Abstract: The invention relates to siRNA molecules and their use in methods and pharmaceutical compositions for inhibiting the expression of the PDK1 gene. The invention also relates to the use of said siRNAs molecules in the treatment and/or prevention of an eye condition characterised by increased expression and/or activity of PDK1 gene, preferably said eye condition is conjunctivitis and/or an ocular allergy such as seasonal allergic conjunctivitis, perennial allergic conjunctivitis, vernal keratoconjunctivitis, atopic keratoconjunctivitis, and giant papillary conjunctivitis.

Abstract: The invention relates to engineering of acetyl-CoA metabolism in yeast and in particular to production of acetyl-CoA in a non-ethanol producing yeast lacking endogenous gene(s) encoding pyruvate decarboxylase and comprising a heterologous pathway for synthesis of cytosolic acetyl-CoA.

Abstract: Described herein are methods and compositions relating to engineered methanotrophic bacterium and the production of carbon products from methane.

Abstract: The present invention discloses methods and systems for producing fungal secondary metabolites. The invention also discloses genetically modified organisms and kits including such organisms for producing fungal secondary metabolites.

Abstract: The present invention relates to the development of genetically engineered yeasts that can produce hydrocarbons in a controllable and economic fashion. More specifically the invention relates to the production of liquid alkanes and alkenes that can be used for liquid transportation fuels, specialty chemicals, or feed stock for further chemical conversion.

Abstract: The disclosure relates to gene expression regulatory sequences from soybean, specifically to recombinant DNA constructs comprising the promoter of a soybean plasma membrane intrinsic protein gene and fragments thereof and their use in promoting the expression of one or more heterologous nucleic acid fragments in a constitutive manner in plants. The disclosure further discloses compositions, polynucleotide constructs, transformed host cells, transgenic plants and seeds containing the recombinant construct with the promoter, and methods for preparing and using the same.

Abstract: Provided are constructs and methods for expressing a transgene in plant cells and/or plant tissues using Zea mays chlorophyll a/b binding gene regulatory elements.

Abstract: This disclosure provides transgenic plants having enhanced traits such as increased yield, increased nitrogen use efficiency and enhanced drought tolerance; propagules, progeny and field crops of such transgenic plants; and methods of making and using such transgenic plants. This disclosure also provides methods of producing hybrid seed from such transgenic plants, growing such seed and selecting progeny plants with enhanced traits. Also disclosed are transgenic plants with altered phenotypes which are useful for screening and selecting transgenic events for the desired enhanced trait.

Abstract: Provided herein are novel acyltransferases and methods of using such novel acyltransferases in making medium-chain fatty acids.

Abstract: Provided are genetic material and nucleic acid sequences useful in increasing yield, biomass, growth rate, vigor, nitrogen use efficiency and/or abiotic stress tolerance, preferably tolerance to nutrient deficiency of a plant. Specifically, the improvement of nitrogen fixation properties in cultivated plants is described.

Abstract: Methods of producing transgenic photosynthetic organisms and plants overexpressing an FMO protein are disclosed. The disclosure also relates to transgenic photosynthetic organisms and plants having between 4 and 37 fold greater expression of an FMO protein compared to wild-type plants, wherein said transgenic photosynthetic organisms and plants have between 1.1 and 3.4 fold greater trimethylamine N-oxide compared to wild-type, and wherein said transgenic photosynthetic organisms plants are drought tolerant. The disclosure further relates to DNA constructs and methods of producing DNA constructs having a promoter operably linked to one or more FMO protein coding sequences. The disclosure further relates to methods of producing drought tolerant plants and photosynthetic organisms by applying an effective amount of trimethylamine N-oxide di-hydrate.

Abstract: Materials and methods for conferring geminivirus resistance to plants, and particularly to materials and methods for using CRISPR/Cas systems to confer resistance to geminiviruses to plants.

