Abstract: Disclosed herein is an improved Gene Site Saturation Mutagenesis (GSSM) method for producing a plurality of modified polynucleotides and/or polypeptides, creating specific changes to a gene, and reassembling mutations or changes at one or more sites.

Abstract: The present invention provides a method to quantitatively measure the response of a patient to an immune-modulator drug that will aid clinicians in the determination of the optimal combination/posology of immunosuppressant/immune-modulator drugs. In addition, this method will open the possibility for clinicians to make the necessary adjustments in immunosuppressive therapy, as a way to avoid organ rejection to actually take place. Furthermore, this method will significantly reduce side effects of immunosuppressant drugs, optimizing therapeutic scheme and dosages, enabling the determination of the most effective immunosuppression regimen at the lower dosages for each patient individually and monitoring of treatment efficiency along time, thus opening the door to treatment personalization.

Abstract: A culture device is applicable to measurement of an electrical resistance of cells. The culture device includes a measurement chamber, a permeable layer, an upper working electrode, and a lower working electrode. The measurement chamber is longer in a first direction than in a second direction intersecting the first direction. The permeable layer partitions the measurement chamber into a first chamber on an upper side and a second chamber on a lower side. The permeable layer is permeable to liquid. The upper working electrode is disposed on the upper side with respect to the measurement chamber, and has working electrode portions longer in the first direction than in the second direction. The lower working electrode is disposed on the lower side with respect to the measurement chamber, and has working electrode portions longer in the first direction than in the second direction.

Abstract: Disclosed are methods, systems, cells and compositions directed to modeling a physiologic or pathologic process in an animal using a set of yeast genes analogous to a set of animal genes and augmenting the physiologic or pathologic process in the animal with predicted gene interactions based on the interactions between the set of yeast genes. Also disclosed are methods of screening for and using therapeutics for neurodegenerative proteinopathies.

Abstract: Provided is a method for preparing mesenchymal stem cell-conditioned medium, including isolating mesenchymal stem cells from a subject, maintaining the mesenchymal stem cells in a mesenchymal stem cell maintenance medium, collecting the mesenchymal stem cells at passages 2 to 5, culturing the mesenchymal stem cells in a medium supplemented with fetal bovine serum and mesenchymal stem cell culture adjuvant for hours to obtain a mesenchymal stem cell-conditioned medium, harvesting the medium and centrifuging followed by filtering. Also provided is a method for preventing or treating epithelial tissue disorder of eyes such as dry eye syndrome, including applying the medium to an eye of a subject. Further provided is a medical composition including the medium.

Abstract: The present disclosure provides, among other things, methods and devices for single cells/particle selection and isolation from a sample in a light-curable biomatrix gel. The individual cells or particles are observed by microscopy and manipulated and isolated by accurately controlling the light transmission from a liquid crystal display (LCD) oriented under the sample to provide a detailed image of the sample. In some embodiments, selected cells or particles are then immobilized by curing the biomatrix gel with blue/violet light transmitted from a LED pixel array. In other embodiments, the selected cells or particles of interest are allowed to remain mobile. In either embodiment, the individual cells or particles of interest are segregated from and isolated from the remainder of the sample.

Abstract: The analysis method includes a step of measuring cytometry parameters for each biological cell contained in a biological sample; a step of determining, for each biological cell of the biological sample, a point in a N-dimensional space whose coordinates are defined depending on the cytometry parameters measured for the corresponding biological cell, where N is an integer greater than or equal to 3; a step of automatic clustering of the points into different cell clusters depending on the measured cytometry parameters, so as to define a sample cluster file; and a step of comparing the sample cluster files with reference cluster files, each of the reference cluster files being defined from cytometry parameters of a respective pathological or abnormal biological sample.

Abstract: The present invention relates to a tissue-specific promoter system for expressing microRNA (miRNA) for RNA interference-based methods of gene therapy. In these systems, the miRNA will inhibit gene expression or replace natural miRNA expression using microRNA.

