Abstract: A process for the use of peracid compositions to eliminate and/or control the growth of undesirable bacteria, including contaminating bacteria, in the fermentation production of alcohol is disclosed. Beneficially, the peracid compositions and methods of use of the same do not interfere or inhibit the growth or replication of yeast and have low or no adverse environmental impact.

Abstract: The present invention relates to a genetically engineered yeast capable of manufacturing a fermentation product using sucrose as a fermentation substrate, and fermentation processes using such a yeast. The yeast has an exogenous invertase gene and has a deletion or disruption of the PDC activity gene. Accordingly, the yeast is useful for manufacturing fermentation products other than ethanol from fermentation substrates containing sucrose.

Abstract: Provided herein is a genetically engineered microbe which accumulates citramalate. In one embodiment, the microbe includes an exogenous polynucleotide encoding a citramalate synthase which catalyzes the condensation of acetyl CoA and pyruvic acid. Optionally, the microbe also includes a second exogenous polynucleotide encoding a citrate synthase which catalyzes the condensation of acetyl CoA and oxaloacetate, and the citrate synthase activity in the microbe is reduced compared to a control microbe. In one embodiment, the citrate synthase includes at least one amino acid substitution in the acetyl-CoA binding pocket, the mobile loop, the NADH binding site, and the oxaloacetate binding site, or a combination thereof. Also provided herein are methods for using the genetically engineered microbe, including a method for producing citramalate. The method can further include isolating the citramalate.

Abstract: The invention relates to a genetically engineered thermophilic bacterial cell that is facultative anaerobic comprising: a) inactivation or deletion of the endogenous (S)-lactate dehydrogenase gene; b) introduction of a (R)-lactate dehydrogenase gene; c) inactivation or deletion of the endogenous pyruvate formate lyase A and/or B gene.

Abstract: The invention provides a recombinant microbial host cell capable of converting a raw material comprising a fermentable carbon substrate to o-aminobenzoate biologically. The invention further provides a method for producing aniline, comprising the steps of: a) producing o-aminobenzoate by fermentation of a raw material comprising at least one fermentable carbon substrate using the recombinant microbial host cell of the capable of converting said raw material comprising at least one fermentable carbon substrate to o-aminobenzoate biologically, wherein said o-aminobenzoate comprises anthranilate anion, b) converting said o-aminobenzoate from said anthranilate anion to anthranilic acid by acid protonation, c) recovering said anthranilic acid by precipitation or by dissolving in an organic solvent, and d) converting said anthranilic acid to aniline by thermal decarboxylation in an organic solvent.

Abstract: The present invention relates to a recombinant nucleic acid molecule, a recombinant microorganism, to a method for producing alanine and to the use of the recombinant nucleic acid molecule or the recombinant microorganism for the fermentative production of alanine.

Abstract: The present disclosure provides engineered proline hydroxylase polypeptides for the production of hydroxylated compounds, polynucleotides encoding the engineered proline hydroxylases, host cells capable of expressing the engineered proline hydroxylases, and methods of using the engineered proline hydroxylases to prepare compounds useful in the production of active pharmaceutical agents.

Abstract: The invention relates to composite components and methods of producing composite components. In yet another embodiment, the present invention relates to a method of producing a composite component using anaerobically digested biomass. In still yet another embodiment, the method further comprises using liquid effluent from the digester. In still yet another embodiment, the method further comprises wet-mat forming and cold pressing the anaerobically digested biomass and wet-mat drying under heat and pressure.

Abstract: Embodiments of the present disclosure involve systems and methods that inhibit the production of lactic acid during propagation of yeast and/or during hydrolysis of cellulose by including a sufficient amount of dissolved oxygen.

Abstract: The invention relates to a process for the preparation of a fermentation product from ligno-cellulosic material, comprising the following steps: a) optionally pre-treatment of the ligno-cellulosic material; b) optionally washing of the optionally pre-treated ligno-cellulosic material; c) enzymatic hydrolysis of the optionally washed and/or optionally pre-treated ligno-cellulosic material using an enzyme composition comprising at least two cellulase and whereby the enzyme composition at least comprises GH61; d) fermentation of the hydrolysed ligno-cellulosic material to produce a fermentation product; and e) optionally recovery of a fermentation product; wherein before and/or during the enzymatic hydrolysis oxygen is added to the ligno-cellulosic material.

Abstract: The invention relates to a genetically modified microorganism for making a recombinant oligosaccharide, preferably of 3-8 monosaccharide units, more preferably of 3-5 monosaccharide units, particularly a HMO, which comprises one or more genes encoding a sucrose utilization system, so the microorganism can use sucrose as a carbon and energy source. The one or more genes encoding a sucrose utilization system are preferably one or more genes encoding a heterologous PTS-dependent sucrose utilization transport system, such as the scr genes.

