Abstract: The present disclosure provides methods for generating sugars from a cellulosic biomass. The methods combine treatment of the biomass using a high-shear milling device and saccharification of the biomass to partially hydrolyze the biomass. The biomass can be saccharified either after or simultaneously with the high-shear milling treatement. The partially hydrolyzed biomass is then separated into a solids stream with saccharification enzymes, and a liquid stream with sugars. The solids stream and associated enzymes are further incubated under saccharification conditions to produce additional sugars, or are recycled and added to fresh biomass, which is saccharified under high-shear milling conditions. The methods result in improved conversion of cellulosic biomass to glucose.

Abstract: A method of digesting a lignocellulosic material is disclosed. In one embodiment, the method comprises the step of exposing the material to an effective amount of Streptomyces sp. ActE secretome such that at least partial lignocellulosic digestion occurs.

Abstract: Biomass (e.g., plant biomass, animal biomass, and municipal waste biomass) is processed to produce useful products, such as fuels. For example, systems can use feedstock materials, such as cellulosic and/or lignocellulosic materials and/or starchy materials, to produce ethanol and/or butanol, e.g., by fermentation.

Abstract: The present invention relates to a novel endoglycoceramidase whose hydrolytic activity has been substantially reduced or eliminated, such that the enzyme is useful for synthesis of glycolipids from a monosaccharide or oligosaccharide and a ceramide. More specifically, the endoglycoceramidase is a mutant version of a naturally occurring endoglycoceramidase, preferably comprising a mutation within the active site or the nucleophilic site of the enzyme and more preferably comprising a substitution mutation of the Glu residue within the active site or the nucleophilic site. Also disclosed are a method for generating the mutant endoglycoceramidase and a method for enzymatically synthesizing glycolipids using this mutant enzyme.

Abstract: The present invention relates to methods of modulating the mannose content of recombinant proteins.

Abstract: The invention described herein generally relates to glycoengineering host cells for the production of glycoproteins for therapeutic use. Host cells are modified to express biosynthetic glycosylation pathways. Novel prokaryotic host cells are engineered to produce N-linked glycoproteins wherein the glycoproteins comprise polysialic acid or blood group antigens.

Abstract: The present invention relates to the field of recombinant protein production in bacterial hosts. It further relates to extraction of soluble, active recombinant protein from an insoluble fraction without the use of denaturation and without the need for a refolding step. In particular, the present invention relates to a production process for obtaining high levels a soluble recombinant Type 1 interferon protein from a bacterial host.

Abstract: The invention relates to a sortase-mediated protein purification and ligation. Specifically, the invention relates to a technique that links protein expression/purification with conjugation to therapeutic agents, imaging agents, or linkers.

Abstract: The present invention is directed to methods and a bio-capacitor sensing device for the detection of toxic chemicals using bacteria. The sensing platform comprises gold interdigitated capacitor with a defined geometry, a layer of carboxy-CNTs immobilized with viable E. coli cells as sensing elements. Also included are methods of making the bio-capacitor device and methods for detecting toxic chemicals that induce cellular stress response. The present innovation discloses the development of a bio capacitor chips immobilized with carboxy-CNTs tethered E. coli bacteria. In addition, the present invention also includes determination of behavior and characteristics of chemically stimulated bacteria on biochip using electric field including frequency and/or amplitude as controlling parameters.

Abstract: The present invention is directed to a separation device or container that can be used in the separation, isolation or pelleting of microorganisms from a test samples known to contain or suspected of containing said microorganisms. Subsequently, the separated, isolated or pelleted microorganism sample can undergo one or more interrogation steps to provide measurements useful for the characterization and/or identification of microorganism. In one aspect of the present invention, the interrogation steps can occur in situ in the separation device or container described herein.

Abstract: The present invention provides a Mitrecin A polypeptide useful in prevention and treatment of one or more bacteria. Also provided is a method to kill or prevent growth of one or more bacteria comprising contacting the one or more bacteria with a Mitrecin A polypeptide. The target bacteria can be selected from the group consisting of a Gram-positive bacterium, a Gram-negative bacterium, or both. In one embodiment, the present invention is drawn to a polynucleotide encoding a Mitrecin A polypeptide, a vector comprising the polynucleotide, a host cell comprising the polynucleotide, or a composition comprising the Mitrecin A polypeptide, the polynucleotide, the vector, or the host cell.