Abstract: Polynucleotides comprising genetic regulatory elements, as well as constructs, host cells, and transgenic organisms comprising the same are described. The polynucleotides can control the expression of an operably linked gene in a host cell or organism, such as a plant cell or a plant. Methods of using the polynucleotide to control the expression of an operably linked gene of interest in a plant or plant cell are further provided.

Abstract: A guide RNA comprising: a gRNA spacer sequence at the 5? end of the guide RNA, wherein the spacer sequence is complementary to a target gene, a scaffold sequence that binds to Cas9, and an RNA capture and sequencing domain comprising: a barcode sequence, and a primer binding sequence; nucleic acids and vectors encoding the guide RNA; cells expressing the guide RNA; and a library comprising a plurality of guide RNAs. Also disclosed are methods of introducing a genetic perturbation into a cell, methods of assessing an effect of at least one genetic perturbation on RNA expression in a cell, methods of identifying nucleic acid sequences associated with a disease state and a method of identifying candidate therapeutic agents.

Abstract: The authors of the present invention designed a new fluorescent fusion polypeptide comprising a membrane localization peptide, a peptide capable of binding G-protein or tyrosine receptors following phosphorylation of these receptors by GRKs or RTKs, a vesicularization peptide and a fluorescent peptide. This biosensor is formed by two peptides targeted to two different cellular compartments, allowing the detection of the translocation of GRKs (G-protein receptor kinases) and/or beta-arrestin or Receptor tyrosine kinases (RTKs) from the cell cytoplasm to the cell cytoplasmic membrane in vivo by monitoring the distribution of the fluorescent polypeptide within the cellular cytoplasm.

Abstract: Provided are vesicles derived from bacteria belonging to the genus Proteus and a use thereof. The inventors of the present invention experimentally confirmed that the vesicles was significantly reduced in samples of patients with cancers, allergic-respiratory diseases, cardiovascular diseases, metabolic diseases, or neuropsychiatric diseases, as compared to that of normal people, and the vesicles inhibited the secretion of inflammatory mediators due to pathogenic vesicles and also exhibited anticancer efficacy. Therefore, it is anticipated that the vesicles derived from bacteria belonging to the genus Proteus, according to the present invention, may be usefully used for the development of a method of diagnosing cancer, cardiovascular diseases, metabolic diseases, neuropsychiatric diseases, allergic-respiratory diseases, and inflammatory bowel diseases, and a composition for prevention, treatment, and/or alleviation.

Abstract: A system for determining the viability of an embryo comprises an imaging device, an excitation device configured to direct an excitation energy at an embryo, a controller communicatively connected to the imaging device and the excitation device, configured to drive the excitation device and collect images from the imaging device at an imaging frequency, a processor performing steps comprising acquiring a set of images from the imaging device, performing a Fourier Transformation to generate a set of phasor coordinates, computing a D-trajectory, computing a set of values of additional parameters, comparing the set of values to a set of stored values related to embryos of known viability, and calculating a viability index factor of the embryo from the set of values and the set of stored values. Methods of calculating embryo viability and determining one or more properties of a tissue are also described.

Abstract: Disclosed herein are microfluidic systems with recirculation of fluid and computer-implemented methods of calculating conditions within the microfluidic systems. The microfluidic systems include a computing device and a microfluidic device having first and second reservoirs, at least one chamber, and a fluid path connecting the first reservoir, the chamber, and the second reservoir. The methods for calculating conditions include receiving a first reservoir fluid volume, a second reservoir fluid volume, a first concentration, and a second concentration. The methods further include receiving a time-dependent imposed pressure difference between the first reservoir and the second reservoir, then determining a hydraulic pressure difference and an effective pressure difference. The effective pressure difference is used to account for reactions occurring within the microfluidic device and to determine the value of the condition within the microfluidic device.

Abstract: The present invention relates to a method for determining or predicting the response of a patient diagnosed with non-small-cell lung carcinoma to targeted pharmacotherapy. The present invention also aims to provide methods and devices for predicting the response of patients diagnosed with non-small-cell lung carcinoma to specific medicaments. More specifically, the present invention provides methods which measure kinase-activity by studying phosphorylation levels and profiles and inhibitions thereof by drugs in blood samples of said patients.

