Abstract: A system and method is provided for enabling demand-based pooling of endpoint resources in a multi-router, multi-application hosting system. The method includes dividing a plurality of endpoints into zones. Each of a plurality of routers is assigned to one of the zones. Each router is enabled to control endpoint assignments within its zone. In the preferred embodiment, for each application hosted by the system, all requests for the application are concentrated on the minimum number of endpoints required to meet demand and fault tolerance requirements. When a request for an application comes into the system, a router will route the request to an endpoint assigned to the application, regardless of whether the endpoint is within the router's zone. If a new endpoint is needed for the application, the router will assign an endpoint within its zone to the application, and inform the other routers of the assignment.

Abstract: A method for determining the ploidy of a test genome is provided. In some embodiments, the method may comprises: a) obtaining a plurality of ratios for polymorphisms that are distributed throughout a test genome, wherein each of the ratios is a ratio of the measured copy number of uncut allele in a polymorphic site relative to the measured copy number of the uncut allele in the reference sample; b) taking the log of the ratios and plotting a distribution of the reference corrected log ratios of the SNP probes; and c) determining the ploidy of said the genome based on the number of peaks in that distribution.

Abstract: This disclosure relates to novel xylose isomerases and their uses, particularly in fermentation processes that employ xylose-containing media.

Abstract: This disclosure relates to novel xylose isomerases and their uses, particularly in fermentation processes that employ xylose-containing media.

Abstract: This disclosure provides, among other things, a method for analyzing a planar cellular sample. In some embodiments, the method comprises: (a) indirectly or directly attaching nucleic acid tags to binding sites in a planar cellular sample; (b) contacting the planar cellular sample with a solid support comprising an array of spatially addressed features that comprise oligonucleotides, wherein each oligonucleotide comprises a molecular barcode that identifies the feature in which the oligonucleotides is present; (c) hybridizing the nucleic acid tags, or a copy of the same, with the oligonucleotides to produce duplexes; and (d) extending the oligonucleotides in the duplexes to produce extension products that each comprises (i) a molecular barcode and (ii) a copy of a nucleic acid tag. Other embodiments, e.g., kits and the like, are also described.

Abstract: A method for sequencing a nucleic acid is provided. In certain embodiments the method comprises obtaining a duplex comprising a nucleic acid and a primer, wherein the primer has a nuclease resistant 3? end, combining the duplex with a chain terminator nucleotide and a proof-reading polymerase to produce a reaction in which the polymerase idles on the added chain terminator nucleotide, identifying the chain terminator nucleotide added to the end of the primer; and adding a nuclease-resistant nucleotide to the end of the primer after the polymerase has idled on and removed the added chain terminator nucleotide, thereby producing a duplex comprising the template and an extended primer that has a nuclease resistant 3? end.

Abstract: This disclosure provides, among other things, a nanofluidic device sensing device is provided. In certain embodiments, the device contains: a) a channel comprising a floor and a ceiling, b) an array of charge sensors in the floor and/or ceiling of the channel, arranged along the longitudinal axis of the channel; c) a capture area in the floor and/or ceiling of the channel at the entrance end of the channel; and d) a first electrode and a second electrode, wherein the first and second electrodes are positioned to provide an electrophoretic force along the longitudinal axis of the channel. Other embodiments, e.g., methods, are also described.

Abstract: The invention generally relates to methods and apparatus for manipulation of charged molecules in solution. More particularly, the invention provides nanofluidic CCD arrays that are capable of manipulate one or a group of molecules on an individual bases such that they undergo controlled physical and/or chemical movements and/or transformations.

Abstract: A system and method is provided for enabling demand-based pooling of endpoint resources in a multi-router, multi-application hosting system. The method includes dividing a plurality of endpoints into zones. Each of a plurality of routers is assigned to one of the zones. Each router is enabled to control endpoint assignments within its zone. In the preferred embodiment, for each application hosted by the system, all requests for the application are concentrated on the minimum number of endpoints required to meet demand and fault tolerance requirements. When a request for an application comes into the system, a router will route the request to an endpoint assigned to the application, regardless of whether the endpoint is within the router's zone. If a new endpoint is needed for the application, the router will assign an endpoint within its zone to the application, and inform the other routers of the assignment.

Abstract: A method of enriching for a fragment of a genome, as well as corresponding compositions and kits, are provided. In certain embodiments, the method comprises: (a) contacting a sample comprising fragmented DNA with a Cas9-gRNA complex comprising mutant Cas9 protein that has inactivated nuclease activity and a Cas9-associated guide RNA that is complementary to a site in the DNA, to produce a Cas9-fragment complex that comprises a fragment of the fragmented DNA; and (b) isolating the complex. In addition, other methods and compositions for Cas9/CRISPR-mediated nucleic acid manipulation are also provided.

Abstract: A method for fragmenting a genome is provided. In certain embodiments, the method comprises: (a) combining a genomic sample containing genomic DNA with a plurality of Cas9-gRNA complexes, wherein the Cas9-gRNA complexes comprise a Cas9 protein and a set of at least 10 Cas9-associated guide RNAs that are complementary to different, pre-defined, sites in a genome, to produce a reaction mixture; and (b) incubating the reaction mixture to produce at least 5 fragments of the genomic DNA. Also provided is a composition comprising at least 100 Cas9-associated guide RNAs that are each complementary to a different, pre-defined, site in a genome. Kits for performing the method are also provided. In addition, other methods, compositions and kits for manipulating nucleic acids are also provided.