Abstract: The present invention is directed to methods and compositions for adding tails of specific lengths to a substrate polynucleotide. The invention also contemplates methods and compositions for immobilization of tailed substrates to a solid support. The disclosure contemplates that the attenuator molecule is any biomolecule that associates with a tail sequence added to a substrate polynucleotide and controls the addition of a tail sequence to the 3? end of the substrate polynucleotide. The sequence that is added to the substrate polynucleotide is referred to herein as a tail sequence, or simply a tail, and the process of adding a nucleotide to a substrate polynucleotide is referred to herein as tailing.

Abstract: The present invention relates generally to the production of steviol glycosides. Provided is a method for enzymatically providing a modified steviol glycoside, comprising incubating a steviol glycoside substrate in the presence of sucrose and the glucansucrase GTF180 of Lactobacillus reuteri strain 180, or a mutant thereof having the desired transglycosylation activity. Also provided are modified steviol glycosides obtainable by a method of the invention, and the use thereof as low-glycemic sweetener.

Abstract: The disclosure provides recombinant cells and methods for producing a ribosomally synthesized and posttranslationally modified peptide (RiPP), as well as RiPP libraries and methods for producing RiPP libraries.

Abstract: The present invention relates to a method for detecting or quantifying CTP in a cell sample comprising at least two nucleotide triphosphates by cationic ion pairing chromatography coupled to mass spectrometry, to a method for detecting or quantifying CTP synthase activity based on the method for detecting or quantifying CTP, and to their use in methods for screening potential immunosuppressive or anti-cancer compounds and in methods for determining the appropriate dose of an immunosuppressive or anti-cancer compound inhibiting CTP synthase activity for a treated subject.

Abstract: A sensor determines whether a specimen includes a first substance. In an exemplary embodiment, the sensor includes a base. In an exemplary embodiment, the sensor is configured to determine whether the specimen includes the first substance and further includes, on the base, a detection unit on which a second substance is immobilized. The second substance includes a bond that is cleft by the reaction with hydrogen peroxide. In an exemplary embodiment, the specimen that is brought in contact with an enzyme that generates the hydrogen peroxide by the reaction with the first substance is introduced to the detection unit in the sensor configured to determine whether the specimen includes the first substance.

Abstract: Aspects of embodiments may include methods for automated enzymatic detection of glucose-6-phosphate dehydrogenase (G6PD) activity. Aspects of embodiments may include methods for enzymatic detection of G6PD activity in droplets in oil. Aspects of embodiments may include a system including a droplet actuator. Aspects of embodiments may include a treatment method.

Abstract: A method of quantifying ammonia, which method includes: performing a first reaction in which a test liquid containing ammonia is reacted with ATP and L-glutamic acid in the presence of glutamine synthetase to produce ADP; performing a second reaction in which the produced ADP is reacted with glucose in the presence of ADP-dependent hexokinase to produce glucose-6-phosphate; performing a third reaction in which the produced glucose-6-phosphate is reacted with an oxidized NAD compound in the presence of glucose-6-phosphate dehydrogenase to produce a reduced NAD compound; and quantifying the reduced NAD compound to quantify ammonia.

Abstract: A microfluidic device includes an input port for inputting a particle-containing liquidic samples into the device, a retention member, and a pressure actuator. The retention member is in communication with the input port and is configured to spatially separate particles of the particle-containing liquidic sample from a first portion of the liquid of the particle containing fluidic sample. The pressure actuator recombines at least some of the separated particles with a subset of the first portion of the liquid separated from the particles. The device can also include a lysing chamber that receives the particles and liquid from the retention member. The lysing chamber thermally lyses the particles to release contents thereof.

Abstract: Methods and systems for identifying binding sites in macromolecules using small molecule mimics of naturally occurring molecules is disclosed. A reactive probe is provided that mimics small molecule cofactors. A target macromolecule is irreversibly bound to the probe in vivo to selectively pull down or precipitate probe-bound macromolecules. The macromolecules may be, but are not limited to, DNA, RNA, and proteins.

Abstract: The present invention relates to the detection of a target nucleic acid sequence by a PCE-SH (PTO Cleavage and Extension-Dependent Signaling Oligonucleotide Hybridization) assay. The present invention does not use probes to be hybridized with target nucleic acid sequences for providing target signals. Interestingly, the present invention uses probes (signaling oligonucleotides) to be hybridized with the extended strand formed in a target-dependent manner in which the extended strand is synthesized using the CTO artificially selected as templates.