Abstract: The subject invention includes methods and plants for controlling European corn borer, said plants comprising a Cry1Ab insecticidal protein and a DIG-3 insecticidal protein to delay or prevent development of resistance by the insect.

Abstract: The present invention is directed to controlling pest infestation by inhibiting one or more biological functions in an invertebrate pest. The invention discloses methods and compositions for use in controlling pest infestation by feeding one or more different recombinant double stranded RNA molecules to the pest in order to achieve a reduction in pest infestation through suppression of gene expression. The invention is also directed to methods for making transgenic plants that express the double stranded RNA molecules, and to particular combinations of transgenic pesticidal agents for use in protecting plants from pest infestation.

Abstract: Provided are nucleic acids and expression vectors having a non-silencing selectable marker gene, and methods of using the same. A subject expression vector includes an expression cassette and a non-silencing selectable marker gene. In some cases, the non-silencing selectable marker gene provides for drug resistance for prokaryotic cells, and includes a nucleotide sequence that (i) encodes a drug selectable marker protein; (ii) is operably linked to a promoter functional in prokaryotic cells, and (iii) includes an increased A/T content relative to a corresponding wild type nucleotide sequence. In some cases, the non-silencing selectable marker gene provides for drug resistance for prokaryotic cells, and includes a nucleotide sequence that (i) encodes a drug selectable marker protein; (ii) is operably linked to a promoter functional in prokaryotic cells, and (iii) has an A/T content in a range of from 52% to 70%.

Abstract: Methods and compositions useful in targeting a payload to or editing a target nucleic acid utilizing CRISPR/Cas9 and guide RNA (gRNA) are disclosed herein

Abstract: Methods of modulating expression of a target nucleic acid in a cell are provided including introducing into the cell a first foreign nucleic acid encoding one or more RNAs complementary to DNA, wherein the DNA includes the target nucleic acid, introducing into the cell a second foreign nucleic acid encoding a nuclease-null Cas9 protein that binds to the DNA and is guided by the one or more RNAs, introducing into the cell a third foreign nucleic acid encoding a transcriptional regulator protein or domain, wherein the one or more RNAs, the nuclease-null Cas9 protein, and the transcriptional regulator protein or domain are expressed, wherein the one or more RNAs, the nuclease-null Cas9 protein and the transcriptional regulator protein or domain co-localize to the DNA and wherein the transcriptional regulator protein or domain regulates expression of the target nucleic acid.

Abstract: Disclosed herein are linear donor molecules comprising homology arms of 50-750 base pairs (e.g., 50-100 base pairs) flanking one or more sequences of interest. The donor molecules and/or compositions comprising these molecules can be used in methods for targeted integration of an exogenous sequence into a specified region of interest in the genome of a cell.

Abstract: A method of producing ethanol is disclosed. The method includes fermentation of carbohydrates from multiple byproduct feedstocks simultaneously during the same fermentation batch by application of a bacterial microbe which converts said carbohydrates to ethanol. A method of producing ethanol from whole stillage is also disclosed comprising converting multiple carbohydrates from multiple feedstocks simultaneously into ethanol without pre-treatment and without added enzymes. A method of producing ethanol with the application of a microbe from the Order Lactobacillales to a byproduct to produce ethanol is also disclosed.

Abstract: A process and system for producing ethanol from a biomass feedstock is provided that improves ethanol production by using a biomass feedstock containing high amounts of solids and starch. The process can involve subjecting the biomass feedstock to a primary fermentation to produce a whole stillage and subjecting this whole stillage to a secondary fermentation. The processes and systems described herein can maximize the amount of ethanol produced in ethanol production facilities.

Abstract: The invention relates to a process of fermenting plant material in a fermentation medium into a fermentation product using a fermenting organism, wherein one or more carbonic anhydrases are present in the fermentation medium.