Abstract: The present invention relates to a synthetic promoter capable of controlling the expression of a target gene at various locations in the genome of an acid-resistant strain, and more particularly to a synthetic promoter including a core promoter derived from an acid-resistant strain and an upstream activating sequence (UAS) element serving as an enhancer. When the present invention is applied to a variety of genetic and metabolic engineering techniques for acid-resistant yeast, various metabolic networks can be configured as desired while controlling the expression level of the target gene, so a method of producing various metabolites using acid-resistant yeast is provided, and the cost of producing the metabolites can be greatly reduced depending on the properties of the acid-resistant yeast.

Abstract: Described are three-dimensional, engineered, biological breast tissues, adipose tissues, and tumor models, including breast cancer models.

Abstract: Methods and systems for determining a dose of an analyte in an unknown sample on an instrument, such as a nucleic acid analyzer, immunoassay analyzer, or clinical chemistry analyzer using a reagent from a selected assay lot are described. The methods and systems use core dose-response information based on measurements of response values to a set of calibrators on a plurality of other instruments and assay lot-specific response information to calibrate the instrument.

Abstract: A honeycomb tube with a planar frame defining a fluidic path between a first planar surface and a second planar surface. A fluidic interface is located at one end of the planar frame. The fluidic interface has a fluidic inlet and fluidic outlet. The fluidic path further includes a well chamber having an well-substrate with a plurality of wells. The well chamber is arranged in the planar frame between the first or second surface and the well-substrate.

Abstract: A functional engineered guide RNA sequence is provided including a spacer sequence and a scaffold sequence, wherein the scaffold sequence includes a primer binding site for reverse transcription.

Abstract: The invention relates to a method for the determination and visualization of the spatial distribution of tissue states of a tissue sample, wherein a mass/mobility map is acquired at each of a plurality of sample sites of the tissue sample, the signal heights at each sample site are determined at characteristic signal positions in the corresponding mass/mobility map, from which a tissue state for each sample site is calculated with the aid of a mathematical/statistical classification algorithm, and the spatial distribution of the tissue states calculated for the sample sites is represented graphically.

Abstract: Several embodiments relate to engineered extracellular vesicles (EVs) using the membrane cloaking platform technology described herein, the cloaking imparting to the EVs enhanced delivery to tissues of interest, such as damaged or dysfunctional tissue. Several embodiments relate to engineering exosomes derived from cardiosphere-derived cells (CDCs) using the membrane cloaking platform technology described herein to confer enhanced tissue homing specificities, thereby leading to repair and regeneration at sites of injury. Uses of engineered EV compositions to treat diseases are also provided for in several embodiments.

Abstract: The present invention relates to a method of determining if a patient is likely to respond to a treatment with a targeted therapy compound selected from protein kinase inhibitors, small molecule inhibitors, and monoclonal antibody-based compounds. The present invention further relates to a method of identifying a targeted therapy compound selected from protein kinase inhibitors, small molecule inhibitors, and monoclonal antibody-based compounds for personalized medicine. The present invention also relates to a method of treatment of cancer in a patient. The present invention also relates to a targeted therapy compound selected from protein kinase inhibitors, small molecule inhibitors, and monoclonal antibody-based compounds for use in a method of treatment of cancer in a patient.

Abstract: The invention relates to the ADH3 promoter; polynucleotide sequences, vectors and expression cassettes including DNA regions responsible for the regulation of the ADH3 promoter; the host cells, including these vectors and expression cassettes, and, the recombinant proteins performed with the developed cells. In the scope of the invention, deletion analyzes in the ADH3 promoter were performed to identify regions that affect promoter strength and significant data was obtained in the formation of mutant ADH3 promoters. Deletion of the nucleotides between 539 and 638 (?361 to ?262) in SEQ ID NO: 1 resulted in a 63% increase in ADH3 promoter activity. Five different synthetic promoters were created using positive regulatory regions identified and approximately 165% to 200% promoter activities were achieved with these promoters.