Abstract: The present invention provides for novel methods for regulating and detecting the cytosine methylation status of DNA. The invention is based upon identification of a novel and surprising catalytic activity for the family of TET proteins, namely TET1, TET2, TET3, and CXXC4. The novel activity is related to the enzymes being capable of converting the cytosine nucleotide 5-methylcytosine into 5-hydroxymethylcytosine by hydroxylation.

Abstract: The present invention relates to a microfluidic device and platform configured to conduct multiplexed analysis within the device. In particular, the device allows multiple targets to be detected on a single-cell level. Also provided are methods of performing multiplexed analyses to detect one or more target nucleic acids, proteins, and post-translational modifications.

Abstract: The present invention relates to a proximity probe based detection assay (“proximity assay”) for an analyte in a sample, specifically a proximity probe extension assay (PEA), an in particular to an improvement in the method to reduce non-specific “background” signals, wherein the improvement comprises the use in such assays of a component comprising 3? exonuclease activity, said method comprising: (a) contacting said sample with at least one set of at least first and second proximity probes, which probes each comprise an analyte-binding domain and a nucleic acid domain and can simultaneously bind to the analyte; (b) allowing the nucleic acid domains of the proximity probes to interact with each other upon binding of said proximity probes to said analyte, wherein said interaction comprises the formation of a duplex; (c) contacting said sample with a component comprising 3? exonuclease activity; (d) extending the 3? end of at least one nucleic acid domain of said duplex to generate an extension product, wherein

Abstract: A portable testing device includes a hosing with an integrated touchscreen display and a receptacle in which a sample holder containing a biological sample and reagent mixture can be placed. The portable testing device further includes an optical assembly positioned in the housing, an electronic assembly that is configured to receive data from the optical assembly and transmit it for display upon the touchscreen display, and a power supply in the housing to power the portable testing device. The optical assembly includes an excitation filter that extends across the entire optical assembly and an emission filter that extends across the entire optical assembly.

Abstract: The present invention provides facile and accurate molecular diagnosis of disease-specific genes capable of the naked eye detection through amplifying the target genes to selectively block the fluid path in a microfluidic device. Specifically, the present invention includes an isothermal amplification of target genes through a rolling circle amplification, a microfluidic device for detecting pathogen genes, and a detection method using the same. Therefore, the present invention can conveniently detect a single target gene, such as a single pathogen, or at the same time, several target genes, such as several pathogens, without complicated mechanical equipment.

Abstract: Methods of loading a molecule of interest into a sample well are provided. In some aspects, methods of loading a molecule of interest into a sample well involve loading a molecule of interest into a sample well in the presence of a crowding agent and/or a condensing agent. In some aspects, methods of loading a sequencing template into a sample well are provided.

Abstract: A DNA sequencing device and related methods, wherein the device includes a substrate, a nanochannel formed in the substrate, a first electrode positioned on a first side of the nanochannel, and a second electrode. The second electrode is positioned on a second side of the nanochannel opposite the first electrode, and is spaced apart from the first electrode to form an electrode gap that is exposed in the nanochannel. At least a portion of first electrode is movable relative to the second electrode to decrease a size of the electrode gap.

Abstract: The present disclosure provides methods, compositions, and systems for distributing polymerase compositions into array regions. In particular, the described methods, compositions, and systems utilize density differentials and/or additives to increase efficiency in the distribution of polymerase compositions to a surface as compared to methods utilizing only diffusion control.

Abstract: Provided herein are methods, compositions, and kits for targeted sequencing of polynucleotides with high accuracy and low amplification and sequencing errors and bias.

Abstract: Improved solid supports and methods for analyzing target nucleotide sequences are provided herein. Certain improvements are directed to efficiently preparing nucleic acids that comprise nucleotide sequences identical to or substantially identical to one or more target nucleotide sequences, or complement thereof. The prepared nucleic acids include a reference sequence that facilitates sequence analysis. The solid supports and methods provided herein minimize the number of steps required by published sequence analysis methodologies, and thereby offer improved sequence analysis efficiency.

Abstract: Provided herein, among other things, is a method of processing a nucleic acid sample. In some embodiments, the method comprises a) hybridizing a sample comprising a target fragment to a nucleic acid probe comprising: i. a head sequence and a tail sequence, wherein the head and tail sequences are at the ends of a first oligonucleotide molecule; and ii.