Abstract: This document describes biochemical pathways for producing methacrylate from precursors such as pyruvate via isobutyraldehyde and isobutyryl-CoA, using enzymes such as one or more thioesterases, transferases, or dehydrogenases, as well as recombinant hosts expressing one or more of such enzymes.

Abstract: An object of the present invention is to provide a microorganism strain that accumulates a high molecular weight PHA, and a PHA production method using the microorganism. The present invention provides a method for producing a PHA copolymer, which includes culturing a microorganism, wherein at least a portion of either of the following genes (a) and (b) of the microorganism has been altered by substitution, deletion, insertion, and/or addition to reduce or eliminate the activity of a PHA degrading enzyme encoded by the gene: (a) a PHA degrading enzyme gene encoding the amino acid sequence of SEQ ID NO:2 in the sequence listing; and (b) a gene encoding a polypeptide having at least 85% sequence identity to the amino acid sequence of SEQ ID NO:2 in the sequence listing and having PHA degrading enzyme activity.

Abstract: Provided is a method of producing a lower alcohol ester of fatty acid-containing composition, the method including treating a raw material oil and fat containing an EPA-containing glyceride with a lipase to obtain a lower alcohol ester of fatty acid-containing composition including a lower alcohol ester of EPA, a content of water in a reaction solution in the treating being 0.4 mass % or more.

Abstract: The present invention provides a method for producing L-amino acids such as L-amino acids belonging to the glutamate family by fermentation using a bacterium of the family Enterobacteriaceae, particularly a bacterium belonging to the genus Escherichia, which has been modified to disrupt the putrescine degradation pathway by, for example, inactivation of one gene or several genes from the puuADRCBE gene cluster.

Abstract: The present invention relates to a method for the production of hyaluronic acid (HA) in Bacillus subtilis and Escherichia coli through plasmid vectors wherein the gene is under the control of strong promoter Pgrac, and a system for the selection of stable bacterial strains for the production of high levels of hyaluronic acid.

Abstract: The present disclosure relates to compositions and methods useful for the production of heterologous proteins in filamentous fungal cells.

Abstract: Surfactin is produced from Bacillus subtilis ssp. containing sfp gene (lipopeptide biosurfactants produced by fermentation). Production of surfactin at present is mainly by liquid fermentation, but the production costs are high due to difficulty in purification resulted from addition of the defoaming agent during the production process. Therefore, present invention conducts physical or chemical mutation on Bacillus subtilis subsp. isolated from Thailand seawater shrimp ponds and screens for the mutant strain of Bacillus subtilis subsp. based on sfp gene expression and then produces surfactin from the mutant strain by semi-solid state fermentation.

Abstract: An analysis bag for receiving a biological sample for microbial culture with a culture broth powder disposed within an inner volume of the container and retained by a porous wall. The culture broth powder can be disposed in at least one pouch comprising an envelope of porous material with an open inner volume. The container can have two compartments sharing a common porous wall with one compartment adapted to receive the culture broth powder and the other compartment adapted to receive the biological sample. The pouch can be manufactured with a panel of porous material folded over and sealed with the culture broth powder retained therein. A microbial culture process can be implemented with such analysis bags retaining at least one pouch or having compartments separated by a common porous wall.

Abstract: The present invention is concerned with a method of identifying microbial strains (e.g. from a cell culture), the method comprising; i) a lipid extraction step, comprising extraction of phospholipids from the microbe, suitably with an extraction composition comprising more than 50 vol % MeOH; ii) a sample preparation step, comprising preparation of a MALDI sample incorporating the extracted lipids; iii) a data gathering step, comprising performing MALDI-based mass spectrometry on the MALDI sample, and iv) a microbe identification step, comprising analysis of the mass spectrometry data to characterise or identify the microbial strain. Suitably the method also includes extracting proteins from the microbes and analysing the extracted proteins using MALDI-based mass spectrometry so as to obtain not only lipid m/z data but also protein m/z data.

