Abstract: Provided herein are novel materials and methods for site-specific incorporation of phosphotyrosines into proteins. The novel methods of the invention encompass the use of a novel aminoacyl tRNA synthetase capable of charging compatible tRNAs with a phosphotyrosine precursor. The phosphotyrosine precursor is then incorporated, site-specifically, into a protein at sites where phosphotyrosine residues are desired. The phosphotyrosine precursors are subsequently treated to convert them into phosphotyrosine residues, yielding proteins with phosphotyrosines at selected sites. The scope of the invention encompasses novel aminoacyl tRNA synthetases, novel phosphotyrosine precursors, and methods of using these materials to create site-specific phosphorylated tyrosine residues in a protein.

Abstract: The present invention relates to chimeric (preferably, bifunctional) compounds, compositions comprising those compounds and methods of treating cancer in a patient or subject, especially including metastatic cancer where cancer cells exhibit overexpression (heightened expression) of cell surface urokinase-type plasminogen activator receptor (urokinase receptor) compared to normal (non-cancerous) cells. The compounds preferably covalently bind to the urokinase receptor and recruit native antibodies of the patient or subject where the antibodies can selectively degrade and/or deactivate targeted cancer cells through antibody-dependent cellular phagocytosis and/or antibody-dependent cellular cytotoxicity (ADCC) against a large number and variety of cancers, thus providing cancer cell death and/or an inhibition of growth, elaboration and/or metastasis of the cancer, including remission and cure of the patient's cancer.

Abstract: The presently disclosed subject matter relates generally to the delivery of electrical stimuli via cell-penetrating nanoelectrodes. Such electrical stimuli leads to differentiation of cells, including but not limited to adipose derived stem cells, to neural lineage, specifically to neural cells.

Abstract: Articles of manufacture, including an apparatus for acoustic wave based agglomeration, are provided. The apparatus may include a well and an acoustic wave device. The well may be configured to hold a suspension that includes a plurality of particles. The acoustic wave device may be configured to generate a plurality of acoustic waves. The plurality of acoustic waves inducing acoustic streaming within the suspension. The acoustic streaming agitating the suspension to form an agglomerate comprising at least a portion of the plurality of particles. Methods for acoustic wave based agglomeration are also provided.

Abstract: A device for electrically stimulating living cells and promoting biological cell growth and differentiation is hereby disclosed, said device being based on the generation of an electrical field due to a piezoelectric effect yielded by a nanostructure made from a piezoelectric material. When a cell contacts the nanostructure, the nanostructure suffers a mechanical stress which in turn produces an electrical field that locally stimulates the cell membrane. This in-situ electrical stimulation allows the activation of voltage-dependent ionic channels present in the membrane of electroconductive cells. It allows the control of key cellular messengers, such as calcium ions, that can lead to the stimulation of neural circuits in neurons, provoking motion in muscle cells or promoting cell growth and differentiation.

Abstract: In accordance with the present disclosure, exposure of a sample to one or more electric pulses via capacitive coupling is described. In certain embodiments, the sample may be a biological sample to be treated or modified using the pulsed electric fields. In certain embodiments, the electric pulses may be delivered to a load using capacitive coupling. In other embodiments, the electric pulses may be bipolar pulses.

Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered RNA-targeting systems comprising a novel RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.

Abstract: The present invention includes compositions and methods for promoting scarless genome editing in a cell. In one aspect, methods of the invention utilize the CRISPR/Cas9 system to introduce a cut site into a genomic location to be edited. In another aspect, methods of the invention integrate an edited sequence into that genomic location in a scarless manner.

Abstract: The invention relates to methods for performing in vitro site-directed mutagenesis of a targeted gene or genes. In another aspect, the invention includes in vitro site-directed mutagenesis kits comprising a ribonucleotide particle (RNP), an oligonucleotide, a buffer, a cell-free extract, and instructional material for use thereof.

Abstract: Methods and apparatuses to non-destructively and periodically sample a small quantity of intracellular proteins and mRNA from the same single cell or cells for an extended period of time. Specifically, describe herein are non-perturbative methods for time-resolved, longitudinal extraction and quantitative measurement of intracellular proteins and nucleic acids from a variety of cell types using systems including nanostraws.

