Abstract: Processes for the bioconversion of syngas to oxygenated organic compound are disclosed that reliably, cost-effectively and efficiently supply sulfur nutrient to microorganisms contained in acidic, aqueous fermentation menstrua. In the processes of this invention, basic, aqueous solution used to maintain the pH of the aqueous fermentation menstruum is used to remove hydrogen sulfide from the off-gas from the fermentation menstruum for recycle to the fermentation menstruum.

Abstract: An improved process for alcohol production includes microbial fermentation using a genetically modified microorganism to produce substantial quantities of aldehydes that are stripped from the fermentation medium and condensed. So produced aldehydes are converted in an ex vivo process to corresponding alcohols.

Abstract: The invention relates to recombinant host cells having at least one integrated polynucleotide encoding a polypeptide that catalyzes a step in a pyruvate-utilizing biosynthetic pathway, e.g., pyruvate to acetolactate conversion. The invention also relates to methods of increasing the biosynthetic production of isobutanol, 2,3-butanediol, 2-butanol or 2-butanone using such host cells.

Abstract: Cells and cell cultures are provided that have improved tolerance to 3-hydroxypropionic acid (3HP). Genetic modifications to provide a mutated or overexpressed SFA1 gene or other enhancement of 3HP detoxification via a glutathione-dependent dehydrogenase reaction, including medium supplementation with glutathione, may be combined with a 3HP producing metabolic pathway.

Abstract: Bio-based renewable 3-hydroxypropionic acid (3-HP) may be produced through fermentation processes utilizing genetically modified microorganisms such as, for example, genetically modified E. coli strains. The practice of the invention may include cultivating or culturing (meant to be synonymous) cells or genetically modified microorganisms, including in large-scale fermentations.

Abstract: An acyl-ACP thioesterase consisting of an amino acid sequence of the 72nd to 233rdmino acids set forth in SEQ ID NO: 1, an acyl-ACP thioesterase gene encoding the protein, a transformant having the gene, and a method of producing a lipid using the transformant.

Abstract: The disclosure relates to omega-hydroxylated fatty acid derivatives and methods of producing them. Herein, the disclosure encompasses a novel and environmentally friendly production method that provides omega-hydroxylated fatty acid derivatives at high purity and yield. Further encompassed are recombinant microorganisms that produce omega-hydroxylated fatty acid derivatives through selective fermentation.

Abstract: Provided is an aniline-producing transformant constructed by introducing a gene which encodes an enzyme having aminobenzoate decarboxylase activity into a coryneform bacterium as a host. Also provided is a process for producing aniline, which comprises a step of allowing the transformant to react in a reaction mixture containing aminobenzoic acid, an ester thereof, and/or a salt thereof under reducing conditions, and a step of recovering aniline from the reaction mixture.

Abstract: A method for producing an objective substance is provided. An objective substance is produced by culturing a microorganism which has been modified so that the activity of a dicarboxylic acid exporter protein is reduced in a medium, and collecting the objective substance from the medium.

Abstract: PHB-deficient Sphingomonas strains having improved sphingan yield are provided. Certain of the Sphingomonas strains are diutan-producing strains that exhibit a dramatic improvement in productivity and yield due to a combination of certain genetic modifications that affect PHB and sphingan synthesis. Moreover, the sphingans produced from such strains have superior characteristics including improved filterability, clarity, and improved rheology-modifying characteristics. The sphingans provided are, thus, highly desirable in a variety of commercial and industrial uses, including personal care items, cement applications, and oilfield applications.

Abstract: The present disclosure relates to a method for simultaneously degrading lignin and cellulose and for boosting effect on the cellulase activity using a specific catalyst. Since the present disclosure allows for the preparation of sugars by degrading not only lignin but also cellulose and hemicellulose using the enzymes which were previously known only as lignin-degrading biocatalysts, it provides the advantage that the preparation of a hydrolysate as a source material for the production of biofuels or biochemicals from lignocellulosic biomass can be simplified and facilitated. As a result, the present disclosure can reduce enzyme cost and can provide improved production efficiency by simplifying the biofuel production process.

