Abstract: Described herein are methods of identifying host factors that modulate Hepatitis B virus (HBV) replication in mammalian, e.g., human cells, as well as factors identified by those methods, and methods of treating HBV infections by targeting those factors. Zinc finger, CCHC domain containing 14 (ZCCHC14) is an exemplary host factor.

Abstract: The invention provides aptamer-gene modulator conjugates, where the aptamer and the gene modulator are linked together. The invention further provides a method for cell-specific delivery of gene modulators to hard to transfect cells such as CD4+ cell.

Abstract: The invention relates to an oligonucleotide including one or more modified nucleoside bases having the structure -B-L-A wherein for each of the modified nucleosides A is independently a monosaccharide or oligosaccharide, L is a linker molecule, and B is independently a pyrimidine or pyridine base linked to the sugar-phosphate backbone of the oligonucleotide; and wherein the oligonucleotide binds specifically to a carbohydrate-binding monoclonal antibody with an affinity of less than 100 nM. Immunogenic conjugates that include the oligonucleotide, and pharmaceutical compositions that include the oligonucleotide or the immunogenic conjugate are also disclosed. Various method of using the oligonucleotides, immunogenic conjugates, and pharmaceutical compositions are disclosed, including inducing an immune response, inhibiting viral or bacterial infection, treating a cancerous condition, and detecting a neutralizing antibody.

Abstract: The present invention is directed towards an artificial RNA nanostructure comprising multiple external strands of RNA, each external strand comprising about 40-50 nucleotides; one internal strand of RNA comprising more than about 50 nucleotides; the internal strands and external strands assembled to form a triangle nanostructure, a square nanostructure, or a polygon nanostructure and a pRNA three-way junction (3WJ) motif at each vertex of the nanostructure. Such nanostructure can be provided in a composition together with an adjuvant for use in inducing the production of high affinity neutralizing antibodies or inhibitory antibodies, inducing the production of cytokines, inducing an immune response in a subject, or a combination thereof.

Abstract: Methods of pre-methylation of foreign DNA to improve genetic transformation in cyanobacterium. Two Type II methyltransferase-encoding genes, i.e., M (sll0729) and C (slr0214), were cloned from the chromosome of Synechocystis sp. PCC 6803 (hereafter Synechocystis 6803) and expressed in E. coli that harbors the integrative plasmid pBS-SPtK or pJU105. After pre-methylation in E. coli, the integrative plasmids were extracted and used for transformation of Synechocystis 6803. The results showed that expression of slr0214 in the integrative-plasmid-harboring E. coli cells before DNA preparation resulted in orders of magnitude higher efficiency in the following integrative transformation of Synechocystis 6803.

Abstract: The inventive technology relates to systems and methods for enhanced in vivo production, accumulation and modification of cannabinoids. In one embodiment, the invention may include systems and methods for enhanced in vivo biosynthesis of chemically-modified water-soluble cannabinoids in a whole plant, or a cell suspension culture system.

Abstract: The invention provides compositions and methods for manipulating the exchange of water and/or carbon dioxide (CO2) through plant stomata by controlling CO2 sensor genes. The invention provides compositions and methods for enhancing or optimizing biomass accumulation in a plant. The invention provides compositions and methods for 10 opening or closing a stomatal pore on a guard cell in the epidermis of a plant. The invention provides compositions and methods for increasing or decreasing oxygenation efficiency and/or carbon fixation in a guard cell in the epidermis of a plant by manipulating expression of a ribulose-1,5-bisphosphate carboxylase/oxygenase. The invention provides promoters for regulating expression of a nucleic acid in a plant guard cell.

Abstract: The present invention includes a seed, a plant, a protoplast, a hybrid and methods of making the same of a cotton cultivar recombinantly modified overexpresses at least one of AtRAV1, AtRAV2 to confer longer fibers to transgenic cotton plants under drought conditions without an effect on yield.

Abstract: The invention relates to biotechnology and provides novel recombinant DNA molecules and engineered proteins for conferring tolerance to protoporphyrinogen oxidase-inhibitor herbicides. The invention also provides herbicide tolerant transgenic plants, seeds, cells, and plant parts containing the recombinant DNA molecules, as well as methods of using the same.

Abstract: Two small proteins with anti-bacterial activity are generated and called optimized thionin and optimized pro-thionin. Optimized pro-thionin contains a signal sequence for intracellular trafficking of the protein and is cleaved off to yield optimized thionin. Genetically altered plants and their progeny expressing a polynucleotide encoding optimized pro-thionin or optimized thionin resist diseases caused by bacteria.