Abstract: The present disclosure provides methods for detecting early Lyme disease. The present disclosure provides a biosignature indicative of the presence or absence of Borrelia burgdorferi infection.

Abstract: Deubiquitinating enzyme (DUB) probes are provided that resemble native diubiquitin (diUB) with a similar linkage size and that may contain a Michael acceptor for trapping the DUB active-site cysteine. For example, both K63- and K48-linked diubiquitin probes are generated using a facile chemical ligation method, utilizing the linker compound 3-(2-(bromomethyl)-1,3-dioxolan-2-yl)prop-2-en-1-amine. The diUb probes are capable of labelling DUBs from different families and may be employed to reveal intrinsic linkage specificities of DUBs.

Abstract: Provided is a primer middle sequence interference PCR method, and the method uses one segment of a non-complemented or same-sequence base of the middle sequence of primers to perform antisense interference inside and outside the primer molecules, so as to competitively destroy the polymerization among the primers to selectively inhibit amplification of the primer dimer (PD).

Abstract: The present invention provides methods to obtain dry compositions of reaction compounds that maintain the biological activity of the compounds upon re-solubilization after a certain storage time. Preferably, the dry composition comprises a polymerase, and the dry composition is usable for polymerase chain reaction (PCR) amplification after re-solubilization.

Abstract: The present teachings relate to a method and system for normalizing spectra across multiple instruments. In an embodiment of the present invention, the method comprises at least one reference instrument and a test instrument. Each instrument comprises at least one excitation filter and at least one emission filter arranged in pairs. Each instrument further comprises a pure dye plate comprising a plurality of wells. Each well contains a plurality of dyes where each dye comprises a fluorescent component. Fluorescent spectra are obtained from each instrument for each dye across multiple filter combinations to contribute to a pure dye matrix Mref for the reference instrument and pure dye matrix M for the test instrument. The pure dye spectra can then be multiplied by correction factors for each filter pair to result in corrected pure dye spectra, then normalized and the multicomponenting data can be extracted.

Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.

Abstract: Systems and methods for in situ laser lysis for analysis of biological tissue (live, fixed, frozen or otherwise preserved) at single cell resolution in 3D. For example, a system and method for lysing individual cells in situ, including the steps of capturing a tissue sample comprising a cellular content, subjecting the tissue sample to a stream of continuous fluid flow, lysing a selected area of the tissue sample with a laser, thereby releasing at least a portion of the cellular content from the tissue sample, recovering at least one target molecule from the cellular content in the stream, and processing at least one target molecule is provided. The system collects cellular contents, performs highly multiplexed (RT-qPCR or RNA-seq), and sequentially (cell-by-cell) reconstructs a 3D spatial map of mRNA expression of the tissue with a large number of genes. A 3D spatial map of the DNA, RNA, and/or proteins can be generated for each cell in the tissue.

Abstract: The present invention provides miniaturized instruments for conducting chemical reactions where control of the reaction temperature is desired or required. Specifically, this invention provides chips and optical systems for performing and monitoring temperature-dependent chemical reactions. The apparatus and methods embodied in the present invention are particularly useful for high-throughput and low-cost amplification of nucleic acids.

Abstract: Disclosed herein are method, materials and kits for detection of B. Burgdorferi infection or determining stage of Lyme disease in a subject. Exemlified is a method of diagnosing an infection in a subject, the method involving exposing a biological sample from the subject to a capture substrate under conditions for an infection marker in said biological sample to associate with the capture substrate to form a capture complex; associating said capture complex with a marker complex, said marker complex comprising an oligonucleotide; and amplifying said oligonucleotide of marker complex associated with said capture complex to produce an amplification signal; wherein an amplification signal above a predetermined signal threshold indicates that said subject is infected.