Abstract: A method and microfluidic device useful for isolating microbes from a blood sample which includes introducing the blood sample into the sample inlet of a spiral microfluidic device; and introducing a second fluid into the sheath inlet of the microfluidic device, wherein the spiral channel terminates in a microbe outlet and a waste outlet, and wherein the spiral channel includes a length, height, and a width that define an aspect ratio adapted to isolate any microbes present in the sample along a first portion of the spiral channel terminating at the microbe outlet, and to isolate red blood cells and leukocytes along a second portion of the spiral channel terminating at the waste outlet; and collecting the microbes from the microbe outlet, thereby isolating the microbes.

Abstract: This invention pertains to the general field of microbiology, and more specifically to transfer, inoculation and/or streaking of micro-organisms, e.g. for the purpose of obtaining individual colonies. Provided is a method for transferring a microbial sample from a first carrier to a second carrier, comprising the steps of: a) contacting at least one ferromagnetic particle with at least part of the sample associated with the first carrier, wherein the particle is a composite bead having a surface roughness (Ra) in the range of 0.1 to 25 ?m, a diameter between 2 to 88 mm and a density below 7 g/cm3, and b) applying a magnetic field gradient to allow for magnetically controlled motion of said particle to said second carrier, such that at least part of the sample is streaked onto the second carrier. Also provided is an apparatus for inoculating petri dishes with the sample according to the method and also inoculating slides and/or tubes with a portion of the sample.

Abstract: The present invention generally relates to air sampling of biological compounds. Specifically, the present invention relates to a device and method for sampling the ambient air for detecting microbial propagules, microbial propagules being any spore, vegetative cell, or virion of microbiological origin including all bacteria, fungi, viruses, protozoans, molds, slime molds, chlamydospores, hyphae, and cysts.

Abstract: Provided herein is a reaction mixture comprising Cas9 and a non-ionic surfactant, e.g., a polyoxyethylene surfactant. In certain embodiments, the reaction mixture may comprise a Cas9 protein, a guide RNA, a salt, a buffering agent, a nucleic acid target and a non-ionic surfactant. Kits are also provided. In certain embodiments, a kit may comprise: a Cas9 protein; and a concentrated reaction buffer comprising salt, a buffering agent and a non-ionic surfactant.

Abstract: It is an object of this invention to provide a simple measurement method capable of detecting indoxyl sulfuric acid in a sample rapidly and at high sensitivity. By causing sulfatase and tetrazolium salt to act on indoxyl sulfuric acid in a sample to generate a formazan dye, and then calculating the generation amount of the formazan dye, indoxyl sulfuric acid in the sample can be measured more simply, more rapidly, and at higher sensitivity as compared with former methods.

Abstract: In some embodiments, the invention provides methods for detecting and/or classifying an anticoagulant at a therapeutically relevant amount or higher in a patient, including subjecting a sample of a control blood component (known not to contain the anticoagulant) to a clotting assay in the presence of a Factor Xa reagent to obtain a control clotting measurement; and subjecting a sample of a blood component from a patient suspected of having the anticoagulant to the clotting assay in the presence of the Factor Xa reagent to obtain a patient clotting measurement, wherein the patient clotting measurement sample greater than the control clotting measurement indicates the presence of the anticoagulant at a therapeutically relevant amount or higher in the patient. In some embodiments, the invention includes methods for classifying an anticoagulant as an anti-Factor Xa or a direct thrombin inhibitor anticoagulant using a clotting assay in the presence of an ecarin reagent.

Abstract: The present invention provides, among other things, methods of quantitating mRNA capping efficiency, particularly for mRNA synthesized in vitro. In some embodiments, the methods comprise chromatographic methods of quantifying capping efficiency and methylation status of the caps.