Abstract: Molecular markers are described for determining the presence or absence of a gene conferring resistance to tomato yellow leaf curl virus from S. chilense (Ty-1) in a host plant. Also described, are methods for producing a host plant comprising a gene conferring resistance to tomato yellow leaf curl virus from S. chilense (Ty-1), including the analysis of the presence or absence of the molecular markers. A plant, and parts thereof, obtained by such a method are also described.

Abstract: The present invention relates to viral transformation method, particularly foamy virus-mediated transformation method. The present invention relates to the transfer of transgene into cells by the safe and efficient transfer of RNA encoding foamy components. The present invention has therefore therapeutic interest, especially in the field of gene therapy.

Abstract: Methods and constructs for RNA-guided targeting of heterologous functional domains such as transcriptional activators to specific genomic loci.

Abstract: The present invention provides a method for fermentative hydrogen production under limited aerobic conditions by utilizing the respiratory interaction between a strictly anaerobic hydrogen producing bacterium, E. harbinense YUAN-3, and a facultative anaerobic bacterium, P. aeruginosa PAO1. The two bacteria are co-cultured to produce hydrogen gas in a culture medium without any anaerobic treatment. Sucrose, lactose or glucose are used as the carbon source for the co-culture which can promote the growth of E. harbinense YUAN-3 and reduce substrate competition between two bacteria. L-cysteine is added to increase the hydrogen yield and the production rate. Using 15 g/L glucose and 5 mmol/L L-cysteine, the invented method achieved the hydrogen production yield of 1.11 mol-hydrogen/mol-glucose.

Abstract: A method produces a chemical product by continuous fermentation including filtering a culture liquid of a microorganism(s) through a separation membrane, retaining unfiltered liquid in, or refluxing unfiltered liquid to, the culture liquid, adding a fermentation feedstock to the culture liquid, and recovering a product in the filtrate, wherein the microorganism(s) is/are a microorganism(s) that undergo(es) catabolite repression, and the fermentation feedstock comprises hexose and pentose.

Abstract: Embodiments of the invention relate generally to processes for the production and processing of polyhydroxyalkanoates (PHA) from carbon sources. In several embodiments, PHAs are produced at high efficiencies from carbon-containing gases or materials.

Abstract: The present disclosure relates to a novel O-acetylhomoserine sulfhydrylase variant, a polynucleotide encoding the same, a vector comprising the polynucleotide, a strain capable of expressing the variant, and a method for producing L-methionine using the variant.

Abstract: The present disclosure relates to a microorganism of the genus Escherichia producing more L-tryptophan by inactivating the activity of phosphatase. Additionally, the present disclosure relates to a method for producing L-tryptophan using the microorganism of the genus Escherichia.

Abstract: The present application relates to reaction mixtures comprising biomass, a solid acid catalyst and cellulolytic enzymes or organisms expressing such enzymes for converting biomass to useful feedstocks and methods of forming products via fermentation using the said reaction mixture.

Abstract: The present invention provides to methods for the production of neuraminic acid or derivatives thereof under alkaline conditions and to the use of neuraminate lyases showing improved characteristics under alkaline conditions in the production of neuraminic acid or its derivatives. More particularly, the present invention employs inter alia a N-acetylneuraminate lyase which has been isolated from the psychrophilic bacterium Aliivibrio salmonicida LFI1238 and has shown to have improved characteristics under alkaline conditions.

Abstract: Methods of in vitro transcription using cyanophage Syn5 RNA polymerase (RNAP) or mutants thereof and transcription conditions are provided.

Abstract: The present invention relates to methods for the enzymatic deacetylation of mannosylerythritol lipids produced by fermentation using lipases. More in particular, the present invention relates to a method for the enzymatic deacetylation of mannosylerythritol lipids using a hydrolyzing enzyme in an organic solvent containing only low amounts of water, preferably, no water. It further provides the use of organic solvents, containing only low amounts of water, more preferably, no water, for the enzymatic deacetylation of mannosylerythritol lipids.

Abstract: A method for engineering and utilizing large DNA vectors to target, via homologous recombination, and modify, in any desirable fashion, endogenous genes and chromosomal loci in eukaryotic cells. These large DNA targeting vectors for eukaryotic cells, termed LTVECs, are derived from fragments of cloned genomic DNA larger than those typically used by other approaches intended to perform homologous targeting in eukaryotic cells. Also provided is a rapid and convenient method of detecting eukaryotic cells in which the LTVEC has correctly targeted and modified the desired endogenous gene(s) or chromosomal locus (loci) as well as the use of these cells to generate organisms bearing the genetic modification.