Abstract: The present invention relates to a method for preparing a sialic acid derivative characterized by performing both of a process for preparing CMP-N-acetylneuraminic acid using N-acetyl-D-glucosamine and a process for preparing the sialic acid (neuraminic acid) derivative that combines a sialic acid with a galactose derivative or a lactose derivative, together, in one reactor. According to the method for preparing a sialic acid derivative of the present invention, expensive cytidine 5?-monophosphate (CMP) is capable of being recycled in a reactor, such that an amount of the CMP introduced into the reactor may be reduced, and the sialic acid derivative is capable of being prepared at a significantly high efficiency by using cheap N-acetyl-D-glucosamine, and pyruvate as substrates.

Abstract: The present invention is directed to an innate DNA sequence within the complete genome sequence of Actinoplanes sp. SE50/110 which resembles the structure of an actinomycete integrative and conjugative element (AICE). Related AICEs were used for establishing genetic manipulation tools for other bacteria in the past. In this document, we describe the unique features of the specific AICE found in Actinoplanes sp. SE50/110 which are clearly distinct from any other known AICE as a whole, but share minor parts with varying sequence similarity with other characterized AICEs from other species.

Abstract: The present invention provides methods of amplifying a target nucleic acid utilizing a clamp oligonucleotide comprising a first target-binding region on the 3?-terminus and a second target-binding region on the 5?-terminus and tether region in between. The tether region may comprise a variety of user-defined sequences or elements that allow for further manipulation of the target nucleic acid. Such as, for example, capture followed by amplification, identification and/or sequencing. The target-binding regions bind to the target nucleic acid, the 3?-terminus functions as a primer to initiate extension across the target nucleic acid sequence and ligation of the gap results in formation of a circularized nucleic acid. This circular template can be used in a variety of processes, including amplification and sequencing.

Abstract: The present invention contemplates a method of producing a recombinant protein comprising (a) fermenting a prokaryotic host cell wherein said prokaryotic host cell has been transformed with a nucleic acid encoding said recombinant protein, and (b) harvesting said recombinant protein under conditions where dO2 levels are greater than 0%, and (c) purifying said recombinant protein to a filtered bulk, wherein said filtered bulk does not contain detectable DHNA-recombinant protein adduct, as measured by an IEC assay at 310 nm.

Abstract: Melanin or inorganic fertilizers are produced from fermentation leachates or from low-cost nutrient-rich solutions. The method for producing the melanin or inorganic fertilizer comprises repetitive trophic cycling in the controlled conditions of primary and secondary bioreactors. Nutrients are cycled between microorganisms such as bacteria, yeast and fungi and black soldier fly larvae, Hermetia illucens. Polysaccharides are partly converted into natural melanins or inorganic fertilizer, which are difficult to biodegrade and hence accumulate in the bioreactors. The method can employ, as a source of nutrients, leachates produced from food waste or from sugar-rich liquid waste of the food industry. These leachates can be used raw or can be augmented with low-cost sugar-rich solutions such as molasses, hydrolyzed cellulose or starch. The method is inexpensive and does not require the use of expensive chemically-defined culture media.

Abstract: The present invention relates to methods of recombinantly producing a natively secreted polypeptide, the method comprising the steps of providing a microorganism host cell comprising an exogenous polynucleotide encoding a natively secreted polypeptide without a translationally fused signal peptide; cultivating the microorganism host cell under conditions conducive to the expression of the polypeptide and, optionally, recovering the polypeptide, as well as microorganisms, certain polynucleotides, expression constructs and protease substitution variants.

Abstract: The technology disclosed herein relates to novel methods and compositions for the production processes of algae cell components from algae of the genus Haematococcus. The extractability of algae cellular components is improved and the process is optimized and accelerated by using the enzyme compositions according to the present invention.

Abstract: The present invention relates to a microorganism comprising a gene for coding an enzyme involved in producing retinoid and a method for producing retinoid by using the same, and more specifically, to: a microorganism capable of mass-producing retinoid at a remarkable efficiency by comprising a gene for coding an enzyme involved in producing retinoid; and a method for producing retinoid by using the same.

Abstract: The present application related to the use of endogenous fluorescent biological markers to determine a parameter of a cell in a liquid Because the techniques provided herein provide accurate results in a relatively short amount of time, the methods described herein can be used to monitor and optimize cell culture online as well determine the presence of a cellular contamination in a cell suspension.

