Abstract: The present invention relates to a method for transformation of a prokaryote or an eukaryote using aminoclay wherein the method includes mixing aminoclay, foreign nucleic acids, and a prokaryote or an eukaryote, and a composition and a kit for transformation of a prokaryote or an eukaryote containing aminoclay, in which the method for transformation of a prokaryote or an eukaryote using aminoclay according to the present invention has a simple and efficient process not requiring expensive equipments, and thus the method for transformation of a prokaryote or an eukaryote according to the present invention can be usefully employed for development of useful microbial strains that can be used in an industry of renewable energy, a food industry, and also for producing high added-value biomaterials and cosmetic raw materials.

Abstract: Described herein are recombinant polynucleotide-binding polypeptides, recombinant fusion proteins made with the described polynucleotide-binding polypeptides, methods of using the described recombinant polynucleotide-binding polypeptides and recombinant fusion proteins to modify genomic DNA of cells and, in some embodiments, create recombinant cells. Methods are also provided herein for genetically modifying a neuronal stem cell. Methods are also provided for treating a neurological disorder in a subject that include the administration of genetically modified neuronal stem cells produced by the methods disclosed herein.

Abstract: Disclosed herein are engineered cleavage half-domains; fusion polypeptides comprising these engineered cleavage half-domains; polynucleotides encoding the engineered cleavage half-domains and fusion proteins; and cells comprising said polynucleotides and/or fusion proteins. Also described are methods of using these polypeptides and polynucleotides, for example for targeted cleavage of a genomic sequence.

Abstract: New semiconductor nanoparticles and manufacturing technologies, including novel methods, systems, and compositions, are provided herein. Robust, reproducible production of large amounts of semiconductor nanoparticles, such as quantum dots, from bacterial cultures during continuous growth is provided, without a need for extensive post growth processing or modification. The result is a novel semiconductor of nanoparticle dimensions and quality that is suitable for commercial applications in lighting, display, imaging, diagnostics, photovoltaics and hydrogen generation, for example. In one embodiment, bacterial-based synthesis methods for producing nanocrystal semiconductor quantum dots are provided by aqueous, environmentally friendly media and methods.

Abstract: Provided are labdenediol diphosphate synthase polypeptides, sclareol synthase polypeptides, nucleic acid molecules encoding the labdenediol diphosphate synthase polypeptides and sclareol synthase polypeptides, and methods of using the labdenediol diphosphate synthase polypeptides, sclareol synthase polypeptides. Also provided are methods for producing labdenediol diphosphate, sclareol and (?)-ambroxide.

Abstract: Provided herein are soluble engineered polypeptides for oxidizing hydrocarbons, and methods of use, manufacture, and design thereof. In particular, soluble, polypeptides capable of oxidizing methane to methanol (e.g., hydroxylation) are provided.

Abstract: This invention provides a method for the prolonged production of ethanol using a metabolically enhanced cyanobacterium.

Abstract: The present invention provides for novel metabolic pathways to detoxify biomass-derived acetate via metabolic conversion to ethanol, acetone, or isopropanol. More specifically, the invention provides for a recombinant microorganism comprising one or more native and/or heterologous enzymes that function in one or more first engineered metabolic pathways to achieve: (1) conversion of acetate to ethanol; (2) conversion of acetate to acetone; or (3) conversion of acetate to isopropanol; and one or more native and/or heterologous enzymes that function in one or more second engineered metabolic pathways to produce an electron donor used in the conversion of acetate to less inhibitory compounds; wherein the one or more native and/or heterologous enzymes is activated, unregulated, or downregulated.

Abstract: Disclosed herein are enzymes and organisms useful for the dealkylation of products derived from lignin depolymerization, including the conversion of guaiacol or guaethol to catechol or the conversion of anisole to phenol. Methods of converting guaiacol or guaethol to catechol or anisole to phenol using enzymes or organisms expressing the same are also disclosed.

Abstract: The invention provides a process for producing 3-hydroxybutyric acid or a salt thereof, the process comprising culturing one or more halophilic bacteria belonging to the genus Halomonas under specific conditions.

Abstract: The invention relates to a process for producing a fuel, in particular a liquid fuel, or another organic product, from a carbon-based matter feedstock, comprising the following steps: a/ gasification of the carbon-based matter feedstock in a first reactor, termed gasifier (1), b/ downstream of the gasification, fermentation of the synthesis gas produced according to step a/, by means of microorganisms, water and nutrients in a second reactor, termed fermenter (2), c/ recovery, downstream of the fermenter, of the microorganisms and of the water, d/ injection of at least a part of the recovered microorganisms and, where appropriate, of at least a part of the recovered water at the inlet (10) of the gasifier.

