Abstract: The invention is directed to apparatus and chips comprising a large scale chemical field effect transistor arrays that include an array of sample-retaining regions capable of retaining a chemical or biological sample from a sample fluid for analysis. In one aspect such transistor arrays have a pitch of 10 ?m or less and each sample-retaining region is positioned on at least one chemical field effect transistor which is configured to generate at least one output signal related to a characteristic of a chemical or biological sample in such sample-retaining region.

Abstract: The construction of a chimeric Pestivirus by the identification of selected regions in the 3?NTR of the viral RNA genome is described where additional RNA sequences can be stably inserted. These sequence insertions in the viral RNA genome were stable in replication and capable of forming infectious, RNase resistant virus particles. This chimeric Pestivirus with a 3?NTR insertion can be utilized as a quality control material in analytical assays for RNA targets, including external, internal controls, quantitative standards in PCR and NAT nucleic acid assays.

Abstract: This disclosure relates to methods of performing activation by polyphosphorolysis (APP) reactions using at least one of the polyphosphorylating agents triphosphate, polyphosphate, imidodiphosphate, thiodiphosphate (or ?-monothiopyrophosphate), and related compounds.

Abstract: Various embodiments of a sequencing system capable of rapidly imaging samples at multiple wavelengths are provided herein. In one embodiment, the system includes a fast-indexing filter wheel having a plurality of excitation and emission filters capable of being rapidly rotated into and out of communication with an excitation source (e.g., an arc lamp, a laser. For example, the filter wheel can be configured to index in an amount of time falling within a range of about 40 ms to about 60 ms, preferably 50 ms. The system can also be configured to account for vibrations resulting from the quick starts and stops of the fast-indexing filter wheel as well as vibrations resulting from other sources. Various methods of rapidly imaging a sample at multiple wavelengths are also provided herein.

Abstract: Disclosed are systems and methods for assessing images in applications such as microscopic scanning of a slide having light emitting objects. In certain embodiments, such scanning can involve objects such as sequencing beads disposed on the slide to facilitate biological analysis such as nucleic acid sequencing. Also disclosed are certain embodiments where images of light emitting objects are assessed for image quality so as to facilitate a feedback response such as a corrective action. In certain embodiments, such assessment and correction can be performed in real-time during the scanning process, and can include re-acquisition of the assessed image. Also disclosed are certain embodiments where such assessment and correction can be triggered dynamically during the scan, or before start of the scan, so as to enhance the scanning performance, including scanning time and throughput.

Abstract: A vertical clamping device is provided that supports a flow cell component in a vertical configuration in which the flow cell is on an opposite side of the vertical support from the electronic interface. The clamp includes a vertical setting to receive the flow cell component and provides an electronic interface on a vertical surface of the vertical setting. A block supports the fluidics interface and can move in a horizontal direction bringing the fluidics interface into contact with the flow cell component.

Abstract: A load cell lockout system includes a lower support, an upper support, and a load cell disposed between the lower support and the upper support. The upper support is movable relative to the lower support between a first position wherein a first load is applied by the upper support to the load cell and a second position wherein either a second load that is lighter than the first load is applied by the upper support to the load cell or no load is applied by the upper support to the load cell. A lockout includes a cam with an eccentric perimeter side edge, the cam being rotatable between a first orientation whereby the upper support is placed in the first position and a second orientation whereby the upper support is placed in the second position.

Abstract: The present teachings provide apparatuses and methods for automated handling of samples, e.g., biological or chemical samples. The apparatuses and the methods of the present teachings allow automated performance of various sample manipulation steps without manual intervention. In a preferred embodiment, the present teachings provide apparatuses and methods for automated enrichment of templated beads produced by PCR.

Abstract: Methods, assays, compositions and kits for the ligation of short polynucleotides are presented herein. The short polynucleotides are optionally no more than 7 nucleotides in length, and can be as short as 3 or 4 nucleotides in length. The ligation is optionally performed by CV ligase.

