Abstract: Apparatus and method for handling biological samples. Segments of ionic liquid can provide voltage across segments of immiscible liquid to concentrate or separate charged species in the biological samples. Reactants in biological samples can be contacted and reacted in segments of immiscible liquid.

Abstract: A camera alignment system that can enable alignment in at least one of three planes and about an axis of at least one of the planes. An alignment mount can mate to a camera and lens. The alignment mount can comprise a mechanism to adjust the camera relative to the lens to that an image plane of the camera aligns with an image plane of the lens in a predetermined orientation. One predetermined orientation can be that the image plane of the camera being parallel to the image plane of the lens.

Abstract: A method of operating an ion trap spectrometer system having an ion trap is provided.

Abstract: In various embodiments, the present teachings provide sequencing methods which facilitate enhancing the efficiency of ligation and/or increasing sequencing reads. Various embodiments of the methods enable sequencing through template regions for which complementary labeled extension probes are unavailable or insufficient. In various embodiments, one or more rounds of ligation with unlabeled extension probes can be used in addition to a round of ligation with labeled extension probe. In various embodiments, for example, such methods can facilitate extension on template polynucleotides that do not bind labeled extension probe in the first round of ligation.

Abstract: The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to immobilized beads. The invention further provides sets of labeled probes containing phosphorothiolate linkages.

Abstract: The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to immobilized beads. The invention further provides sets of labeled probes containing phosphorothiolate linkages.

Abstract: A heated platen assembly for use in a biological testing device is disclosed having a heated platen defining a plurality of optical openings configured to permit radiation to pass through the heated platen, a light transmissive slip cover configured to cover at least one of the plurality of optical openings, and means for retaining the slip cover over the at least one of the plurality of optical openings.

Abstract: Fluorescent phenyl xanthene dyes are described that comprise any fluorescein, rhodamine or rhodol comprising a particular C9 phenyl ring. One or both of the ortho groups on the lower C9 phenyl ring is ortho substituted with a group selected from alkyl, heteroalkyl, alkoxy, halo, haloalkyl, amino, mercapto, alkylthio, cyano, isocyano, cyanato, mercaptocyanato, nitroso, nitro, azido, sulfeno, sulfinyl, and sulfino. In one embodiment, halo and/or hydroxy groups are used. Optimal dyes contain a lower C9 phenyl ring in which both ortho groups are the same and the lower ring exhibits some form a symmetry relative to an imaginary axis running from the phenyl rings point of attachment to the remainder of the xanthene dye through a point para to the point of attachment. The phenyl xanthene dyes may be activated. Furthermore, the phenyl xanthene dyes may be conjugated to one or more substances including other dyes.

Abstract: The present teachings provide novel methods for amplifying short nucleic acids. In some embodiments, the present teachings provide novel methods for linearly amplifying a collection of micro RNAs by using temperature cycling during a reverse transcription reaction. The cycling can comprise at least 20 cycles of an annealing temperature segment of 10 C-30 C, and a denaturation temperature segment of 35 C-60 C. In some embodiments, the temperature cycled reaction can comprise an osmolyte.

Abstract: The present teachings provide methods, compositions, and kits for synthesizing and sequencing nucleic acids. In some embodiments, elaborated nucleotide phosphorothiolate compounds are employed along with efficient cleaving reactions. Improved sequencing efficiency is achieved by the rapid polymerase-mediated incorporation of elaborated nucleotide phosphorothiolate compounds. Increased sequencing efficiency is also achieved by the ability of the cleaving reactions to restore the incorporated nucleotides to their natural structure prior to subsequent elongation.

Abstract: Ion trap apparatus and methods for efficiently addressing the effects of charge space caused by ion trap overfilling, useful in linear ion traps of mass spectrometers.

Abstract: Disclosed herein a reversible terminator nucleotides and methods of use.

Abstract: A set of 4,7-dichlororhodamine compounds useful as fluorescent dyes are disclosed having the structures wherein R1-R6 are hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, sulfonate, sulfone, amino, amido, nitrile, lower alkoxy, linking group, or, when taken together, R1 and R6 is benzo, or, when taken together, R4 and R5 is benzo; R7-R10, R12-R16 and R18 may be hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, sulfonate, sulfone, amino, amido, nitrile, lower alkoxy, linking group; R11 and R17 may be hydrogen, lower alkyl, lower alkene, lower alkyne, phenyl, aryl, linking group; Y1-Y4 are hydrogen, lower alkyl, or cycloalkyl, or, when taken together, Y1 and R2, Y2 and R1 Y3 and R3, and/or Y4 and R4 is propano, ethano, or substituted forms thereof; and X1-X3 taken separately are hydrogen, chlorine, fluorine, lower alkyl, carboxylate, sulfonate, hydroxymethyl, and linking group, or any combinations thereof.

Abstract: A thermal cycler for automatic performance of the polymerase chain reaction is provided. The thermal cycler comprises a heater control that provides close temperature control of the reaction.

Abstract: Apparatus comprising a plurality of channels and a plurality of deposition units and methods for depositing fluids on a support are disclosed.

Abstract: System and methods for detecting analytes such as pathogenic cells are described. The methods allow for the direct measurement of analytes such as pathogenic organisms without the need for sample preparation and/or PCR. The devices can be used individually as point-of-use sensors for airborne pathogens and other pathogenic organisms in foods and agriculture products.

Abstract: An instrument is provided that can monitor nucleic acid sequence amplification reactions, for example, PCR amplification of DNA and DNA fragments. The instrument includes a multi-notch filter disposed along one or both of an excitation beam path and an emission beam path. Methods are also provided for monitoring nucleic acid sequence amplifications using an instrument that includes a multi-notch filter disposed along a beam path.

Abstract: An embodiment relates generally to resonant structure. The resonant structure includes a substrate and a nano-bowtie antenna deposited over the substrate. The resonant structure also includes an enclosure deposited over the substrate and surrounding the nano-bowtie antenna, where the enclosure is configured to raise an enhancement level in the nano-bowtie antenna.

Abstract: A device for performing biological sample reactions may include a plurality of flow cells configured to be mounted to a common microscope translation stage, wherein each flow cell is configured to receive at least one sample holder containing biological sample. Each flow cell also may be configured to be selectively placed in an open position for positioning the at least one sample holder into the flow cell and a closed position for reacting biological sample contained in the at least one sample holder. The plurality of flow cells may be configured to be selectively placed in the open position and the closed position independently of each other.

Abstract: Methods and materials are disclosed for use in simultaneously amplifying at least 11 specific STR loci of genomic DNA in a single multiplex reaction, as are methods and materials for use in the analysis of the products of such reactions. Included in the present invention are materials and methods for the simultaneous amplification of 16 specific loci in a single multiplex reaction, comprising the 10 AmpFISTR® SGMplus® STR loci, the Amelogenin locus, and 5 new STR loci, including methods and materials for the analysis of these loci.