| LIFE TECHNOLOGIES CORPORATION Patent applications |
| Patent application number | Title | Published |
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| 20120136073 | Amine-Containing Transfection Reagents and methods for making and using same - There are provided for herein novel amine-containing transfection compounds and methods for making and using same. The compounds are generally obtained by reacting a primary amine with an unsaturated compound. Transfection complexes made using the amine-containing transfection compounds in combination with additional compounds to encapsulate biologically active agents such as nucleic acids are also provided for herein. Methods of using the transfection complexes for the in vivo or in vitro delivery of biologically active agents are also described. The transfection complexes of the present invention are highly potent, thereby allowing effective modulation of a biological activity at relatively low doses compared to analogous transfection compounds known in the art. | 05-31-2012 |
| 20120135885 | Methods and Kits Using Extended Rhodamine Dyes - Extended rhodamine compounds exhibiting favorable fluorescence characteristics having the structure | 05-31-2012 |
| 20120135870 | Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 05-31-2012 |
| 20120135426 | Method for quantifying phosphokinase activity on proteins - The invention involves a method for measuring phosphorylation of proteins at specific sites and, as such, is an indicator of the protein kinase activity of enzymes capable of phosphorylating those sites. The method involves the in vitro or in vivo phosphorylation of a target protein at a specific serine, threonine or tyrosine residue, subjecting that protein (non-phosphorylated) to reaction mixture containing all reagents, including phosphokinase which allow the creation of a phosphorylated form of protein. The phosphorylated protein is measured by contacting it with an antibody specific for the phosphorylation site(s). The invention includes antibodies useful in practicing the methods of the invention. The invention particularly relates to all proteins modified by phosphorylation and dephosphorylation as illustrated by Tau, Rb and EGFR proteins and antibodies specific for the site of phosphorylation of the Tau, Rb or EGFR proteins. | 05-31-2012 |
| 20120135414 | CHEMICALLY-ENHANCED PRIMER COMPOSITIONS, METHODS AND KITS - A composition is provided comprising a negatively charged group, an oligonucleotide sequence and at least none or one nuclease-resistant linkage group to form a chemically-enhanced primer. The chemically-enhanced primer can be used for sequencing and fragment analysis. Methods for synthesizing the primer as well as a method of preparing DNA for sequencing and 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 under conditions in which excess amplification primer is degraded by the nuclease and the chemically-enhanced primer is essentially non-degraded. | 05-31-2012 |
| 20120129732 | Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 05-24-2012 |
| 20120129728 | Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 05-24-2012 |
| 20120129703 | Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 05-24-2012 |
| 20120129225 | METHODS AND REAGENTS FOR MOLECULAR CLONING - The present invention provides compositions, methods, and kits for covalently linking nucleic acid molecules. The methods include a strand invasion step, and the compositions and kits are useful for performing such methods. For example, a method of covalently linking double stranded (ds) nucleic acid molecules can include contacting a first ds nucleic acid molecule, which has a topoisomerase linked to a 3′ terminus of one end and has a single stranded 5′ overhang at the same end, with a second ds nucleic acid molecule having a blunt end, such that the 5′ overhang can hybridize to a complementary sequence of the blunt end of the second nucleic acid molecule, and the topoisomerase can covalently link the ds nucleic acid molecules. The methods are simpler and more efficient than previous methods for covalently linking nucleic acid sequences. | 05-24-2012 |
| 20120123997 | SYSTEMS AND METHODS FOR LABORATORY ASSAY VALIDATION OR VERIFICATION - Systems and methods are used to generate a protocol for an assay. At least one performance characteristic parameter of an assay and at least one standardized protocol for each assay of a plurality of assays and assay types are stored. A performance characteristic parameter selection and an assay selection are received from a client device of a laboratory. One or more performance characteristic parameters and a standardized protocol are retrieved from the database device. The client device is sent the one or more performance characteristic parameters and one or more study variable values. One or more amendments to the one or more performance characteristic parameters and one or more study variable values are received from the client device. A protocol for the assay is generated based on the one or more amendments. | 05-17-2012 |
| 20120122093 | METHODS AND KITS FOR MULTIPLEX AMPLIFICATION OF SHORT TANDEM REPEAT LOCI - Compositions, methods and kits are disclosed for use in simultaneously amplifying at least 20 specific STR loci of genomic nucleic acid 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 23 and 24 specific loci in a single multiplex reaction, comprising the 13 CODIS loci, the Amelogenin locus, an InDel and at least six to ten additional STR loci, including methods, kits and materials for the analysis of these loci. | 05-17-2012 |
| 20120115744 | METHODS FOR GENERATING TARGET SPECIFIC PROBES FOR SOLUTION BASED CAPTURE - Provided herein are compositions and kits for single-stranded nucleic acid probes, and methods for making the single-stranded nucleic acid probes, where the single-stranded nucleic acid probes comprise a probe region having a predetermined sequence which is flanked by a 5′ region having a first restriction enzyme recognition sequence and flanked by a 3′ region having a second restriction enzyme recognition sequence, and a region which hybridizes to a capture nucleic acid molecule. The single-stranded nucleic acid probes are useful for solution-based capture methods. | 05-10-2012 |