Abstract: A method for engineering and utilizing large DNA vectors to target, via homologous recombination, and modify, in any desirable fashion, endogenous genes and chromosomal loci in eukaryotic cells. These large DNA targeting vectors for eukaryotic cells, termed LTVECs, are derived from fragments of cloned genomic DNA larger than those typically used by other approaches intended to perform homologous targeting in eukaryotic cells. Also provided is a rapid and convenient method of detecting eukaryotic cells in which the LTVEC has correctly targeted and modified the desired endogenous gene(s) or chromosomal locus (loci) as well as the use of these cells to generate organisms bearing the genetic modification.

Abstract: A method for engineering and utilizing large DNA vectors to target, via homologous recombination, and modify, in any desirable fashion, endogenous genes and chromosomal loci in eukaryotic cells. These large DNA targeting vectors for eukaryotic cells, termed LTVECs, are derived from fragments of cloned genomic DNA larger than those typically used by other approaches intended to perform homologous targeting in eukaryotic cells. Also provided is a rapid and convenient method of detecting eukaryotic cells in which the LTVEC has correctly targeted and modified the desired endogenous gene(s) or chromosomal locus (loci) as well as the use of these cells to generate organisms bearing the genetic modification.

Abstract: A method for engineering and utilizing large DNA vectors to target, via homologous recombination, and modify, in any desirable fashion, endogenous genes and chromosomal loci in eukaryotic cells. These large DNA targeting vectors for eukaryotic cells, termed LTVECs, are derived from fragments of cloned genomic DNA larger than those typically used by other approaches intended to perform homologous targeting in eukaryotic cells. Also provided is a rapid and convenient method of detecting eukaryotic cells in which the LTVEC has correctly targeted and modified the desired endogenous gene(s) or chromosomal locus (loci) as well as the use of these cells to generate organisms bearing the genetic modification.

Abstract: A latent effervescent body comprising a selective agent is disclosed. A method of using the latent effervescent body in a method to selectively enrich a target microorganism is also disclosed. The method comprises providing a sample, a culture medium, and the latent effervescent body. The method further comprises contacting the sample, the culture medium, and the latent effervescent body under conditions to facilitate growth of the target microorganism. The method further comprises releasing the selective agent from the latent effervescent body. Optionally, the method includes detecting a microorganism.

Abstract: An aerosol collection system and method. The system includes a bio-aerosol delivery device configured to supply bioparticles in a gas stream, a moisture exchange device including a partition member coupled to the gas stream and configured to humidify or dehumidify the bioparticles in the gas stream, and an aerosol collection medium downstream from the moisture exchange device and configured to collect the bioparticles. The method includes delivering bioparticles in a gas stream, humidifying or dehumidifying the bioparticles in the gas stream by transport of water across a partition member and into a vapor phase of the gas stream, and collecting the bioparticles by a collection medium.

Abstract: Devices and methods are provided for electrically lysing cells and releasing macromolecules from the cells. A microfluidic device is provided that includes a planar channel having a thickness on a submillimeter scale, and including electrodes on its upper and lower inner surfaces. After filling the channel with a liquid, such that the channel contains cells within the liquid, a series of voltage pulses of alternating polarity are applied between the channel electrodes, where the amplitude of the voltage pulses and a pulsewidth of the voltage pulses are effective for causing irreversible electroporation of the cells. The channel is configured to possess thermal properties such that the application of the voltage produces a rapid temperature rise as a result of Joule heating for releasing the macromolecules from the electroplated cells. The channel may also include an internal filter for capturing and concentrating the cells prior to electrical processing.

Abstract: Systems and methods for detecting a target species using a semiconductor nanosensor are generally described.

Abstract: A disposable cartridge for preparing a nucleic acid sample including a stationary cartridge body and a cylindrical rotor rotationally mounted to the cartridge body. The cartridge body includes: (i) a cylindrical surface defining a fixed port and (ii) a syringe barrel defining a bore in fluid communication with the fixed port. When the disposable cartridge is disposed in combination with an assay system, syringe barrel is configured to receive a moveable plunger, i.e., to stroke the plunger into and out of the barrel. The rotor is seated within a cavity of the cartridge body such that a mating surface thereof slideably engages a cylindrical surface of the cavity. The rotor comprises a plurality of chambers fluidly connecting to a plurality of ports along the mating surface at different radial positions such that at least one of the chambers is fluidly connected to one of the ports by a connecting channel.