Abstract: A method for separating a target allele from a mixture of nucleic acids by (a) providing a mixture of nucleic acids in fluidic contact with a stabilized ternary complex that is attached to a solid support, wherein the stabilized ternary complex includes a polymerase, primed nucleic acid template, and next correct nucleotide, wherein the template has a target allele, wherein the next correct nucleotide is a cognate nucleotide for the target allele, and wherein the stabilized ternary complex is attached to the solid support via a linkage between the polymerase and the solid support or via a linkage between the next correct nucleotide and the solid support; and (b) separating the solid support from the mixture of nucleic acids, thereby separating the target allele from the mixture of nucleic acids.

Abstract: Disclosed herein are engineered nucleases and nuclease systems, including chimeric nucleases and chimeric nuclease systems. Engineered and chimeric nucleases disclosed herein include nucleic acid guided nucleases. Additionally disclosed herein are methods of generating engineered nucleases and methods of using the same.

Abstract: This application provides a system and related methods that determine residue sequences for engineered proteins that facilitate genome engineering, including transcription activator-like effector nucleases. The system may receive an input DNA sequence for a region of a given genome and desired cleavage positions within the region. The system may determine candidate residue sequences for proteins that bind to the region and cleave the region at the desired cleavage positions, such as transcription activator-like effector nucleases (TALENs). The determination may be based on how the proteins may interact with the region and perform other biological functions. A selection can be made from the candidate residue sequences to achieve high accuracy and efficiency in the genome engineering tasks. The system may thus allow development of proteins that incorporate the selected residue sequences to perform the genome engineering tasks.

Abstract: This invention is in the field of molecular biology, gene expression, functional genomics, and bioinformatics and relates to novel RNA and related structures and methods of use thereof that enables modulation of gene expression and preservation of particular transcriptome targets. The invention contemplates various applications of RNA sequences derived from the genomic RNA of flaviviruses (FVs) and the application of such features in combination with heterologous sequences.

Abstract: The present disclosure provides oligomeric compounds comprising at least one ?-?-constrained nucleic acid as provided herein. More particularly, the ?-?-constrained nucleic acid provided herein comprise an optionally modified nucleoside with a phosphorus containing constrained internucleoside linkage such as for example a cyclic phosphate internucleoside linkage. The ?-?-constrained nucleic acid provided herein are expected to be useful for enhancing one or more properties of oligomeric compounds they are incorporated into such as for example nuclease resistance. In certain embodiments, the oligomeric compounds provided herein hybridize to a portion of a target RNA resulting in loss of normal function of the target RNA.

Abstract: The present invention provides oligonucleotide inhibitors of miR-155 and compositions thereof. The invention further provides methods for treating cancer such as a T cell lymphoma in a subject by administering to the subject an oligonucleotide inhibitor of miR-155. The invention also provides methods for reducing or inhibiting the proliferation of malignant T cells by administering an oligonucleotide inhibitor of miR-155.

Abstract: The present embodiments provide methods, compounds, and compositions useful for inhibiting APOL1 expression, which may be useful for treating, preventing, or ameliorating a disease associated with APOL1.

Abstract: Improved compositions and methods for treating muscular dystrophy by administering antisense molecules capable of binding to a selected target site in the human dystrophin gene to induce exon skipping are described.

Abstract: Methods and compositions are provided for oligonucleotides that bind targets of interest. The targets include cells and microvesicles, such as those derived from various diseases. The oligonucleotides can be used for diagnostic and therapeutic purposes. The target of the oligonucleotides can be a member of a ribonucleoprotein or spliceosomal complex such heterologous nuclear ribonucleoprotein U (hnRNP U).

Abstract: RNA interference (RNAi) triggers for inhibiting the expression of Factor XII (F12) gene through the mechanism of RNA interference are described. Pharmaceutical compositions comprising one or more F12 RNAi triggers together with one or more excipients capable of delivering the RNAi trigger(s) to a liver cell in vivo are also described. Delivery of the F12 RNAi trigger(s) to liver cells in vivo provides for inhibition of F12 gene expression and treatment of angioedema, including hereditary angioedema (HAE) and venous thromboembolism (VTE), and diseases associated with angioedema.

Abstract: A method of achieving sustainable, general-purpose cognitive enhancement in mentally-healthy adults comprising administering a gene-editing endonuclease complexed with a gene-expression inhibiting nucleotide and a synthetic guide RNA to lower the population of 5-hydroxytryptamine 2A receptors in the brain.