Abstract: The present invention provides for the use of oleaginous yeast strains that are capable of converting lignocellulosic hydrolysates to lipids. More specifically, under specific molar carbon to nitrogen ratios of treated biomass hydrolysates, oleaginous yeasts are able to accumulate lipids that are suitable for the manufacture of biofuels and other products of interest. Additionally, some yeast species provided herein produce carotenoids when grown utilizing the disclosed methodologies.

Abstract: There is provided a recombinant bacterium comprising at least one overexpressed acyl-ACP thioesterase gene, and wherein at least one gene from the tricarboxylic acid cycle or glycolysis or both is inactivated. There is also provided a method for producing fatty acids, said method comprising culturing bacteria comprising at least one overexpressed acyl-ACP thioesterase gene in a growth medium in a container having walls; allowing said bacteria to secrete fatty acids; and collecting said fatty acids. Acid supplementation is also shown to increase productivity.

Abstract: The present disclosure relates to a process of production and extra-cellular secretion of lipids from an oleaginous microorganism by using a modified growth medium deficient in nitrogen and iron.

Abstract: The present invention relates to agarooligosaccharide hydrolase and a method for producing 3,6-anhydro-L-galactose and galactose from agarose by using the same. More specifically, the production yield of 3,6-anhydro-L-galactose and galactose from agarose, that is, the saccharification yield, is improved by using ?-agarooligosaccharide hydrolase having an agarotriose hydrolytic activity.

Abstract: The present invention relates to the use of ?-glucan branching enzymes in transglycosylation reactions.

Abstract: Provided herein are mispriming prevention reagents, compositions and kits comprising such reagents and methods of use thereof.

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: This invention concerns microorganisms, to be precise Archaea, which, in case of cultivation at 25° C., indicate unsaturated ether lipids in quantities of at least 10% with reference to the total amount of ether lipids. In a further aspect, this invention is directed towards microorganisms within the Archaea, in particular from those of the class halomebacteria, in particular the order of Halobacteriales, in particular the family Halobacteriaceae, in particular the genus Haloarcula and Haloferax containing lipid compositions. These lipid compositions, in particular liposomes, are characterized by the presence of large quantities of unsaturated ether lipids. In a further aspect, the existing invention concerns a process for the extraction of these unsaturated ether lipids from the designated Archaea.

Abstract: The invention relates to a process for the culturing of cells, preferably E1-immortalized HER cells, more preferably PER.C6 cells in a reactor in suspension in a cell culture medium, wherein the cells produce a biological substance, preferably an antibody, wherein at least one cell culture medium component is fed to the cell culture and wherein the cell culture comprising the cells, the biological substance and cell culture medium is circulated over a separation system and wherein the separation system separates the biological substance from substances having a lower molecular weight than the biological substance and wherein the biological substance is retained in or fed back into the reactor. Preferably part of the substances of lower molecular weight is continuously removed from the cell culture.

Abstract: The present disclosure is directed to expression vectors, comprising a weakened SV40 promoter, and recombinant mammalian cells capable of producing high levels of a polypeptide of interest, methods of generating and using such recombinant mammalian cells.

Abstract: A method for producing an L-amino acid is described, for example, L-phenylalanine and L-histidine, by fermentation using a bacterium of the Enterobacteriaceae family, wherein the bacterium has been modified by attaching a DNA fragment able to be transcribed encoding the peptide represented in SEQ ID NO: 2, or a variant thereof, particularly a portion of the ssrA gene, to the 3?-end of gene encoding for the bacterial enzyme, which influences on the L-amino acid biosynthesis, such as chorismate mutase/prephenate dehydrogenase or phosphoglucose isomerase.

Abstract: The embodiments herein disclose a method of synthesizing protein nanoparticles from waste chicken feathers by enzymatic hydrolysis followed by ultrasonic treatment. The steps for the synthesis of the protein nanoparticles include pretreatment of the chicken feathers. The next step is hydrolyzing the feather fibres enzymatically. Further the effect of the enzyme concentration, hydrolysis time and substrate concentration are analyzed. Also the protein nanoparticles are characterized. The effects of enzyme concentration, hydrolysis time, and substrate concentration on particle mean size are analyzed to optimize the best condition in order to attain the smallest particles by a Box-Behnken Design. It was found that minimum particle size can be obtained by using 5 g/l feather and 3.6% enzyme at hydrolysis time of 243 h. A validation assay confirmed the predictive response value under the optimal conditions.