Abstract: Disclosed herein are methods and compositions (e.g., oligonucleotide primers) for isothermal amplification and detection of M. pneumoniae nucleic acids in a sample. In some embodiments, the methods include contacting a sample with a set of LAMP primers specific for a M. pneumoniae CARDS toxin-encoding nucleic acid under conditions sufficient to produce an M. pneumoniae nucleic acid amplification product and detecting the resulting M. pneumoniae amplification product. Kits including sets of LAMP primers for detection of M. pneumoniae CARDS toxin nucleic acids are also provided herein.

Abstract: A cleavage-based real-time PCR assay method is provided. In general terms, the assay method includes subjecting a reaction mixture comprising a) PCR reagents for amplifying a nucleic acid target, and b) flap cleavage reagents for performing a flap cleavage assay on the amplified nucleic acid target to two sets of thermocycling conditions. No additional reagents are added to the reaction between said first and second sets of cycles and, in each cycle of the second set of cycles, cleavage of a flap probe is measured.

Abstract: A method and an oligonucleotide probe are described for determining the presence or absence of mutant alleles in a genomic locus. The probe binds to different alleles of a target sequence with different melting temperatures (Tm). The method determines the Tm of the probe when it is hybridized to the target sequence to establish whether a variant nucleic acid such as a mutant allele is present or absent in the target sequence. There may be variants in a target sequence that are not of interest, for example phenotypically silent mutations. To ensure that these variants do not influence the Tm of the probe, the probe contains universal base sites where such variants of no interest occur.

Abstract: The invention relates to devices and methods for the detection of specific interactions between probe and target molecules. In particular, the invention relates to methods for the qualitative and/or quantitative detection of targets, including: introducing a sample containing targets into a reaction chamber formed between a first surface of the device and a second surface of a device, which is preferably located opposite to the first surface, wherein the distance between the first and the second surface is variable; and detecting the targets.

Abstract: Provided herein is a method for reducing amplification of non-template molecules in a nucleic acid sample. In certain embodiments, the method involves adding a helicase to a reaction mixture for non-helicase-dependent amplification of target nucleic acid.

Abstract: The present teachings provide methods, compositions, and kits for nucleic acid amplification. In some embodiments of the present teachings, amplification reactions are performed with at least one high stability primer. In some embodiments, the present teachings provide a method comprising a high stability primer for amplification of a nucleic acid sequence in a sample comprising a target nucleic acid sequence and a PCR inhibitor.

Abstract: Methods obtaining a single molecule consensus sequence for a single template molecule, and for obtaining a plurality of single molecule consensus sequences for a plurality of single template molecules is provided. Template molecules having two complementary regions connected with a linker are sequenced. A single read from each template molecule can be obtained, the read containing sequence information for each of the complementary regions. Single molecule consensus sequences can be determined from these reads by comparing the sequence information of the two complementary regions.

Abstract: The present invention provides methods for native extension parallel sequencing of polynucleotide.

Abstract: The present disclosure includes a method for predicting differential alternative splicing events from ribonucleic acid (RNA) sequencing data that includes receiving RNA sequence reads for two or more samples; generating directed acyclic graphs from the RNA sequence reads, wherein each directed acyclic graph represents at least a portion of a gene model; extracting count data from the directed acyclic graphs; and generating differential alternative splicing event information from the count data using a Dirichlet multinomial (DMN) regression.

Abstract: This application discloses methods of producing a DNA strand for sequencing, as well as genetic constructs, libraries, and arrays using DNA strands produced according to these methods. The application also discloses methods of sequencing using the DNA strands, genetic constructs, libraries, and arrays produced. In certain aspects, DNA being sequenced includes a target sequence and at least one adaptor sequence.

Abstract: Provided are methods and apparatuses for performing sequencing using droplet manipulation, for example, via electrowetting-based techniques. Also provided are integrated methods and apparatuses for performing sample preparation and sequencing on the same apparatus. In addition, provided are methods of reducing reagent waste and preloaded consumable cartridges comprising reagents for sample preparation and/or sequencing.