Abstract: Provided herein are methods and compositions for batch production of producer cells using fluorescence activated cell sorting (FACS). In some aspects, the disclosure provides a drug-selection-free method for batch production of producer cells using FACS. Such batch production methods and compositions can be further utilized to generate clonal populations of producer cells, e.g., for large-scale manufacturing of a polypeptide of interest.

Abstract: Some aspects of this disclosure relate to systems, apparatuses, compositions (e.g., isolated nucleic acids and vectors), and methods for improving the stability and/or solubility of proteins evolved using phage-assisted continuous evolution (PACE). In some embodiments, vectors described herein comprise nucleic acids encoding selection systems (e.g., positive and/or negative selection systems) that link expression of genes required for production of infectious phage particles to a desirable physiochemical (e.g., stability or solubility) and/or desired function of an evolved protein.

Abstract: A method of characterizing a glioblastoma multiforme (GBM) stem cell (GSC), comprising culturing the GSC to provide a culture, contacting a first set of aliquots of the culture with individual compounds selected from a panel of compounds, identifying two or more of the selected compounds that cause more than a threshold level of cell death in the first set of aliquots, and characterizing the GSC as suitable for treatment with one or more combinations comprising the two or more identified compounds. A panel of chemical compounds, the compounds selected by a method comprising surgically resecting the tumor, culturing a GSC derived from GBM tissue derived from a GBM tumor, contacting aliquots thereof with individual compounds selected from a panel of compounds, and identifying two or more of the selected compounds that cause more than a threshold level of cell death in the aliquots, thereby identifying the compounds.

Abstract: Kits and methods are provided for performing multiplex LAMP reactions. These kits and methods are directed to specific and sensitive methods of target nucleic acid detection and more specifically pathogen diagnostics such as detection of Coronavirus. The kits and methods utilize a plurality of sets of oligonucleotide primers for targeting the viral nucleic acid target.

Abstract: Provided are epithelial cell spheroids including spheroids that have apical membranes and cilia that face towards the interior core of the spheroid and spheroids that have apical membranes and cilia that face away from the interior core of the spheroid. Also provided methods of making and using such spheroids.

Abstract: Provided are methods of producing nucleic acid libraries. In certain aspects, the methods include combining target nucleic acids (e.g., 5? phosphorylated nucleic acids) and an oligonucleotide pool. Oligonucleotides of the oligonucleotide pool may include complementarity regions of varying length and nucleotide sequence, and a complementarity region identification sequence. In such aspects, the combining is under conditions in which oligonucleotides of the oligonucleotide pool hybridize to nucleic acids of the target nucleic acids (e.g., 5? phosphorylated nucleic acids) having overhang regions that are complementary in sequence and have corresponding lengths with respect to the complementarity regions of the oligonucleotides. Compositions and kits that find use, e.g., in practicing the methods of the present disclosure are also provided.

Abstract: The invention relates to microbial host cells engineered to produce glycoconjugate vaccines by stable integration of an acceptor protein and an oligosaccharyltransferase into the host's genome, wherein expression of the oligosaccharyltransferase is regulated.

Abstract: The present invention provides a method to quantitatively measure the response of a patient to an immune-modulator drug that will aid clinicians in the determination of the optimal combination/posology of immunosuppressant/immune-modulator drugs. In addition, this method will open the possibility for clinicians to make the necessary adjustments in immunosuppressive therapy, as a way to avoid organ rejection to actually take place. Furthermore, this method will significantly reduce side effects of immunosuppressant drugs, optimizing therapeutic scheme and dosages, enabling the determination of the most effective immunosuppression regimen at the lower dosages for each patient individually and monitoring of treatment efficiency along time, thus opening the door to treatment personalization.

Abstract: A kit includes a microfabricated device having a top surface defining an array of microwells for receiving a sample comprising at least one cell, and a membrane for applying on the top surface of the microfabricated device to retain the at least one cell in at least one microwell of the array of microwells after the sample is loaded on the microfabricated device.