Abstract: Provided is a flavin adenine dinucleotide-dependent glucose dehydrogenase comprising a polypeptide having an amino acid sequence with 78% or more identity to the amino acid sequence of SEQ ID NO: 3, and having glucose dehydrogenase activity.

Abstract: An apparatus and associated methods of use for a controlled combination of reagents is disclosed. The apparatus includes a vessel 400, a vessel insert 220, and a cap element 200. The vessel 400 has a body portion 410 for receiving a biological sample. The vessel insert 220 receives at least one reagent therein. Preferably, the vessel insert 220 is received in a portion 420 of the vessel 400. The cap element 200 is attached to the vessel 400 to secure the vessel insert 220 in the vessel 400. During use, the vessel insert 220 is adapted to release its contents when the biological sample is introduced into the body portion 410 of the vessel 400 upon application of an intermixing force to the vessel insert 220. A variety of intermixing forces may be applied, depending upon the embodiment of the present invention and its associated methods of use.

Abstract: Liposomal detection devices and methods of making and using such devices are disclosed. Such liposomal detection devices may be used to detect microbes by detecting a byproduct of microbial metabolism, or may be used to detect changes in pH and/or changes in temperature. Liposomal detection devices may include a first liposome encapsulating a first destabilizing compound and a second liposome encapsulating a second destabilizing compound. The first liposome may destabilize in response to the detection of the target compound or change to release the first destabilizing compound which may destabilize the second liposome. A matrix, such as a hydrogel matrix, may encase the first liposome and the second liposome.

Abstract: A lactate dehydrogenase detector, which is used to detect a content of lactate dehydrogenase in a biological sample, comprises a substrate, an electrode assembly, a hydrophobic insulation layer, a cover and a reagent-containing membrane. The electrode assembly is disposed on the substrate and including a working electrode and a reference electrode. The hydrophobic insulation layer is arranged over the substrate and has a notch. The cover hoods the notch and cooperates with the substrate to form a sample channel accommodating the reagent-containing membrane. The reagent-containing membrane is made of materials selected from a group consisting of a lactic acid, nicotinamide adenine dinucleotide (NAD), diaphorase, and potassium ferricyanide. A bioelectrochemical reaction between the reagent-containing membrane and the lactate dehydrogenase induces an electrical signal variation in the electrode assembly, which indicates the content of the lactate dehydrogenase.

Abstract: The present invention relates to compositions and methods for detection and quantification of individual target molecules in biomolecular samples. In particular, the invention relates to coded, labeled probes that are capable of binding to and identifying target molecules based on the probes' label codes. Methods of making and using such probes are also provided. The probes can be used in diagnostic, prognostic, quality control and screening applications.

Abstract: An analysis unit for performing a polymerase chain reaction includes a cover element, a bottom element, at least one fluid channel, at least one pressure channel, and a film. The bottom element has at least one bottom hollow that defines a fluid-accommodating surface and an arrangement of microcavities, and that faces toward the cover element. The fluid channel is formed between the cover element and the bottom element in order to conduct a fluid onto the fluid-accommodating surface. The pressure channel is formed in the cover element in order to conduct a pressure into a region of the fluid-accommodating surface. The film is positioned between the cover element and the bottom element in a region of the bottom hollow, and is configured to deform in response to the pressure conducted through the pressure channel such that the fluid is moved through the fluid-accommodating surface into the arrangement of microcavities.

Abstract: Embodiments provided herein relate to methods and compositions for preparing nucleic acid libraries. Some embodiments include preparing libraries from nucleic acids obtained from degraded samples, such as ancient samples and fixed samples.

Abstract: A porous structure according to the present invention has a polymerase chain reaction (PCT) primer inside pores thereof, and hence, even an inner portion thereof can be used unlike general structures of which only surfaces are used for amplification and detection, thereby maximizing reactivity. In addition, the differentiating of the kinds of primers contained in respective structures leads to detection of several kinds of target nucleic acids at the same and real-time analysis thereof at the same time, and thus is useful for multiplex real-time PCR.

Abstract: A colorimetric-based DNA diagnostic system which includes a detector module, a processor and a memory is provided. The detector module is disposed to record an image of a DNA sample illuminated by a light source. The memory includes computer program code which along with the memory is configured, with the processor, to perform (a) sending a signal to adjust the temperature of the DNA sample to be within an approximate temperature range over which the color of the DNA sample changes, (b) sending a signal to the detector module to capture an image of the DNA sample at defined intervals within the approximate temperature range, (c) processing the captured images to extract color information, and (d) processing the extracted color information to objectively determine a melting temperature within the approximate temperature range at which the color of the DNA sample changes.