Abstract: Aspects of the present invention relate to compositions and methods for providing DNA fragments from a remote sample. In particular aspects a remote sample comprising DNA is provided, DNA is isolated from the remote sample, and the isolated DNA is treated in a way which allows differentiation of methylated and unmethylated cytosine. Additional, particular embodiments provide compositions and methods for methylation analysis of DNA derived from a remote sample. Other aspects provide for compositions and methods of whole genome amplification of bisulfite treated DNA. Other aspects provide methods for determining the presence or absence of methylation of at least one cytosine, or a series of cytosines in cis, in human DNA of a blood sample, a plasma sample, a serum sample or a urine sample from a human individual.

Abstract: The present invention relates to a method of diagnosing depression (even at an early stage that may precede clinical symptoms), for determining the pharmacoresponse to antidepressants, for managing treatment of psychiatric disorders, including depression, and for treatment of depression in patients. Further provided is a method for screening antidepressants.

Abstract: Methods and kits are provided for diagnosing, monitoring, or predicting preeclaimpsia in a pregnant woman, trisomy 18 and trisomy 21 in a fetus, as well as for detecting pregnancy in a woman, by quantitatively measuring in the maternal blood the amount of one or more RNA species derived from a set of genetic loci and comparing the amount of the RNA species with a standard control.

Abstract: The present invention relates generally to the fields of reproductive medicine. More specifically, the present invention relates to methods for determining the ovarian reserve and ovarian function by determining the level of cell-free nucleic acids or the level of a miRNA species selected from miR_30_a or miR_140 or let_7_b or miR_191 or miR_320_a or miR_21 or miR_30_d or miR_574_3p. The method may also be used in predicting the efficacy of controlled ovarian hyperstimulation.

Abstract: The method for preventing progression to metabolic syndrome includes determining whether a subject possesses at least one allele of the caveolin-1 rs1997623 C to A SNP, and providing an intervention to prevent progression to metabolic syndrome, including modifications of diet and exercise, administration of one or more pharmaceutical compounds, or a combination thereof. The method may be useful to reduce the risk of developing complications associated with MetS, such as heart disease, stroke, or diabetes. The method may include monitoring additional metabolic risk factors. The pharmaceutical compound may be a pharmaceutical capable of inhibiting the expression of caveolin-1.

Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

Abstract: The invention relates to classification, diagnosis and treatment of cancers. In one embodiment, the present invention provides methods and kits that classify cancers into various subtypes based on expression patterns of AKT pathway components. In another embodiment, the present invention provides methods and kits that diagnose cancer subtypes by evaluating expression patterns of AKT pathway components. In still another embodiment, the present invention provides methods and kits that treat a cancer subtype by administering an alkylating agent or a PI3K/AKT/mTOR inhibitor to a patient. Cancers suitable with various embodiments of the invention include but are not limited to brain tumors, gliomas and GBM.

Abstract: A method for the prediction and/or prognosis of survival time of a patient suffering from cancer, comprising the steps of: a) measuring a RDA score in a tumor tissue sample comprising cellular RNA from said patient after said patient has received one or more doses of a cancer treatment; b) comparing said RDA score to one or more predetermined RNA disruption reference values; and c) providing a favorable prediction and/or prognosis of survival time for said patient when said RDA score is higher than said predetermined RNA disruption reference value; or providing an unfavorable prediction and/or prognosis of survival time for said patient when said RDA score is lower than said predetermined RNA disruption reference value, wherein the RDA score is proportional to the degree of RNA disruption.

Abstract: The present invention relates to compositions and methods for molecular profiling and diagnostics for genetic disorders and cancer, including but not limited to gene expression product markers associated with cancer or genetic disorders. In particular, the present invention provides algorithms and methods of classifying cancer, for example, thyroid cancer, methods of determining molecular profiles, and methods of analyzing results to provide a diagnosis.

Abstract: Cell-free DNA molecules in a mixture of a biological sample can be analyzed to detect viral DNA. Methylation of viral DNA molecules at one or more sites in the viral genome can be determined. Mixture methylation level(s) can be measured based on one or more amounts of the plurality of cell-free DNA molecules methylated at a set of site(s) of the particular viral genome. The mixture methylation level(s) can be determined in various ways, e.g., as a density of cell-free DNA molecules that are methylated at a site or across multiple sites or regions. The mixture methylation level(s) can be compared to reference methylation level(s), e.g., determined from at least two cohorts of other subjects. The cohorts can have different classifications (including the first condition) associated with the particular viral genome. A first classification of whether the subject has the first condition can be determined based on the comparing.