| 20120109598 | Predictive Model for Use in Sequencing-by-Synthesis - A method of obtaining a more accurate estimate of a signal correction parameter(s) in sequencing-by-synthesis operations, such as incomplete extension rates, carry forward rates, and/or signal droop rates. The sequencing operation produces signal data. A model is constructed to simulate a population of template strands as it undergoes the sequencing process and becomes divided into different phase-states as the sequencing-by-synthesis progresses. For example, the model may be a phase-state model. The output from the model is used to adjust the signal correction parameter(s). For example, the model may be fitted to the signal data. This fitting results in a more accurate estimate of the signal correction parameter(s). In another embodiment, the signal droop rate is modeled as a decaying function and this decaying function is fitted to the signal data to obtain an improved estimate of the signal droop rate. | 05-03-2012 |
| 20120108804 | COMPOSITIONS AND METHODS FOR PREPARING SHORT RNA MOLECULES AND OTHER NUCLEIC ACIDS - The invention provides methods of preparing nucleic acids, such as RNA molecules, of a defined size or range of sizes. The invention provides compositions, methods and kits for use in the production and preparation of small RNA molecules (including without limitation micro-RNA, siRNA, d-siRNA and e-siRNA) and other nucleic acids of various sizes. | 05-03-2012 |
| 20120108452 | Semi-Invasive Method for Characterizing Lung Injury - Described and disclosed are methods for determining, predicting, diagnosing, treating, and monitoring lung diseases, including bronchiolitis obliterans syndrome and acute cellular rejection in a lung transplant recipient by measuring chemokine levels in bronchoalveolar lavage (BAL) samples. The chemokine CXCL10 is measured in combination with at least one analyte selected from the group consisting of IL1RA, CXCL11, MCP-1, CXCL9, RANTES, IL-13, IL-17, IL-22, fractalkine, and eotaxin; and/or biomarkers. The present teachings also relate to methods, treatment decisions and kits for detecting and monitoring onset of lung transplant rejection in advance of clinically recognized symptoms. | 05-03-2012 |
| 20120107897 | DOUBLE-STRANDED OLIGONUCLEOTIDES - Antisense sequences, including duplex RNAi compositions, which possess improved properties over those taught in the prior art are disclosed. The invention provides optimized antisense oligomer compositions and method for making and using the both in in vitro systems and therapeutically. The invention also provides methods of making and using the improved antisense oligomer compositions. | 05-03-2012 |
| 20120107879 | METHODS FOR PRODUCTION AND PURIFICATION OF NUCLEIC ACID MOLECULES - The present invention is directed to methods for the production and isolation of nucleic acid molecules. In particular, the invention concerns isolation of mRNA molecules and the production and isolation of nucleic acid molecules (e.g., cDNA molecules or libraries), which may be single- or double-stranded. Additionally, the invention concerns selection and isolation of particular nucleic acid molecules of interest from a sample which may contain a population of molecules. Specifically, the invention concerns affinity-labeled primer-adapter molecules which allow improved isolation and production of such nucleic acid molecules, increasing both product recovery and speed of isolation. | 05-03-2012 |
| 20120107844 | IMMUNOSORBENT ASSAY SUPPORT AND METHOD OF USE - Embodiments of the present invention provide an immunosorbent assay support immobilized with an intermediate binding antibody and their method of use in an improved immunoassay format. | 05-03-2012 |
| 20120102054 | Systems and Methods for Annotating Biomolecule Data - Systems, methods, software and computer-usable media for annotating biomolecule-related data are disclosed. In certain exemplified embodiments, the biomolecules can be nucleic acids and the data can be sequence-related data. In various embodiments, systems can include one or more public or private biological attributes (e.g., annotation information databases, data storage devices and systems, etc.) sources, one or more genomic features data sources (e.g., genomic variant tools, genomic variant databases, genomic variant data storage devices and systems, etc.), a computing device (e.g., workstation, server, personal computer, mobile device, etc.) hosting an annotations module and/or a reporting module, and a client terminal. | 04-26-2012 |
| 20120100566 | CHEMILUMINESCENT COMPOSITIONS, METHODS, ASSAYS AND KITS FOR OXIDATIVE ENZYMES - Chemiluminescent compositions, methods, assays and kits for oxidative enzymes are described. Further disclosed are dioxetane compounds of the form: 0-0 ΛR R R T (i) where R can independently be any branched alkyl or cycloalkyl group which provides stabilization for the dioxetane or where both R groups together form a cycloalkyl or polycycloalkyl moiety spiro bound to the dioxetane ring, wherein each R group or the spiro bound moiety can be unsubstituted or substituted with one or more electron-withdrawing groups or electron donating groups, or groups providing preferential oxidative isozyme substrate recognition, and wherein Ri is an aryl group, or an alkyl group of 1-20 carbon atoms, which can be optionally substituted with 1 or more halogen atoms, and wherein T is an aryl or heteroaryl ring capable of emitting light upon enzyme activated decomposition of the dioxetane I. Kits, methods and assays are also disclosed that comprise the dioxetane compounds. | 04-26-2012 |
| 20120097257 | SURFACE TENSION CONTROLLED VALVES - The present teachings relate to surface tension controlled valves used for handling biological fluids. The valves controlled by optically actuating an electro-wetting circuit. | 04-26-2012 |