Abstract: The present disclosure relates to biofragment compositions that comprise bioparticle fragments and at least one heterologous antigen-binding molecule. In some embodiments, the biofragment is typically derived from a larger, intact bioparticle that express the at least one heterologous antigen-binding molecule at the surface, and the biofragment has increased solubility to facilitate assays for antigen detection. The disclosure also relates the related methods of using and making the biofragment compositions, as well as systems and devices implementing the biofragment compositions. In some embodiments, the related methods, systems and devices do not require additional detection reagents, such as animal derived detection antibodies.

Abstract: Apparatus and methods for determining whether a test compound induces cell activity, changes cell activity, prevents cell activity, or inhibits cell activity. An embodiment comprises placing a test compound solution in contact with a cell suspension media containing cells, diffusing the test compound solution into the cell suspension from one or more sides, and detecting activity in the cells with respect to their distance from the side from which the test compound is diffusing. Embodiments may provide an apparatus that allows a side source, a point source, or both, from which a test compound solution diffuses into a cell suspension media and contacts cells. Detecting cell activity may involve detecting activity in a first cell group proximate to the side from which the test compound is diffusing, and detecting activity in a second cell group farther than the first cell group from the side from which the test compound is diffusing.

Abstract: Yeast having modified chromosomes are provided. The chromosomes are modified such that at least one of yeast histones H3, H4, H2A or H2B are fully or partially replaced by their human histone counterparts H3, H4, H2A or H2B, respectively. Histone amino acid substitutions are included. Cell fusions with the yeast having the modified chromosomes and non-yeast cells are provided. Methods for screening test agents using the yeast are also provided. Yeast with a mutated yeast DAD1 gene, the mutated DAD1 gene encoding an E50D mutation in yeast DAD1 protein, are provided, and provide a useful genetic background for making the yeast with partially or fully replaced histone(s).

Abstract: The present invention relates to production of renewable fuels and fuel components from plant oil originating from at least one Brassica species, where said Brassica species, doped with at least one nitrogen-fixing bacteria, is cultivated to obtain Brassica seed oil, and feedstock comprising the Brassica seed oil is converted in a converting step, whereby renewable fuel or renewable fuel components are obtained. The invention also relates to a method for reducing nitrate release in renewable fuel production. Further, the invention relates to a method for reducing greenhouse gases in renewable fuel production.

Abstract: A method of detecting cells is provided. The method includes the following steps. A sensor device including a base and at least one response electrode is provided, wherein the response electrode is spaced apart from the base with respect to a gate end of the base. A test solution containing a target cell is placed on the response electrode, a first pulse voltage is applied to the response electrode, and a first detection current generated from the base is measured. A membrane potential of the target cell is changed, a second pulse voltage is applied to the response electrode, and a second detection current generated from the base is measured, wherein a sign of the first detection current and a sign of the second detection current are opposite.

Abstract: The present invention provides assays and compositions to identify the risk of toxicity in a patient population with genotypic variations in specific proteins and/or protein complexes within the patient population.

Abstract: The majority of clinically used antibiotics and anticancer agents are derived from bacterial small molecules. These molecules are produced by dedicated biosynthetic gene clusters, sets of genes that are responsible for the step-wise generation of the target small molecule. Recent investigations have indicated, to the surprise of many experts, that the majority of these biosynthetic genes are inactive or ‘silent’ for unknown reasons. Thus under typical bacterial culturing conditions, these genes are not expressed and consequently the bioactive small molecule products are not synthesized. Disclosed is a method for high throughput screening of elicitors of cryptic metabolites, a method for producing cryptic metabolites, and a new family of cryptic metabolites, the acybolins, as well as their complete structural elucidation.

Abstract: Compositions and methods related to anucelate cells (e.g., bacterial minicells) for pesticide degradation applications including related cells, polypeptides, and vectors.

Abstract: A honeycomb tube with a planar frame defining a fluidic path between a first planar surface and a second planar surface. A fluidic interface is located at one end of the planar frame. The fluidic interface has a fluidic inlet and fluidic outlet. The fluidic path further includes a well chamber having an well-substrate with a plurality of wells. The well chamber is arranged in the planar frame between the first or second surface and the well-substrate. The well chamber is in fluidic communication between the pre-amplification chamber and the fluidic outlet.