Abstract: This invention relates to polynucleotide sequences encoding genes that can confer resistance to the plant pathogen Colletotrichum, which causes anthracnose stalk rot, leaf blight and top dieback in corn and other cereals. It further relates to plants and seeds of plants carrying chimeric genes comprising said polynucleotide sequences, which enhance or confer resistance to the plant pathogen Colletotrichum, and processes of making said plants and seeds. The invention further presents sequences that can be used as molecular markers that in turn can be used to identify the region of interest in corn lines resulting from new crosses and to quickly and efficiently introgress the genes from corn lines carrying said genes into other corn lines that do not carry said genes, in order to make them resistant to Colletotrichum and resistant to stalk rot.

Abstract: A method for quantification of an adeno-associated virus genome, including the steps of (a) preparing a composition containing a sample, at least one primer pair for use in amplification of only a nucleotide sequence contained in inverted terminal repeats of an adeno-associated virus, and an intercalating dye; (b) performing nucleic acid amplification reaction using the composition prepared in the step (a); and (c) detecting an amplified product obtained in the step (b). The present invention is especially useful in the fields of medicine, gene engineering, and biology.

Abstract: Provided herein include compositions comprising a primer having the nucleic acid sequence of ACeIN-F3_c, a primer having the nucleic acid sequence of ACeIN-B3_a, a primer having the nucleic acid sequence of ACeIN-B3_b, a primer having the nucleic acid sequence of ACeIN-FIP_e, a primer having the nucleic acid sequence of ACeIN-FIP_f, a primer having the nucleic acid sequence of ACeIN-BIP (or ACeIN-BIP-song), a primer having the nucleic acid sequence of ACeIN-LF; and a primer having the nucleic acid sequence of ACeIN-LB. Also provided are methods of detecting human immunodeficiency virus (HIV) nucleic acids in a sample comprising performing reverse transcription-based loop mediated isothermal amplification (RT-LAMP) on a sample using the previously disclosed compositions.

Abstract: The present invention relates to a method for differentiating in a subject with HR-HPV between a severe form of HR-HPV infection and a mild form of HR-HPV infection. It further is concerned with a composition comprising a probe oligonucleotide mixture, a device, and a kit for use in conjunction with the method of the invention.

Abstract: Methods and systems for pretreating lignocellulosic biomass are disclosed. An acid solution between 1% to 1.6% sulfuric acid is applied to the biomass. The biomass is subjected to an elevated temperature to cause the production of xylose, glucose, and furfural. Adjustments to temperature, acid concentration, and time can generate at least 80% or 90% of theoretical xylose, 45% or 50% of the theoretical glucose, and less than 4000 ppm of furfural in the xylose liquor. A portion of the resulting xylose liquor may be separated from the glucan solids. The xylose liquor, still highly acidic, can be recycled to reduce subsequent acid loading requirements. Makeup acid solution is added to the xylose liquor and subsequent biomass to ensure a proper solids to liquids ratio. The biomass is again treated to higher temperatures to yield sugars. The process may be repeated for each subsequent cycle.

Abstract: The invention concerns a process for tanning hide to obtain leather. The general process for obtaining the intermediary wet blue stage comprises the following steps: a) a picking step with acid and salt, followed by b) a tanning step with chromium salt, followed by c) a basification step. The invention is characterized in that the bath of the pickling step comprises organic acids selected from 2-Methyl glutaric acid (MGA), ethyl succinic acid (ESA) and mixture thereof instead of the traditional strong acid, generally sulfuric acid This process requires less basification agent and enables an increase of the up-taking of the re-tanning products. This invention provides leather with improved mechanical properties.

Abstract: Disclosed is a steel whose composition includes specified wt % of: Ni, Mo, Co, Mo+Co+Si+Mn+Cu+W+V+Nb+Zr+Y+Ta+Cr+C+Al+B+Ti+N, Ni+Co+Mo, Al, Ti, N, Si, Mn, C, S, P, B, H, O, Cr, Cu, W, Zr, Ca, Mg, Nb, V, Ta, Y, the remainder being iron and impurities resulting from production. The inclusion population, observed by image analysis on a polished surface of 650 mm2 if the steel is in the form of a hot-formed part or a hot-rolled sheet and 800 mm2 if the steel is in the form of a cold-rolled sheet, does not include non-metal inclusions of an equivalent diameter greater than 10 ?m. Also disclosed are a product created from the steel, and a manufacturing method.

Abstract: The present invention provides a method for efficiently leaching copper from copper sulfide ore by separating and recovering iodine, and iron(III) ions to be used are regenerated by a heap of stacked ore in the method for leaching copper from copper sulfide using a sulfuric acid solution containing iodide ions and iron(III) ions as a leaching solution.