Abstract: A detection device includes a PCR processor for conducting a PCR process on a first drop to a fourth drop flowing in a flow channel, a boundary detector for detecting intensities of fluorescence outputted from the first drop to the fourth drop after the PCR process and acquiring boundaries between the first drop to the fourth drop flowing in a flow channel based on the intensities of fluorescence, and a detector for acquiring a number of the second drop and the fourth drop having an intensity of fluorescence greater than or equal to a first threshold based on the intensity of fluorescence and boundaries between the first drop to the fourth drop, and detecting whether or not the objective nucleic acid target includes at least one selected from the group consisting of a first nucleic acid target and a second nucleic acid target based on the number of the second drop and the fourth drop.

Abstract: Methods, compositions and kits for capturing, detecting and quantifying mature small RNAs are provided herein. Embodiments of the methods comprise tailing both the 5? and 3? ends of mature small RNA by ligating a 5? ligation adaptor to the 5? end and polyadenylating the 3? end. Other embodiments comprise reverse transcribing the adaptor ligated, polyadenylated mature small RNA with a universal reverse transcription primer and amplifying the cDNA with universal primers.

Abstract: Aspects of the present disclosure relate to DNA amplification systems, e.g., PCR chips used to hold a testing solution and sample, and systems and methods for testing the sample including thermocycling and detection. The system can include a containment chip capable of holding a sample and reagents for amplifying a nucleic acid in the sample and containing a unique identifier used to choose a nucleic acid amplification protocol. The system can also include a nucleic acid detection component which may contain a light source, a light sensor, a temperature control unit and a processor.

Abstract: Provided herein is technology related to the chemical modification and purification of DNA. Specifically, the technology provides methods for performing a bisulfite conversion reaction on small amounts of single-stranded, fragmented DNA and performing the subsequent desulfonation and purification steps on magnetic beads.

Abstract: Methods for producing a paired tag from a nucleic acid sequence are provided in which the paired tag comprises the 5? end tag and 3? end tag of the nucleic acid sequence. In one embodiment, the nucleic acid sequence comprises two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence distally to the restriction endonuclease recognition sites. In another embodiment, the nucleic acid sequence further comprises restriction endonuclease recognition sites specific for a rare cutting restriction endonuclease. Methods of using paired tags are also provided. In one embodiment, paired tags are used to characterize a nucleic acid sequence. In a particular embodiment, the nucleic acid sequence is a genome. In one embodiment, the characterization of a nucleic acid sequence is karyotyping. Alternatively, in another embodiment, the characterization of a nucleic acid sequence is mapping of the sequence.

Abstract: At least one nucleic acid from a sulphate-reducing bacterium may be extracted from a sample and may be amplified by a PCR amplification method in the presence of at least one primer to form an amplification product. The primer(s) may include a sequence essentially identical to SEQ ID NO:1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, and mixtures thereof. A probe may hybridize with the amplification product from the PCR amplification method where the probe includes a sequence essentially identical to SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, and mixtures thereof.

Abstract: Disclosed herein are methods for detecting a target nucleic acid molecule in a sample. The methods can include contacting a sample with a detectably labeled probe (detection probe) that specifically binds to a first target sequence in the target nucleic acid molecule, a bifunctional oligonucleotide including a portion that specifically binds to a second target sequence in the target nucleic acid molecule and a portion that specifically binds to an anchor, and a surface comprising the anchor. Specifically bound detection probe and bifunctional oligonucleotide are ligated and a reagent that specifically removes substantially all of the target nucleic acid is added. Unligated detection probe is removed and presence of the detectable label is detected. In other embodiments, the ligation and/or removal of target nucleic acid are omitted and the detection probe specifically bound to the target nucleic acid is detected.

Abstract: A buffer composition for hybridization of a target nucleic acid is provided. The nucleic acid can include a nucleotide to be detected with a nucleic acid probe. The probe can contain a nucleotide sequence complementary to the target nucleic acid. The buffer can include a blocking nucleic acid having a nucleotide sequence complementary to a non-target nucleic acid having a nucleotide not to be detected corresponding to the nucleotide to be detected. The buffer composition can suppress non-specific hybridization to the nucleic acid probe even when a non-target nucleic acid is present. The use of the buffer composition can achieve excellent detection efficiency of the target nucleic acid.