Abstract: The present invention is directed to methods for identifying the presence of one or more methylated or unmethylated target nucleotide sequences in a sample that involve a nuclease-ligation reaction. In some embodiments, the ligation products formed in the nuclease-ligation process of the present invention are subsequently amplified using a polymerase chain reaction. The ligated product sequences or extension products thereof are detected, and the presence of one or more methylated or unmethylated target nucleotide sequences in the sample is identified based on the detection.

Abstract: A processing module is configured to extend the capabilities of an analyzer configured to process substances within each of a plurality of receptacles. The module includes a container transport configured to transport a container from a location within the processing module to a location within the analyzer that is accessible to a substance transfer device of the analyzer. A receptacle distribution system is configured to receive a receptacle from the analyzer, transfer the receptacle into the processing module, and to move the receptacle between different locations within the analyzer. A substance transfer device of the module is configured to dispense substances into or remove substances from the receptacle within the processing module. A reagent card exchanger provides an input device for inserting reagent cards into and removing reagent cards from the module, stores reagent cards within the module, and transfers reagent cards to different location within the module.

Abstract: The invention provides methods for generating nucleic acid molecule fragments having a customized distribution. In one aspect, a method of generating nucleic acid fragments having a customized fragment size distribution is provided comprising obtaining a master pool of nucleic acid molecules to be fragmented; fragmenting at least two independent aliquots of the master pool of nucleic acid molecules in separate reactions, wherein the fragmentation conditions are identical except for a single variable.

Abstract: The invention relates to a method for single cell analysis of relative telomere length using multiplex pre-PCR followed by a qPCR (SCT-pqPCR).

Abstract: Systems and methods are provided for sample processing. A device may be provided, capable of receiving the sample, and performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing multiple assays. The device may comprise one or more modules that may be capable of performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing the steps using a small volume of sample.

Abstract: Compositions and methods are provided for facilitating the enrichment of single-stranded DNA containing methylated CpG in a mixture containing methylated and unmethylated DNA. The compositions relate to methylation-binding protein domains that selectively bind to methylated single strand DNA. In embodiments of the invention, the methylated DNA is eluted in 0.4M-0.6M NaCl while the unmethylated single strand DNA is eluted in less than 0.4M salt. The ability to readily enrich for methylated DNA permits high throughput sequencing of the methylated DNA and identification of abnormal methylation patterns associated with disease.

Abstract: There is provided methods and compositions to diagnose, classify and treat inflammatory bowel disease including ulcerative colitis and Crohn's disease by measuring the levels of certain bacterial taxa and proteins collected from the gut.

Abstract: The present disclosure relates to method of distinguishing between two or more species of one or more organisms in a sample, by contacting a biological sample comprising ribosomal ribonucleic acid (rRNA) with a set of antisense probes, wherein the set of probes contains at least one detectable probe that is specific for a target rRNA sequence of each species to be tested, and wherein the individual probes specific for each species comprises less than about 85% sequence identity; and, detecting hybridization between one or more of the probes and the rRNA, thereby distinguishing between two or more species in a sample.

Abstract: The invention is directed to methods of extracting nucleic acids from microorganisms or mammalian cells adhered to polymers that are malleable within a living organism and particularly malleable in the oral cavity of the living organism. The invention also provides for method of detecting and quantitating microorganisms that adhere to malleable polymers, such as chewing gum.

Abstract: The invention provides a rapid, accurate, sensitive, and low-cost detection method for screening a biological sample for one or more desired bacterial species. The inventive method employs a two-step multiplex real-time PCR assay that comprises an internal amplification control and specific primer sets to detect and discriminate bacterial species based the unique melting temperatures of specific DNA sequences of each strain.

Abstract: An object of the disclosure of the present specification is to provide a method for detection of a target nucleic acid which allows construction of an effective detection system of a target nucleic acid. For this purpose, in the disclosure of the present specification, a first primer comprising an identification sequence complementary to a target sequence in a target nucleic acid and a tag addition sequence, and a second primer having a label are prepared. The first primer and the second primer are used for the target nucleic acid in a sample to amplify a chimeric DNA having a tag sequence and the label. The chimeric DNA is hybridized with a detection probe on a solid phase to obtain signal intensity information based on the label, and the target nucleic acid is detected based on the signal intensity information.