Abstract: A chemically-enhanced primer is provided comprising a negatively charged moiety (NCM), an oligonucleotide sequence having a) non-nuclease resistant inter-nucleotide linkages or b) at least one nuclease resistance inter-nucleotide linkage. The chemically-enhanced primer can be used for sequencing and fragment analysis. Methods for synthesizing the chemically-enhanced primer as well as a method of preparing DNA for sequencing, a method of sequencing DNA, and kits containing the chemically-enhanced primer are also provided. The method of sequencing DNA can comprise contacting amplification reaction products with the composition wherein excess amplification primer is degraded by the nuclease and the chemically-enhanced primer is essentially non-degraded.

Abstract: An array of sensors arranged in matched pairs of transistors with an output formed on a first transistor and a sensor formed on the second transistor of the matched pair. The matched pairs are arranged such that the second transistor in the matched pair is read through the output of the first transistor in the matched pair. The first transistor in the matched pair is forced into the saturation (active) region to prevent interference from the second transistor on the output of the first transistor. A sample is taken of the output. The first transistor is then placed into the linear region allowing the sensor formed on the second transistor to be read through the output of the first transistor. A sample is taken from the output of the sensor reading of the second transistor. A difference is formed of the two samples.

Abstract: Methods and apparatus relating to FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.

Abstract: Cell permeable metal ion indicator compounds and methods of their use and synthesis are described. The compound comprises a metal chelating moiety (Mc), a reporter molecule and two or more lipophilic groups (GL) covalently bonded through a linker to the reporter molecule, wherein the lipophilic groups, when present in a live cell, are cleaved resulting in two or more negatively charged groups.

Abstract: In one embodiment, a device is described. The device includes a material defining a reaction region. The device also includes a plurality of chemically-sensitive field effect transistors have a common floating gate in communication with the reaction region. The device also includes a circuit to obtain respective output signals from the chemically-sensitive field effect transistors indicating an analyte within the reaction region.

Abstract: The invention provides apparatuses and methods of use thereof for sequencing nucleic acids subjected to a force, and thus considered under tension. The methods may employ but are not dependent upon incorporation of extrinsically detectably labeled nucleotides.

Abstract: Disclosed are methods and kits for the specific detection of E. coli O157:H7 and not E. coli O55:H7 from samples such as: complex food matrices, water, beverages, fermentation broths, forensic & biological samples, and environmental samples including food processing and manufacturing surfaces. In some embodiments, a method of the disclosure comprises: hybridizing at least a first pair of polynucleotide primers to at least a first target polynucleotide sequence, hybridizing at least a second pair of polynucleotide primers to at least a second target polynucleotide sequence, amplifying the at least first and at least second target polynucleotide sequences, and detecting the first and second amplified target polynucleotide sequence products, wherein the detection of both the first amplified target polynucleotide sequence product and the second amplified target polynucleotide sequence product is indicative of the presence of E. coli O157:H7 in a sample and not E. coli O55:H7.

Abstract: The present invention provides for functionalized fluorescent nanocrystal compositions and methods for making these compositions. The compositions are fluorescent nanocrystals coated with at least one material. The coating material has chemical compounds or ligands with functional groups or moieties with conjugated electrons and moieties for imparting solubility to coated fluorescent nanocrystals in aqueous solutions. The coating material provides for functionalized fluorescent nanocrystal compositions which are water soluble, chemically stable, and emit light with a high quantum yield and/or luminescence efficiency when excited with light. The coating material may also have chemical compounds or ligands with moieties for bonding to target molecules and cells as well as moieties for cross-linking the coating.

Abstract: Methods for predicting clinical outcome for a human subject diagnosed with squamous cell lung carcinoma using a panel of molecular markers that includes CDKN2A and CCND1. The markers are related to the subject's increased likelihood of a negative clinical outcome.