Abstract: A nucleic acid ligand “biochip” is disclosed, consisting of a solid support to which one or more specific nucleic acid ligands is attached in a spatially defined manner. Each nucleic acid ligand binds specifically and avidly to a particular target molecule contained within a test mixture, such as a bodily fluid. The target molecules include, but are not limited to, proteins (cellular, viral, bacterial, etc.) hormones, sugars, metabolic byproducts, cofactor, and intermediates, drugs, and toxins. Contacting the test mixture with the biochip leads to the binding of a target molecule to its cognate nucleic acid ligand. The biochip may then be contacted with a reagent(s) that reacts covalently with proteins and not with nucleic acids. Each protein target in the test mixture may then detected by detecting the presence of the reagent at the appropriate address on the biochip.

Abstract: Provided herein are methods and devices for accurate sequencing and detection of epigenetic information from template polynucleotides. Also provided are methods for long-range strand displacement amplification of polynucleotides, microfluidic devices with selectively permeable barriers for multistep processing, and methods for polynucleotide amplification using the microfluidic devices.

Abstract: A portable testing device includes a housing 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 on 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: Methods of detecting or quantifying short RNA or DNA molecules using split cycle amplification are provided.

Abstract: Provided herein are methods, compositions and kits for the generation of bisulfite-converted next generation sequencing (NGS) libraries. The methods, compositions and kits provided herein can be useful, for example, for the production of libraries from genomic DNA that allow for determination of the methylation status across the genome, i.e. the methylome. The methods, compositions and kits provided herein can also be utilized to query methylation status at a particular genomic locus or loci. Moreover, the methods provided herein can be employed for high-throughput sequencing of bisulfite-converted DNA while maintaining the directional (strandedness) information of the original nucleic acid sample.

Abstract: A short tandem repeat (STR) typing method and system are developed for forensic identification of individual cells. Agarose-in-oil droplets are produced with a high frequency using a microfluidic droplet generator. Statistically dilute single cells, along with primer-functionalized microbeads, are randomly compartmentalized in the droplets. Massively parallel single-cell droplet PCR is performed to transfer replicas of desired STR targets from the single-cell genomic DNA onto a coencapsulated microbead. These DNA-conjugated beads are subsequently harvested and reamplified under statistically dilute conditions for conventional capillary electrophoresis STR fragment size analysis. The methods and systems described herein are valuable for the STR analysis of samples containing mixtures of cells/DNA from multiple contributors and for low concentration samples.

Abstract: Disclosed herein are conjugates comprising a biomolecule linked to a label that have biological activity and are useful in a wide variety of biological applications. For example, provided herein are polymerase-nanoparticle conjugates including a polymerase linked to a nanoparticle, wherein the conjugate has polymerase activity. Such conjugates can exhibit reduced aggregation and improved stochiometries wherein the average biomolecule:nanoparticle ratio approaches or equals 1:1. Also disclosed herein are improved methods for preparing such conjugates, and methods and systems for using such conjugates in biological applications such as nucleotide incorporation, primer extension and single molecule sequencing.

Abstract: Disclosed herein are modified polymerase compositions exhibiting altered polymerase activity, which can be useful in a variety of biological applications. Also disclosed herein are methods of making and using such compositions. In some embodiments, the compositions exhibit altered properties that can enhance their utility in a variety of biological applications. Such altered properties, can include, for example, altered nucleotide binding affinities, altered nucleotide incorporation kinetics, altered photostability and/or altered nanoparticle tolerance, as well as a range of other properties as disclosed herein.

Abstract: The present invention relates to molecular microscopy or volumetric imaging by proximal unique molecular identifiers (“UID”) reaction (“VIPUR”) microscopy methods to record the cellular co-localization and/or spatial distributions of arbitrary nucleic acid sequences, or other biomolecules tagged with nucleic sequences. The method involves one or both of two DNA sequence-components such as an ?-UID, which may identify the targeted sequences-of-interest themselves and/or spatial beacons relative to which their distances are measured, and a ??-UID, which labels ?-UID association events.

Abstract: Provided herein are devices, systems, and methods of employing the same for the performance of bioinformatics analysis. The apparatuses and methods of the disclosure are directed in part to large scale graphene FET sensors, arrays, and integrated circuits employing the same for analyte measurements. The present GFET sensors, arrays, and integrated circuits may be fabricated using conventional CMOS processing techniques based on improved GFET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense GFET sensor based arrays. Improved fabrication techniques employing graphene as a reaction layer provide for rapid data acquisition from small sensors to large and dense arrays of sensors. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes, including DNA hybridization and/or sequencing reactions.