Abstract: Methods and systems are provided for using time-frequency warping to analyze a physiological signal. One embodiment includes applying a warping operator to the physiological signal based on the energy density of the signal. The warped physiological signal may be analyzed to determine whether non-physiological signal components are present. Further, the same warping operator may be applied to signal quality indicators, and the warped physiological signal may be analyzed based on the warped signal quality indicators. Non-physiological signal components, or types of non-physiological noise sources, may be identified based on a comparison of the physiological signal with the signal quality indicators. Non-physiological signal components may also be identified based on a neural network of known noise functions. In some embodiments, the non-physiological signal components may be removed to increase accuracy in estimating physiological parameters.

Abstract: A system and method is provided for enabling demand-based pooling of endpoint resources in a multi-router, multi-application hosting system. The method includes dividing a plurality of endpoints into zones. Each of a plurality of routers is assigned to one of the zones. Each router is enabled to control endpoint assignments within its zone. In the preferred embodiment, for each application hosted by the system, all requests for the application are concentrated on the minimum number of endpoints required to meet demand and fault tolerance requirements. When a request for an application comes into the system, a router will route the request to an endpoint assigned to the application, regardless of whether the endpoint is within the router's zone. If a new endpoint is needed for the application, the router will assign an endpoint within its zone to the application, and inform the other routers of the assignment.

Abstract: Provided herein is a method for enriching a target nucleic acid molecule. In one embodiment, the method may involve hybridizing a C-probe to a strand of a target nucleic acid to produce a complex, enzymatically removing any 3? overhanging end from the target nucleic acid of the complex to produce a 3? hydroxyl group at the 3? end; extending the 3? end of the first sequence using the oligonucleotide sequence of the C-probe as a template; enzymatically removing any 5? overhanging end from the target nucleic acid, either before or after the extending step, to produce an 5? phosphate group at the end of the second sequence; and ligating the 5? phosphate group at the end of the second sequence to the 3? hydroxyl group at the end of the first sequence to produce a circular DNA molecule that contains the target sequence and the complement of the oligonucleotide sequence.

Abstract: A vitrector that includes an adjustable illumination aperture is described. The vitrector may include a probe and a light sleeve assembly extending along and substantially surrounding the probe. The light sleeve assembly may include a plurality of optical fibers. At least a portion of the optical fibers are operable to provide illumination so as to define an illumination aperture about the vitrectomy probe. A portion of the optical fibers may be encapsulated. The light sleeve assembly may be adjustable along a length of the probe, providing adjustment of the illumination aperture to increase or decrease an area of illumination provided thereby.

Abstract: This disclosure provides a method comprising: a) clamping the top and bottom strands of a double stranded DNA molecule to produce a duplex in which the top and bottom strands are linked; b) denaturing the duplex to produce a denatured product; and c) renaturing the denatured product in the presence of a labeled oligonucleotide that is complementary to a sequence of nucleotides in the double stranded DNA molecule, thereby producing a D-loop-containing product. Kits for performing the method and products made by the method are also provided.

Abstract: A method for determining the ploidy of a test genome is provided. In some embodiments, the method may comprises: a) obtaining a plurality of ratios for polymorphisms that are distributed throughout a test genome, wherein each of the ratios is a ratio of the measured copy number of uncut allele in a polymorphic site relative to the measured copy number of the uncut allele in the reference sample; b) taking the log of the ratios and plotting a distribution of the reference corrected log ratios of the SNP probes; and c) determining the ploidy of said the genome based on the number of peaks in that distribution.

Abstract: A system and method is provided for enabling demand-based pooling of endpoint resources in a multi-router, multi-application hosting system. The method includes dividing a plurality of endpoints into zones. Each of a plurality of routers is assigned to one of the zones. Each router is enabled to control endpoint assignments within its zone. In the preferred embodiment, for each application hosted by the system, all requests for the application are concentrated on the minimum number of endpoints required to meet demand and fault tolerance requirements. When a request for an application comes into the system, a router will route the request to an endpoint assigned to the application, regardless of whether the endpoint is within the router's zone. If a new endpoint is needed for the application, the router will assign an endpoint within its zone to the application, and inform the other routers of the assignment.

Abstract: Certain embodiments described in this disclosure relate to a method of sample analysis. In certain cases, the method comprises: a) contacting a genomic sample comprising double-stranded genomic DNA with a first restriction endonuclease that recognizes a nucleotide sequence that comprises a SNP site in the double stranded genomic DNA, wherein: i. the restriction endonuclease cleaves the genomic DNA at the sequence regardless of the allele of the SNP present at the SNP site; and ii. cleavage of the sequence by the restriction enzyme creates a 5? overhang that comprises the SNP site; b) contacting the digested genomic sample with a extension enzyme and a first labeled nucleotide that is used by the extension enzyme to fill in the overhang only if the overhang comprises a first allele of the SNP.

Abstract: A method of genome analysis is provided. In certain embodiments, the method comprises: a) contacting a double-stranded genomic DNA with a site-specific nicking endonuclease that recognizes a sequence comprising a single nucleotide polymorphism (SNP), in which the endonuclease nicks the genomic DNA at a nick site only if a first allele of the SNP is present; b) denaturing the genomic sample; c) contacting the denatured genomic sample with an array comprising a first probe and a second probe, in which nicking results in less binding of the denatured sample to the first probe relative to a sample that is not nicked; and d) comparing the amount of hybridization to the first probe to the amount of hybridization to said second probe, in which decreased binding of the denatured genomic samples to the first probe relative to the second probe indicates that the first allele of the SNP is present.