Abstract: A real-time method of detecting the presence and/or amount of a methylated or unmethylated gene of interest in a DNA-containing sample, comprises the steps of (a) contacting the DNA-containing sample with a reagent which selectively modifies unmethylated cytosine residues in the DNA to produce detectable modified residues but which does not modify methylated cytosine residues (b) amplifying at least a portion of the methylated or unmethylated gene of interest using at least one primer pair, at least one primer of which is designed to bind only to the sequence of methylated or unmethylated DNA following treatment with the reagent, wherein at least one primer in the primer pair produces a detectable fluorescence signal during amplification which is detected in real-time (c) quantifying the results of the real-time detection against a standard curve for the methylated or unmethylated gene of interest to produce an output of gene copy number.

Abstract: Methods and kits for assessing severity index for alcohol abuse, drug abuse, and other reward deficiency syndromes. It has been discovered that a multifaceted non-specific RDS behaviors should be considered as the true “reward” phenotype (endophenotype) instead of a single subset RDS behavior such as alcoholism. In an embodiment of the present invention, it has been discovered that there are at least eleven risk alleles associated with ten candidate genes. The methods and kits of the present invention satisfy the need to classify patients at genetic risk for drug/alcohol seeking behavior prior to or upon entry to residential and or non-residential chemical dependency and pain programs.

Abstract: The present invention relates to methods of elongating chromosomes. Embodiments of the present disclosure are directed to methods of elongating DNA by immobilizing or attaching the DNA to a substrate.

Abstract: A method of forming a polymer matrix array includes applying an aqueous solution into wells of a well array. The aqueous solution includes polymer precursors. The method further includes applying an immiscible fluid over the well array to isolate the aqueous solution within the wells of the well array and polymerizing the polymer precursors isolated in the wells of the well array to form the polymer matrix array. An apparatus includes a sensor array, a well array corresponding to the sensor array, and an array of polymer matrices disposed in the well array.

Abstract: This invention provides novel compositions and processes for analyte detection, quantification and amplification. Nucleic acid arrays and libraries of analytes are usefully incorporated into such compositions and processes. Universal detection elements, signaling entities and the like are employed to detect and if necessary or desirable, to quantify analytes. Amplification of target analytes are also provided by the compositions and processes of this invention.

Abstract: The present invention provides methods and systems for real-time measurements of PCR with multiplexing capability. Certain embodiments relate to methods and systems that use fluorescently encoded superparamagnetic microspheres for the immobilization of amplification products during the PCR process, and an imaging chamber of a measurement device that is also capable of controllable thermal cycling for assisting the PCR process.

Abstract: This disclosure describes related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of recombinase and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods have the advantage of not requiring thermocycling or thermophilic enzymes. Further, the improved processivity of the disclosed methods may allow amplification of DNA up to hundreds of megabases in length.

Abstract: In some embodiments, the present teachings provide methods for nucleic acid amplification, comprising forming a reaction mixture, and subjecting the reaction mixture to conditions suitable for nucleic acid amplification. In some embodiments, methods for nucleic acid amplification include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, methods for nucleic acid amplification include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the methods for nucleic acid amplification employ an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be conducted in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components.

Abstract: Provided herein is technology relating to sequencing nucleic acids, but not exclusively, to compositions, methods, systems, and kits related to nucleotides comprising an electrochemically detectable moiety and one or more photolabile synthesis-inhibiting moieties.

Abstract: Presented herein are polymerase enzymes for improved incorporation of nucleotide analogues, in particular nucleotides which are modified at the 3? sugar hydroxyl, as well as methods and kits using the same.

