of the RCA products on the membrane; wherein the sample contains at least a first population of RCA products and a second population of RCA products, wherein the first and second populations of labeled RCA products are distinguishably labeled; and (b) determining the amount of the first labeled population of RCA products and the amount of the second labeled population of RCA products in an area of the membrane.

Abstract: Provided is a nucleic acid isothermal self-amplification method comprising, adding suitable palindrome complementary sequences at both ends of a target template to form a stem-loop structure spontaneously, and providing reagents and conditions as needed to perform self-amplification. The method does not require addition of additional amplification primers. The reagent comprises a DNA polymerase having a strand displacement activity. The method does not rely on exogenous amplification primers for amplification, has a constant amplification temperature without a complex temperature control equipment, and achieves rapid amplification. The amplification product is a long single-stranded DNA of a continuous complementary sequence and can be applied to special occasions. In addition, the amplification has no GC bias.

Abstract: This present disclosure provides methods and compositions that can be used to quantify cfDNA in biofluids using a hybridization approach.

Abstract: Methods for primer switching during amplification reactions are provided. In particular, methods are provided for converting single primer PCR amplicons to dual primer PCR amplicons.

Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.

Abstract: Methods and compositions are provided for improved nucleic acid amplification assays. In some embodiments, the nucleic acid amplification assay is a tagged amplicon primer extension (TAPE) nucleic acid amplification reaction.

Abstract: Apparatus and techniques for electrokinetic loading of samples of interest into sub-micron-scale reaction chambers are described. Embodiments include an integrated device and related apparatus for analyzing samples in parallel. The integrated device may include at least one reaction chamber formed through a surface of the integrated device and configured to receive a sample of interest, such as a molecule of nucleic acid. The integrated device may further include electrodes patterned adjacent to the reaction chamber that produce one or more electric fields that assist loading the sample into the reaction chamber. The apparatus may further include a sample reservoir having a fluid seal with the surface of the integrated device and configured to hold a suspension containing the samples.

Abstract: The invention relates to new methods of moving helicases past spacers on polynucleotides and controlling the loading of helicases on polynucleotides. The invention also relates to new methods of characterising target polynucleotides using helicases.

Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.

Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.

Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.