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: Described herein is an adapter comprising a population of first oligonucleotides, a second oligonucleotide and a third oligonucleotide, wherein the first oligonucleotides, the second oligonucleotide and the third oligonucleotide are hybridized together to produce a complex that comprises: (i) a first end comprising a transposase recognition sequence, (ii) a central single-stranded region of variable sequence and (iii) a second end comprising sequences that are non-complementary. A method, as well as a kit for practicing the method, are also provided.

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

Abstract: A method for making an asymmetrically-tagged sequencing library is provided. In some embodiments, the method may comprise: obtaining a symmetrically-tagged library of cDNA or genomic DNA fragments, hybridizing a tailed first primer to the 3? sequence tag of the library and extending the same to produce primer extension products, and amplifying the primer extension products using a prior of tailed primers to produce asymmetrically-tagged library.

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

Abstract: In some embodiments, the amplification method may comprise producing a reaction mix comprising: a nucleic acid sample, a polymerase, nucleotides, a forward primer that hybridizes to a sequence in the bottom strand of a fragment in the sample, and a reverse primer. The reverse primer has a hairpin structure comprising a loop, a stem and a 3? overhang of at least 8 nucleotides, wherein the 3? overhang hybridizes to a sequence in the top strand of the fragment. Subjecting the reaction mix at least two rounds of denaturation, renaturation and primer extension conditions results in extension the forward and reverse primers to produce an amplification product that contains: a double stranded region comprising a nick adjacent to the 5? end of the reverse primer, and the loop of the first hairpin primer. Primer sets and kits for performing the methods 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: 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: Described herein, among other things, is an adapter comprising a population of first oligonucleotides, a second oligonucleotide and a third oligonucleotide, wherein the first oligonucleotides, the second oligonucleotide and the third oligonucleotide are hybridized together to produce a complex that comprises: (i) a first end comprising a transposase recognition sequence, (ii) a central single-stranded region of variable sequence and (iii) a second end comprising sequences that are non-complementary. A method, as well as a kit for practicing the method, are also provided.

Abstract: Provided herein, among other things, are a variety of methods that comprise inserting a plurality of barcoded transposons into a population of DNA fragments that comprise DNA fragments of less than 1 kb in length, to produce transposon-tagged fragments that each comprise a barcoded transposon. Kits for performing this method are also provided.

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: Systems and methods for a real time embedded trace are provided. In certain embodiments, a system for acquiring data that uses a real time embedded trace includes a first computing system. The first computing system includes a memory unit; and a processing unit executing software, wherein the software comprises at least one real time trace instruction. Further, the at least one real time trace instruction directs the processing unit to directly store data onto the memory unit; and wherein the stored data is translated for a user after it is stored onto the memory unit.

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

Abstract: The present disclosure relates to variant ?-glucosidase polypeptides that have enhanced thermostability, and compositions, e.g., cellulase compositions, comprising variant ?-glucosidase polypeptides. The variant ?-glucosidase polypeptides and related compositions can be used in variety of agricultural and industrial applications. The present disclosure further relates to nucleic acids encoding variant ?-glucosidase polypeptides and host cells that recombinantly express the variant ?-glucosidase polypeptides.