Abstract: Disclosed are methods of using d8 square planar metal complexes containing tridentate ?-conjugated ligands and ancillary ligand of N-heterocyclic carbene or di-phosphine ligand to target mismatched DNA. Targeting of mismatched DNA can be revealed by monitoring the differences in emission enhancement of metal complexes toward mismatched DNA and matched DNA; or the gradually heat release from isothermal titration calorimetry (ITC) when complexes bind toward mismatch DNA; or the significant increase in melting temperature of the mismatched DNA after adding complexes.

Abstract: Provided is a method for analyzing the prognosis of cervical cancer according to the human papillomavirus (HPV) DNA integration pattern. The method of analyzing the prognosis of cervical cancer according to the human papillomavirus DNA integration pattern of the present invention enables an observation of the HPV DNA integration pattern with accuracy and convenience via in situ hybridization (ISH) compared to qPCR analysis. Since the prognosis of cervical cancer having the tumors with an episomal pattern and an integrated pattern can be significantly distinguished when the HPV DNA integration patterns are classified by the above method, the survival rate after radiotherapy of cervical cancer, and in particular invasive cervical cancer, can be more accurately analyzed.

Abstract: System, including methods, apparatus, compositions, and kits, for making and using a stabilized emulsion. A method of generating a stabilized emulsion is provided. In the method, an aqueous phase may be provided. The aqueous phase may include an effective concentration of one or more skin-forming proteins. An emulsion may be formed. The emulsion may include droplets of a dispersed phase disposed in a continuous phase, with the aqueous phase being the continuous phase or the dispersed phase. The emulsion may be heated to create an interfacial skin between each droplet and the continuous phase, to transform the droplets into capsules.

Abstract: Disclosed herein are apparatuses and methods for conducting multiple simultaneous micro-volume chemical and biochemical reactions in an array format. In one embodiment, the format comprises an array of microholes in a substrate. Besides serving as an ordered array of sample chambers allowing the performance of multiple parallel reactions, the arrays can be used for reagent storage and transfer, library display, reagent synthesis, assembly of multiple identical reactions, dilution and desalting. Use of the arrays facilitates optical analysis of reactions, and allows optical analysis to be conducted in real time. Included within the invention are kits comprising a microhole apparatus and a reaction component of the method(s) to be carried out in the apparatus.

Abstract: This disclosure relates to the use of one or more proteins (e.g., globular proteins) having a low isoelectric point and/or a limited number (e.g., zero) of modifying groups in nucleic acid polymerization and/or amplification reactions such as polymerase chain reaction (PCR).

Abstract: A reaction mixture including (a) a nucleic acid having a primer hybridized to a template, (b) nucleotide analogs, wherein the nucleotide analogs have a blocking moiety; (c) a polymerase that is capable of forming an extended primer by adding the nucleotide analogs to the primer, and (d) a deblocking agent that is capable of removing the blocking moiety from the extended primer. Also provided is a method of synthesizing a polynucleotide including sequentially adding a plurality of the different nucleotides analogs to the nucleic acid via several reaction cycles in the reaction mixture, wherein each reaction cycle includes (i) the polymerase adding a nucleotide analog to the nucleic acid to form a transient nucleic acid species comprising a blocking moiety, and (ii) the deblocking agent modifying the transient nucleic acid species to remove the blocking moiety.

Abstract: A whole-genome sequencing method, including: 1) extracting a whole-genome DNA and constructing a BAC library; 2) constructing mixing pools; 3) extracting DNA of the mixing pools; 4) performing pair-end sequencing for the DNA from the mixing pools; 5) scanning sequences of each mixing pool to obtain a feature sequence set and a k-mer set of each mixing pool; 6) analyzing a corresponding feature sequence set and a corresponding k-mer set of each clone; 7) constructing clone contigs; 8) dividing the k-mer sets of the clones into small k-mer sets and positioning the small k-mer sets; 9) assembling the NGS sequences to yield sequence contigs; 10) positioning the sequence contigs, connecting the sequence contigs and determining directions thereof; and 11) determining relative positions and directions of the clone contigs, and connecting the sequences of clone contigs as whole stripe of chromosome sequences.

Abstract: Disclosed herein are methods and systems for detection and discrimination of optical signals from a densely packed substrate. These have broad applications for biomolecule detection near or below the diffraction limit of optical systems, including in improving the efficiency and accuracy of polynucleotide sequencing applications.