Abstract: The invention provides modified nucleotide or nucleoside molecule comprising a purine or pyrimidine base and a ribose or deoxyribose sugar moiety having a removable 3?-OH blocking group covalently attached thereto, such that the 3? carbon atom has attached a group of the structure —O—Z wherein Z is any of —C(R?)2-O—R?, —C(R?)2-N(R?)2, —C(R?)2-N(H)R?, —C(R?)2-S—R? and —C(R?)2-F, wherein each R? is or is part of a removable protecting group; each R? is independently a hydrogen atom, an alkyl, substituted alkyl, arylalkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclic, acyl, cyano, alkoxy, aryloxy, heteroaryloxy or amido group, or a detectable label attached through a linking group; or (R?)2 represents an alkylidene group of formula ?C(R??)2 wherein each R?? may be the same or different and is selected from the group comprising hydrogen and halogen atoms and alkyl groups; and wherein said molecule may be reacted to yield an intermediate in which each R? is exchanged for H or, where Z is —C(R?)2-F, the F is ex

Abstract: Presented herein are polymerase-linked nucleotides for improved distinguishing nucleotide sequences for different nucleic acid molecules. Also presented are methods and systems using the polymerase-linked nucleotides for improved distinguishing nucleotide sequences for different nucleic acid molecules.

Abstract: The present invention relates to compositions, methods, and uses for obtaining sequence information from nucleic acid molecules.

Abstract: There is provided a method of screening for susceptibility to complement dysregulation in an individual, the method including screening for the presence or absence of a genetic profile characterized by polymorphisms in the genome of the individual associated with complement dysregulation. The presence of a genetic profile is indicative of the individual's risk of complement dysregulation.

Abstract: The present invention relates to a method for diagnosing or predicting a non syndromic autosomal recessive optic atrophy, or a risk of a non syndromic autosomal recessive optic atrophy.

Abstract: Methods are provided for determining if a subject is likely to develop an age-related disease based on miRNA signatures. Related methods of treatment are also provided.

Abstract: A method for identifying the risk of developing Chronic Allograft Nephropathy (CAN) in a patient that received a kidney transplant from a donor which comprises identifying the race of the donor; determining the levels of SHROOM 3 expression in a kidney biopsy specimen obtained from the patient at a predetermined time after transplant; comparing the level of SHROOM 3 expression in the biopsy specimen with the levels of SHROOM 3 expression in a control; determining if the level of SHROOM 3 expression in the allograft is significantly higher than in the control, and diagnosing the patient as being at risk for CAN if the level of SHROOM 3 expression in the specimen is significantly higher than in the control.

Abstract: The present invention relates to methods for simultaneously determining the presence or absence of mutations, deletions, duplications and single nucleotide polymorphisms in a cystic fibrosis transmembrane regulator (CFTR) nucleic acid. Oligo nucleotide primers and kits used to amplify regions of a CFTR nucleic acid for high throughput, massively parallel sequencing and methods of determining an individual's cystic fibrosis status are also disclosed.

Abstract: A method for predicting the severity or progression of OA in a human subject, comprising: determining the identity of at least one allele at each of at least 4 positions of single nucleotide polymorphism (SNPs) selected from the group consisting of: rs2206593, rs10465850, rs780094, rs1374281, rs1143634, rs2073508, rs2243250, rs4720262, rs917760, rs7838918, rs12009, rs730720, rs874692, rs893953, rs1799750, rs10845493, rs11054704, rs7986347, rs1802536, rs10519263, rs7342880, rs16947882 and rs10413815, and one or more SNPs in linkage disequilibrium at a level of at least R2?0.8 therewith, as well as products, in particular systems and kits for use in such a method.

Abstract: Aspects and embodiments disclosed herein are directed to providing methods and systems for evaluating target genes and/or associated super enhancers and or super-enhance components. In some embodiments, the method includes selecting a gene associated with a super-enhancer, to provide a selected gene, evaluating the selected gene for contribution to a cell state, e.g., a state characterized by a disease or disorder (a disease/disorder state), and responsive to the evaluation, classifying the selected gene and/or associated super-enhancer.

Abstract: The present invention is based on the discovery of genetic polymorphisms that are associated with liver fibrosis and related pathologies. In particular, the present invention relates to nucleic acid molecules containing the polymorphisms, variant proteins encoded by such nucleic acid molecules, reagents for detecting the polymorphic nucleic acid molecules and proteins, and methods of using the nucleic acid and proteins as well as methods of using reagents for their detection.