Abstract: A system and method for processing long scan data from a mass spectrometer is described. The long scan data is broken into multiple discrete subsets and each of the multiple subsets are padded by adding additional strings of data on either end of the subset. Each of the multiple subsets is deconvolved and overhang errors are corrected for on each deconvolved subset. A deconvolved full data set is then assembled from the deconvolved subsets.

Abstract: Disclosed are methods for cell transfection and regulating cellular behavior. More particularly, the present disclosure relates to methods of non-viral cell transfection and regulating cellular behavior using mineral coatings that allow for the enhanced transfection of cells. The mineral coatings bind polynucleotides and provide a source of calcium and phosphate ions to enhance transfection. The present disclosure also provides a high throughput platform for screening non-viral transfection of cells. The methods of the present disclosure also provide an advantageous polynucleotide delivery platform because the mineral coatings may be deposited on various medical device materials after being specifically developed using the high throughput screening platform.

Abstract: The present invention relates to a method for determining a decrease in the functions of the hippocampus by using the correlation between a micro RNA (miRNA) and an N-methyl-D-aspartate receptor (NMDAR), a method for inhibiting the decrease in the functions, and a method for screening for inhibitors of the decrease in the functions.

Abstract: The present invention relates to purified and isolated DNA sequences having protein production increasing activity and more specifically to the use of matrix attachment regions (MARs) for increasing protein production activity in a eukaryotic cell. Also disclosed is a method for the identification of said active regions, in particular MAR nucleotide sequences, and the use of these characterized active MAR sequences in a new multiple transfection method.

Abstract: The present invention provides methods for the identification, isolation and/or enrichment of human corneal endothelial cells (HCECs). In some embodiments, the method comprises a positive selection process in which a cell population containing human corneal cells is contacted with a positive affinity reagent that selectively binds to HCECs relative to cells other than HCECs (e.g., corneal keratocytes, etc.) in the population and/or a negative selection process in which a cell population containing HCECs is contacted with a negative affinity reagent that selectively binds to cells other than HCECs in the population relative to HCECs. The present invention also provides reagents and kits for the identification, isolation and/or enrichment of HCECs as well as compositions that are enriched in HCECs.

Abstract: A method for evaluating in vitro the effect of a xenobiotic (e.g., a drug) on drug metabolism in hepatocytes. The kit comprises a first culture of hepatocytes, a portion of in vitro xenobiotic-stimulated biological sample, and instructions for incubating the first culture of hepatocytes with the portion of in vitro xenobiotic-stimulated biological sample, and analyzing the activity, expression, or a combination thereof of a biomarker in the hepatocytes to evaluate the effect of the xenobiotic on drug metabolism in the hepatocytes.

Abstract: The present invention provides for a system comprising (a) a first nucleic acid comprising a nucleotide sequence encoding a nucleotide sequence of interest operatively linked to a promoter comprising a repressor polypeptide binding site, and (b) a second nucleic acid comprising a nucleotide sequence encoding a repressor polypeptide having at least 70% amino acid identity with EilR, SmvR, KmrR, RcdA, or QacR; wherein expression of the nucleotide sequence of interest from the promoter is induced by the presence of a hydrophobic inducer, such as a hydrophobic cation inducer, such as a triarylmethane, acridine, phenazine, phenothiazine, or xanthene.

Abstract: Biomarkers are not as commonly used in ALS drug development as in the drug development process for oncology. Biomarkers are important component of the ALS drug development pathway to demonstrate drug effect and target engagement. In a recent Phase 2A double-blind, randomized, placebo controlled clinical trial with GM604 (AKA MNTF, GM6), where ALS patients were treated with six doses of GM604 for two weeks and then continued to be evaluated for disease progression until 10 weeks after cessation of GM604 treatment, it was demonstrated that GM604 can modulate expression of ALS disease related genes, through pathways that bring about homeostasis of pertinent ALS biomarkers. The statistical significance in biomarker changes also correlate with treatment effects in clinical observations.