Abstract: There is provided a sol-gel chip using a porous substrate for entrapping small molecules and a method for screening a small molecule-specific material using the same, and more particularly, a porous substrate sol-gel chip characterized in that a sol-gel composition for entrapping small molecules is spotted on a surface of the porous substrate, a method for manufacturing the porous substrate sol-gel chip for entrapping small molecules, and a method for screening a material specifically binding to the small molecules using the porous substrate sol-gel chip for entrapping small molecules. According to the present invention, the small molecules can be effectively entrapped in the chip and the inflow of aptamers can be maintained as compared with the existing methods and thus aptamers specific to an extensive range of small molecules can be more easily selected.

Abstract: Provided herein are, inter alia, nucleic acids, methods, and kits for detecting unmethylated DNA in body fluid sample of a subject. The disclosure includes compositions, methods, and kits for detecting unmethylation at a CpG site in an insulin gene promoter of a subject.

Abstract: The present invention provides a method of identifying a human subject as having an increased risk of altered effectiveness of beta blocker therapy, comprising detecting in the subject one or more single nucleotide polymorphism associated with increased risk of altered effectiveness of beta blocker therapy.

Abstract: The present invention provides methods for predicting the pattern of locomotion in a horse including the ability of a horse to use different gaits and the ability to trot at a fast speed. The methods comprise determining in a sample of DNA obtained from a horse the presence or absence of at least one genetic marker, wherein said at least one genetic marker is located on horse chromosome 23, said marker being associated with the ability to use different gaits. The invention further provides primers that amplify markers being associated with the ability to use different gaits and hybridization probes to detect markers being associated with the ability to use different gaits and the ability to trot at a fast speed.

Abstract: Patients with ErbB2-overexpressing cancers can be given an ErbB2 targeting agent as a therapeutic regimen but not all patients are responsive. The present invention concerns the diagnostic, prognostic and therapeutic methods and compositions for evaluating potential efficacy of an ErbB2 targeting agent in an ErbB2-overexpressing cancers by evaluating PTEN expression, which is predictive of responsiveness or resistance to ErbB2 targeting agents such as trastuzumab. Low PTEN expression is predictive of a patient who will respond poorly to trastuzumab.

Abstract: This invention provides methods, pharmacodynamics biomarker signatures for multiple signaling pathways in a cell sample such as anagen hair, in response to carboxyamidotriazole orotate (CTO) from a subject. CTO has demonstrated response in several cancers having different genomic mutations in clinical studies. This invention provides a diagnostic and prognostic assay for monitoring response to CTO ranging from ?100 fold to +25 fold differential expression in several transcriptional signatures associated with tumor inhibition including EGFR, MEK, HDAC, RAS, GFS, WNT, HSP90 or non-voltage dependent calcium signaling, while inducing tumor suppressors signatures such as P53 or EGR1 in the anagen hair assay.

Abstract: The present invention is based on the identification of novel biomarkers predictive of response to anti-cancer therapies.

Abstract: A method of predicting an effect of an anti-c-Met antibody and/or selecting a subject for application of an anti-c-Met antibody including measuring a level of the biomarker in a biological sample, is provided.

Abstract: Natural-KilleifT-Cell Lymphoma (NKTCL) susceptibility prediction, diagnosis and therapy. The invention relates to a method for predicting Natural Killer T-cell Lymphoma (NKTCL) susceptibility and/or diagnosing NKTCL in a subject comprising testing for JAK mutations. The invention also relates to a method of screening for candidate agents capable of treating NKTCL using a cell line comprising at least one JAK mutation. The invention includes an NKTCL animal model comprising at least one JAK mutation. The invention also includes JAK inhibitors for treating NKTCL.

Abstract: The invention provides to RAF1 gene fusions, RAF1 fusion proteins, and fragments of those genes and polypeptides. The invention further provides methods of diagnosing and treating diseases or disorders associated with RAF1 fusions, such as conditions mediated by aberrant RAF1 expression or activity, or overexpression of RAF1.

Abstract: CNA biomarkers can include nucleic acid sequences that are present in circulating nucleic acids obtained from circulatory systems of a population known to have cancer, but that are rarely present, if at all, in circulating nucleic acids obtained from circulatory systems of a control population. Information is received describing one or more sequences obtained from circulating nucleic acids in a population known to have cancer. Information is also received describing one or more sequences obtained from circulating nucleic acids in a control population. A cluster analysis within a predetermined portion of a genome uses the one or more sequences in the circulating nucleic acids obtained from the population known to have cancer and the one or more sequences in the circulating nucleic acids obtained from the control population. Information is generated identifying one or more biomarkers for the cancer based on a cluster search within results of the cluster analysis.