Abstract: The present invention relates to compositions and methods for preparing splice variants of TNFalpha receptor (TNFR) in vivo or in vitro, and the resulting TNFR protein variants. Such variants may be prepared by controlling the splicing of pre-mRNA molecules and regulating protein expression with splice switching oligonucleotides or splice switching oligomers (SSOs) The preferred SSOs according to the invention target exon 7 or 8 of TNFR1 (TNFRSF1A) or TNFR2 (TNFRSF1A) pre-MRNA, typically resulting in the production of TNFR variants which comprise a deletion in part or the entire exon 7 or 8 respectfully. SSOs targeting exon 7 are found to result in a soluble form of the TNFR, which has therapeutic benefit for treatment of inflammatory diseases. The SSO's are characterised in that they are substantially incapable or incapable of recruiting RNaseH.

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 concerns a genetically modified microorganism expressing a functional type I or II RuBisCO enzyme and a functional phosphoribulokinase (PRK), and in which the non-oxidative branch of the pentose phosphate pathway is at least partially inhibited, said microorganism being genetically modified so as to produce an exogenous molecule and/or to overproduce an endogenous molecule. The invention also concerns the use of such a genetically modified microorganism for the production or overproduction of a molecule of interest and processes for the synthesis or bioconversion of molecules of interest.

Abstract: Provided are a fusion protein comprising an antibody binding area and an endocytic functional area, the encoding nucleic acid of the protein, an expression vector of same, a host cell thereof, and an immune effector cell expressing the fusion protein or the endocytic functional area or further expressing a chimeric antigen receptors. Also provided are an immunoconjugate comprising a cell-killing part and an antibody conjugate in a specifically-binding immune effector cell or an antibody of the endocytic functional area, a reagent kit and uses of the immunoconjugate, and a method for specifically removing, selecting, or enriching and detecting the immune effector cell.

Abstract: Nucleic acid molecules comprising a coding sequence with at least one codon substituted to a synonymous codon, a modified form of a virus comprising the nucleic acid molecules of the invention, and methods for producing these nucleic acid molecules, and viruses, are provided.

Abstract: The present invention provides a method for efficiently preparing a mutant filamentous fungus. The present invention also provides a method for producing a mutant filamentous fungus, comprising transferring a programmable DNA nuclease and single-stranded DNA to a host filamentous fungus, and substituting an upstream region and a downstream region of a cleavage site for the programmable DNA nuclease in genomic DNA of the host by the single-stranded DNA through homologous recombination.

Abstract: Materials and methods for changing expression of a gene product in a plant are provided, and in an embodiment for creating herbicide tolerant plants are described herein. The methods provide for inserting into a plant genome, at a different locus than an endogenous gene, a genomic or coding sequence of the gene, which may be modified, into a genetic location that is different from the endogenous gene and where there is a desired transcriptional activity. The methods described herein can include the targeted insertion of an endogenous 5-enolpyruvylshikimate-3-phosphate synthase gene into a genomic locus that enables sufficient expression to confer herbicide tolerance.

Abstract: A combination of virus vectors for genome editing is formed by arranging a polynucleotide encoding a split genome editing enzyme in each of a Tobamovirus vector and a Potexvirus vector and arranging a polynucleotide encoding a guide RNA in one of the vectors. It is found that when these virus vectors are introduced into a plant cell, a complex of a functional Cas9 protein and the guide RNA is formed in the plant cell, and a genome is edited in a target site-specific manner.

Abstract: Disclosed are double stranded RNA molecules that are toxic to coleopteran insects. In particular, dsRNA molecules that capable of interfering with pest IAP genes and that are toxic to the target pest are provided. Further, methods of making and using the interfering RNA, for example in transgenic plants to confer protection from insect damage are disclosed.

Abstract: The present disclosure provides genetic constructs containing a promoter that is useful in driving fruit-specific expression in plants. Further provided are expression vectors, transgenic plants and plant parts containing such genetic constructs, as well as uses thereof.

Abstract: A polynucleotide having at least 80% sequence identity with the full-length nucleotide sequence of SEQ ID NO: 1 and substantially identical polynucleotides; an isolated polypeptide having at least 80% sequence identity with the full-length amino acid sequence of SEQ ID NO: 2 and substantially identical polypeptides; and polynucleotides encoding the HaWRKY76 polypeptide and substantially identical polypeptides are described. Also described are vectors and recombinant expression cassettes containing the cDNA polynucleotide, a polynucleotide encoding the HaWRKY76 polypeptide, or substantially identical polynucleotides. Transgenic plants containing such expression cassettes, related methods and uses are also provided.