Abstract: A selective isolation medium that is not influenced by existence of ESBL-producing bacteria and can clearly detect Campylobacter bacteria. Cefoperazone and Cefoxitin are incorporated into the culture medium for detecting Campylobacter bacteria.

Abstract: The invention mainly relates to the mass spectrometric identification of pathogens in blood cultures from bloodstream infections (septicemia). The invention provides a method with which microbial pathogens can be separated in purified form from blood after a relatively brief cultivation in a blood culture flask, without any interfering human proteins or any residual fractions of blood particles such as erythrocytes and leukocytes, and can be directly identified by mass spectrometric measurement of their protein profiles. The method is based on the use of relatively strong tensides to destroy the blood particles by dissolving the weak cell membranes and most of the internal structures of the blood particles; in spite of the fact that tensides are regarded as strong ionization inhibitors in MALDI and other ionization processes required for mass spectrometric measurements.

Abstract: Methods for determining whether certain compounds, in particular crystals, are present in a sample of a biological fluid that indicates an individual has a particular disease or condition, such as but not limited to gout, pseudogout or urinary tract stones. In some embodiments, the methods include the steps of digestion and filtration of a sample of synovial fluid in order to isolate, if present, monosodium urate monohydrate (MSU), calcium pyrophosphate dihydrate (CPPD), or calcium phosphate crystals from the sample, wherein the filtrate is analyzed with a Raman device to ascertain the presence and type of the crystals. Devices for performing steps of the method are disclosed.

Abstract: The present invention provides a method and apparatus based on a DNA fragment amplified by changing the pH value of a control reaction solution. Specifically, the present invention provides a method for nucleic acid amplification, comprising the following steps: (a) under conditions of pH 10-14 alkalinity, melting of a double-stranded nucleic acid molecule; (b) under conditions of pH 5-8 neutrality and near-neutrality, annealing of the melted nucleic acid molecule and a primer; and in the presence of a nucleic acid polymerase, causing the primer bound to the single-stranded nucleic acid molecule to extend to form an amplified double-stranded nucleic acid molecule.

Abstract: This invention relates to a process for synthesis of a cDNA in a sample, in an enzymatic reaction, whereby the process comprises the steps: simultaneous preparation of a first enzyme with polyadenylation activity, a second enzyme with reverse transcriptase activity, a buffer, at least one ribonucleotide, at least one deoxyribonucleotide, an anchor oligonucleotide; addition of a sample that comprises a ribonucleic acid; and incubation of the agents of the previous steps in one or more temperature steps, which are selected such that the first enzyme and the second enzyme show activity. The invention further relates to a reaction mixture that comprises a first enzyme with polyadenylation activity, a second enzyme with reverse transcriptase activity, optionally a buffer, optionally at least one ribonucleotide, optionally at least one deoxyribonucleotide, and optionally an anchor oligonucleotide. Moreover, the invention relates to a kit that comprises a corresponding reaction mixture.

Abstract: Provided herein is technology relating to isolating nucleic acids. In particular, the technology relates to methods and kits for extracting nucleic acids from problematic samples such as stool.

Abstract: The present invention provides systems, devices, methods, kits, and compositions for nucleic acid analysis using digital PCR. In particular, methods are provided to analyze high titer samples that cannot be divided into a sufficient number of partitions containing zero nucleic acid molecules per partition to allow for Poisson analysis (digital PCR analysis).

Abstract: The present invention provides a method for measuring cellular nascent nucleic acid synthesis by dual pulse labeling of nucleic acid. The first pulse labeling of nucleic acid with a nucleoside analog allows establishment of a baseline nucleic acid synthesis rate. Pulse labeling of the nucleic acid with a second nucleoside analog then allows measurement of any changes to nucleic acid synthesis. The nucleic acid synthesis can be measured as cell proliferation, DNA, or gene expression, RNA. This method does not require a potentially artifact-inducing intermediary wash step between pulse labels. Additionally, this method may be used to screen compounds for their affect on cellular proliferation by treating cells or an organism with the test compound simultaneous to or before treatment with a competitive nucleoside analog.

Abstract: The present invention relates to methods for the diagnosis of bacterial vaginosis based on an analysis of a patient sample. For example, patient test samples are analyzed for the presence or absence of one or more lactobacilli and two or more pathogenic organisms. The presence or absence of one or more lactobacilli and two or more pathogenic organisms may be detected using PCR analysis of nucleic acid segments corresponding to each target organism. The quantity of the target organisms can then be used to determine a score which is indicative of a diagnosis of bacterial vaginosis.