Abstract: The present invention relates to a method of increasing resistance against fungal pathogens of the family Phacosporaceae plants and/or plant cells. This is achieved for instance by increasing the expression of a hydrophobin protein or fragment thereof in a plant, plant part and/or plant cell in comparison to wild type plants, wild type plant parts and/or wild type plant cells. In the transgenic plants hydrophobin can be expressed as a fusion protein to facilitate and/or enhance expression. Furthermore, the hydrophobin protein can be expressed including a secretion signal sequence which mediates secretion of the protein into the apoplast and/or into the cuticule.

Abstract: Compositions and methods and for enhancing the resistance of plants to a plant disease caused by a Phytophthora species are provided. The compositions comprise nucleic acid molecules encoding resistance (R) gene products and variants thereof and plants, seeds, and plant cells comprising such nucleic acid molecules. The methods for enhancing the resistance of a plant to a plant disease caused by a Phytophthora species comprise introducing a nucleic acid molecule encoding an R gene product into a plant cell. Additionally provided are methods for using the plants in agriculture to limit plant disease.

Abstract: Hypersensitive PYR/PYL receptor polypeptides comprising an amino acid substitution in a type 2 protein phosphatase (PP2C) binding interface are provided. Compositions and plants comprising the hypersensitive PYR/PYL receptor polypeptides and methods of producing plants comprising a hypersensitive PYR/PYL receptor polypeptide are also provided.

Abstract: This disclosure provides replication-incompetent adenoviral vectors useful in vaccine development and gene therapy. The disclosed vectors comprise a selective deletion of E3 and are particularly useful for preparation of vaccines development and for gene therapy using toxic transgene products that result in vector instability that occurs when the entire E3 domain is deleted.

Abstract: Disclosed herein are nucleic acid-guided nucleases, guide nucleic acids, and targetable nuclease systems, and methods of use. Disclosed herein are engineered non-naturally occurring nucleic acid-guided nucleases, guide nucleic acids, and targetable nuclease systems, and methods of use. Targetable nuclease systems can be used to edit genetic targets, including recursive genetic engineering and trackable genetic engineering methods.

Abstract: A polynucleotide encoding a ThermoCas9 protein from Geobacillus thermodenitrificans and a constitutive promoter are used to engineer eukaryotic cells, e.g. fungi, yeast or algae, so that the ThermoCas9 endonuclease is integrated and expressed from the genome of the cell. Then, a second expression plasmid is used to transfect these ThermoCas9 expressing cells, the second plasmid containing an inducible promoter and a polynucleotide encoding a guide RNA. The guide RNA combines with the ThermoCas9 to provide the targeted endonuclease activity to cleave the cell DNA at a desired locus or gene of interest. A repair-oligo is also provided to the cell whereby following DNA cleavage, homologous recombination takes place in the cell with the repair-oligo so that either a deletion or substitution of nucleotides in the locus or gene of interest is achieved. Expression vectors and methods of using the vectors to achieve ThermoCas9 mediated gene editing are described whereby higher temperatures, e.g. greater than 30° C.

Abstract: The present invention relates to the field of fungal production fatty alcohols. More specifically, the present invention relates to genetically modified host cells, nucleic acid constructs and culture medium for the production of fatty alcohols in Rhodosporidium.

Abstract: The invention relates to an integrated process for alcohol production and organic acid production from lignocellulosic material.

Abstract: Various embodiments include a method for producing hydrocarbons, the method comprising: producing carbon monoxide and carbon dioxide with addition of oxygen in a first reaction unit; fermenting the carbon monoxide, the carbon dioxide, and hydrogen in a second reaction unit; adding biogas provided from a biogas system and oxygen from an electrolyzer as reactants to the first reaction unit; and adding hydrogen from the electrolyzer as a reactant to the second reaction unit.

Abstract: A low-cost process is provided to render lignocellulosic biomass accessible to cellulase enzymes, to produce fermentable sugars. Some variations provide a process to produce ethanol from lignocellulosic biomass (such as sugarcane bagasse or corn stover), comprising introducing a lignocellulosic biomass feedstock to a single-stage digestor; exposing the feedstock to a reaction solution comprising steam or liquid hot water within the digestor, to solubilize the hemicellulose in a liquid phase and to provide a cellulose-rich solid phase; refining the cellulose-rich solid phase, together with the liquid phase, in a mechanical refiner, thereby providing a mixture of refined cellulose-rich solids and the liquid phase; enzymatically hydrolyzing the mixture in a hydrolysis reactor with cellulase enzymes, to generate fermentable sugars; and fermenting the fermentable sugars to produce ethanol. Many alternative process configurations are described.