Abstract: Embodiments provide detection systems and methods for detecting the presence of a nucleic acid in one or more samples. In a detection method, a sample and one or more nucleic acid probes are introduced into a channel. A first potential difference is applied across the length of the channel in a first direction, and a first electrical property value is detected. Subsequently, a second potential difference is applied across the length of the channel in a second opposite direction, and a second electrical property value is detected. Presence or absence of a nucleic acid in the channel is determined based on a comparison between the first and second electrical property values.

Abstract: In one embodiment, a multiplex fluid processing cartridge includes a sample well, a deformable fluid chamber, a mixing well with a mixer disposed therein, a lysis chamber including a lysis mixer, an electrowetting grid for microdroplet manipulation, and electrosensor arrays configured to detect analytes of interest. An instrument for processing the cartridge is configured to receive the cartridge and to selectively apply thermal energy, magnetic force, and electrical connections to one or more discrete locations on the cartridge and is further configured to compress the deformable chamber(s) in a specified sequence.

Abstract: The disclosed edge-blocker oligonucleotide based AS-NEPB-PCR method amplifies allele specific DNA (or RNA) while dramatically blocking amplification of wild type (WT) DNA (or RNA). The AS-NEPB-PCR design allows ready modification of an existing PCR reaction setup with an edge-blocker oligonucleotide together with an allele specific primer complementary to the mutant sequence to achieve allele specific amplification. The method simplifies assay optimization procedures and achieved sensitivity sufficient to detect a signal present at 0.1% level with close to 100% specificity, which is useful in detecting SNP or genetic mutations. The method was used to detect three different genetic mutations in cancer, in KRAS, BRAF, and EGFR, with three different types of modified edge-blocker oligonucleotides (phosphate, inverted dT and amino-C7). It was possible to detect one copy of mutant DNA in 1000-copy of normal DNA background of a heterogeneous sample, and was far more sensitive than the other blocking method.

Abstract: A method for carrying out nucleic acid amplification, includes providing a reaction chamber, accommodating an array of nucleic acid probes at respective locations, for hybridizing to respective target nucleic acids; and introducing a solution into the reaction chamber, wherein the solution contains primers, capable of binding to target nucleic acids, nucleotides, nucleic acid extending enzymes and a sample including nucleic acids. The a structure of the nucleic acid probes and of the primers so that a hybridization temperature of the probes is higher than an annealing temperature of the primers, whereby hybridization and annealing take place in respective separate temperature ranges.

Abstract: A method of copying a methylated nucleic acid molecule is provided. The method includes copying a nucleic acid molecule into a plurality of nucleic acid molecules; and contacting the plurality of nucleic acid molecules with a DNA methyltransferase enzyme and an E3 ubiquitin ligase. The method results in the copying of the methylated nucleic acid molecule.

Abstract: The present disclosure provide systems, compositions, methods, reagents, kits and products for extending a nucleic acid that includes incorporating a nucleotide residue at a terminus of a nucleic acid using a polymerase enzyme and at least one nucleotide, wherein the at least one nucleotide includes a thiophosphate moiety, and wherein the at least one nucleotide is resistant to hydrolysis by phosphatase. In some embodiments, the nucleotide incorporation can be conducted in the presence of a phosphatase. In some embodiments, the nucleotide incorporation can be conducted in the presence of at least on chelation moiety that is configured to bind an orthophosphate moiety.

Abstract: Methods and systems for sequencing a biological molecule or polymer, e.g., a nucleic acid, are provided. One or more donor labels, which are attached to a pore or nanopore, may be illuminated or otherwise excited. A polymer having a monomer labeled with one or more acceptor labels, may be translocated through the pore. Either before, after or while the labeled monomer of the polymer passes through, exits or enters the pore, energy may be transferred from the excited donor label to the acceptor label of the monomer. As a result of the energy transfer, the acceptor label emits energy, and the emitted energy is detected in order to identify the labeled monomer of the translocated polymer and to thereby sequence the polymer.

Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.

Abstract: Novel fluorescent nucleotide analogues are provided herein. Also provided herein are methods of using the nucleotide analogues in sequencing-by-synthesis and signal confinement methods.