Abstract: The present disclosure discloses a production method of Danshensu, belonging to the technical field of bioengineering. The present disclosure constructs a novel genetic engineering strain co-expressed by three enzymes, which can be applied to the production of optically pure 3-(3,4-dihydroxyphenyl)-2-hydroxypropionic acid. All of the (D/L)-?-hydroxycarboxylic acid dehydrogenase selected by the present disclosure have the characteristics of poor substrate specificity and strong optical specificity, and can produce optically pure D-danshensu and L-danshensu. Further, the production efficiency of the recombinant strain is improved by knocking out or enhancing the expression of a related gene on the E. coli genome to promote substrate transport and reduce product decomposition.

Abstract: According to one broad aspect of this disclosure, a method is provided for producing polyhydroxyalkanoates (PHA) from organic waste. The method comprises homogenizing organic waste to obtain a feedstock that has about 0.01% to about 99.99% (w/w) dry mass solids. The feedstock is inoculated with an inoculum of acidogenic fermentative bacteria in order to obtain an inoculated feedstock. The inoculated feedstock is incubated for at least 1 day to obtain a fermentation broth. The fermentation broth comprises volatile fatty acids (VFAs) and undigested organic waste. The fermentation broth is filtered with a filter with a pore size ranging from 0.2 ?m to 500,000 NMWC to remove the acidogenic fermentative bacteria and undigested organic waste, to obtain a clarified broth comprising concentrated VFAs. The clarified broth and high-PHA producing bacteria are incubated to produce intracellular PHA granules in the high-PHA producing bacteria. PHA polymers are extracted from the intracellular PHA granules.

Abstract: Compositions and methods for producing aldehydes, alkanes, and alkenes are described herein. The aldehydes, alkanes, and alkenes can be used in biofuels.

Abstract: Genes encoding mutant 3-ketoacyl-CoA synthases are introduced into host cells. Certain of the mutants enhance the production of shorter-chain fatty acids and derivatives by the cell than do the wild-type (unmutated) enzymes. In other cases, the chain length is not significantly affected, but productivity is enhanced. In specific cases, both a shift toward lower chain length and higher productivity is seen. Cells producing the mutant 3-ketoacyl-CoA synthases are especially suitable for producing C6-C10 fatty acids and derivatives.

Abstract: Methylopila sp. and use thereof in the selective resolution preparation of (S)-?-ethyl-2-oxo-1-pyrrolidineacetate. Methylopila sp. that produces enzymes is subjected to cell immobilization, and is then applied to the biological resolution of a racemate (R,S)-?-ethyl-2-oxo-1-pyrrolidineacetic acid ethyl ester to prepare high optically pure (S)-?-ethyl-2-oxo-1-pyrrolidineacetic acid ethyl ester, which is further subjected to a hydrolysis reaction to obtain (S)-?-ethyl-2-oxo-1-pyrrolidineacetate. The present invention achieves a high conversion yield up to 50.0% or more, a good stereoselectivity, and an enantiomeric excess value e.e.s(%) of (S)-?-ethyl-2-oxo-1-pyrrolidineacetic acid ethyl ester not less than 99.5; the catalytic efficiency is high; the concentration of the racemic substrate in the resolution reaction is up to 500 g/L, the reaction time does not exceed 15 h, the number of reuse times of the immobilized cells is not lower than 35.

Abstract: The present invention relates to enzyme compositions comprising a polypeptide having cellobiohydrolase II activity, a polypeptide having xylanase activity, and one or more cellulolytic proteins and their use in the degradation or conversion of cellulosic material.

Abstract: An enzymatic method of making a polynucleotide is provided. The method includes combining a selected nucleotide triphosphate, one or more cations, a template-independent polymerase, and an associated processivity factor in an aqueous reaction medium including a target substrate comprising an initiator sequence and having a 3? terminal nucleotide attached to a single stranded portion, such that the template-independent polymerase and the associated processivity factor interact with the target substrate under conditions which covalently add one or more of the selected nucleotide triphosphate to the 3? terminal nucleotide. Also provided are mutant template-independent polymerases having a processivity factor attached thereto.

Abstract: The current invention reports a promoter that has the nucleic acid sequence of SEQ ID NO: 02 or SEQ ID NO: 03 which is a human CMV major immediate-early (hCMV-MIE) promoter/enhancer with C to G point mutation at position ?41 and/or ?179 relative to the transcription start site. This new promoter is especially useful for the production of polypeptides at large scale as it shows reduced promoter silencing and improved polypeptide production.