Abstract: Methods are provided for treating, managing, diagnosing and monitoring myelodysplastic syndrome and other hematologic malignancies. These methods comprise the next generation sequencing analysis conducted on cell-free DNA from peripheral blood plasma or serum.

Abstract: Methods and compositions for digital profiling of nucleic acid sequences present in a sample are provided.

Abstract: System for detection and/or analysis of nucleic acids using nanowires to detect covalent modification of nucleic acids.

Abstract: A device for performing biological sample reactions may include a plurality of flow cells configured to be mounted to a common microscope translation stage, wherein each flow cell is configured to receive at least one sample holder containing biological sample. Each flow cell also may be configured to be selectively placed in an open position for positioning the at least one sample holder into the flow cell and a closed position for reacting biological sample contained in the at least one sample holder. The plurality of flow cells may be configured to be selectively placed in the open position and the closed position independently of each other.

Abstract: The invention relates to the diagnosis of HIV-associated nephropathy (HIVAN) based on determining the expression level of HIV nucleic acids (HIV RNA and/or DNA) in combination with the renal function of a patient. The invention also relates to a method for distinguishing between HIVAN and non-HIVAN kidney disease in a patient based on the expression level of urinary HIV nucleic acids.

Abstract: The present invention provides a method for detecting a target nucleic acid that comprises a step of providing a sample; contacting the sample with a polynucleotide probe comprising a first sequence and a second sequence complementary to the target nucleic acid; and adding a nuclease for cleaving the second sequence of the polynucleotide probe. The present invention further provides a polynucleotide probe for detecting a target nucleic acid that comprises a first sequence and a second sequence complementary to the target nucleic acid. Moreover, the present invention provides a kit for detecting a target nucleic acid.

Abstract: Embodiments of the invention provide a method detecting and treating cancer, such as lung cancer. In some aspects, the method may include detecting cancer in a subject, which may comprise assessing the expression of a marker in a sample from the subject. For example, the marker may comprise Mcl-1. In some embodiments, if the subject is diagnosed as having cancer, the method may further provide administering a therapeutically effective amount of a substance that reduces the expression level of Mcl-1 to the subject and then administering a treatment modality that is known to treat the cancer.

Abstract: The invention described herein relates to novel genes and their encoded proteins, termed Mutants Associated with Resistance to STI-571 (e.g., T315I Bu-Abl), and to diagnostic and therapeutic methods and compositions useful in the management of various cancers that express MARS. The invention further provides methods for identifying molecules that bind to and/or modulate the functional activity of MARS.

Abstract: The disclosure in some aspects provides methods of determining the likelihood that a subject has lung cancer based on the expression of informative-genes. In other aspects, the disclosure provides methods for determining an appropriate diagnostic intervention plan for a subject based on the expression of informative-genes. Related compositions and kits are provided in other aspects of the disclosure.

Abstract: The present invention relates generally to a nucleic acid molecule, the RNA and protein expression profiles of which are indicative of the onset, predisposition to the onset and/or progression of a large intestine neoplasm. More particularly, the present invention is directed to a nucleic acid molecule, the expression profiles of which are indicative of the onset and/or progression of a colorectal neoplasm, such as an adenoma or an adenocarcinoma. The expression profiles of the present invention are useful in a range of applications including, but not limited to, those relating to the diagnosis and/or monitoring of colorectal neoplasms, such as colorectal adenomas and adenocarcinomas. Accordingly, in a related aspect the present invention is directed to a method of screening a subject for the onset, predisposition to the onset and/or progression of a large intestine neoplasm by screening for modulation in the expression profile of said nucleic acid molecule markers.

Abstract: Disclosed herein are assays and methods for distinguishing a keratoacanthoma from squamous cell carcinoma. Methods for diagnosing a keratoacanthoma are also provided. Methods for treating variants of seborrheic keratoses (i.e., keratoacanthoma, acanthosis nigricans, or epidermal nevus) are also provided.

Abstract: The instant invention relates to methods for the treatment of B-cell lymphomas and leukemia by administering a SYK inhibitor. In another embodiment, the invention relates to a method for treating a patient diagnosed with a B-cell lymphoma or leukemia, comprising administering a SYK inhibitor, wherein the B-cells of said patient to be treated are characterized by elevated expression levels of CD86.