| 20120094871 | Particle Population and Methods of Making and Using - The invention provides particle compositions having applications in nucleic acid analysis. Nucleic acid polymer particles of the invention allow polynucleotides to be attached throughout their volumes for higher loading capacities than those achievable solely with surface attachment. In one aspect, nucleic acid polymer particles of the invention comprise polyacrylamide particles with uniform size distributions having low coefficients of variations, which result in reduced particle-to-particle variation in analytical assays. Such particle compositions are used in various amplification reactions to make amplicon libraries from nucleic acid fragment libraries. | 04-19-2012 |
| 20120094851 | Multi-through Hole Testing Plate for High Throughput Screening - A method for holding samples for analysis and an apparatus thereof includes a testing plate with a pair of opposing surfaces and a plurality of holes. Each of the holes extends from one of the opposing surfaces to the other one of the opposing surfaces. The holes are arranged in groups, where each group has at least two rows and two columns of holes. The groups are arranged in sets, where each set has at least two rows and two columns of groups. To analyze samples, at least one of the opposing surfaces of the testing plate is immersed in a solution to be analyzed. A portion of the solution enters openings for each of the holes in the immersed opposing surface. Once the holes are filled with solution, the testing plate is removed and is held above a supporting surface. Surface tension holds the solution in each of the holes. The solution in one or more of the holes is then analyzed and the solution in one of these holes is identified for further study. The location of the identified solution is marked based upon its location within a particular set and group of holes. | 04-19-2012 |
| 20120094332 | DNA POLYMERASES AND MUTANTS THEREOF - The present invention provides polypeptides having a nucleotide polymerase activity and method of enhancing polymerase activity. The polypeptides of the present invention may possess both a DNA-dependent DNA polymerase activity and an RNA-dependent DNA polymerase activity, i.e., a reverse transcriptase activity. The polypeptides of the present invention may be used in any application including, but not limited to, DNA sequencing reactions, amplification reactions, cDNA synthesis reactions, and combined cDNA synthesis and amplification reactions, e.g., RT-PCR. | 04-19-2012 |
| 20120089338 | COMPUTER IMPLEMENTED METHOD FOR INDEXING REFERENCE GENOME - A method for indexing a reference genome is provided. The method includes selecting a reference genome to index, calculating a first minimum index region size, assigning a first position number to a first index region of the reference genome, assigning a second position number to a second index region of the reference genome, and storing the association of the first and second position numbers to index regions in a hash table. The size of the first index region can be greater than or equal to the first minimum index region size. The second index region can overlap with at least one base included in the first index region. The first minimum index region size can be calculated based on the reference genome size. In yet other embodiments of the present teachings, a method for mapping a sequence read to a reference genome is provided wherein a sequence read is compared to the index regions stored in the indexing hash table, and the sequence read is mapped to and aligned against a location on the reference genome. Systems configured to carry out the methods are also provided. | 04-12-2012 |
| 20120088682 | Methods and Apparatus for Detecting Molecular Interactions Using FET Arrays - Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. | 04-12-2012 |
| 20120088233 | Method of Preparing Quality Control Material for FFPE - This specification relates to Formalin-fixed embedded quality control material for use for validation, verification, and to run controls for molecular assays. The quality control material can be used for a variety of tissues and for a variety of molecular assays. The quality control material can be used in commercial labs for validation and limit-of-detection analyses. | 04-12-2012 |
| 20120087832 | Apparatus and Method for Differentiating Multiple Fluorescence Signals by Excitation Wavelength - An apparatus and method are provided for differentiating multiple detectable signals by excitation wavelength. The apparatus can include a light source that can emit respective excitation light wavelengths or wavelength ranges towards a sample in a sample retaining region, for example, in a well. The sample can contain two or more detectable markers, for example, fluorescent dyes, each of which can be capable of generating increased detectable emissions when excited in the presence of a target component. The detectable markers can have excitation wavelength ranges and/or emission wavelength ranges that overlap with the ranges of the other detectable markers. A detector can be arranged for detecting an emission wavelength or wavelength range emitted from a first marker within the overlapping wavelength range of at least one of the other markers. | 04-12-2012 |
| 20120085660 | METHODS AND APPARATUS FOR DETECTING MOLECULAR INTERACTIONS USING FET ARRAYS - Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. | 04-12-2012 |
| 20120083427 | KINASE AND PHOSPHATASE ASSAYS - Compositions, methods, and kits for detecting and monitoring kinase, phosphatase and protein post-translational modification activity are described. The compositions typically include a peptide, a detectable moiety, and a protease cleavage site. Modification of a peptide by a kinase, phosphatase or other protein post-translational modification alters the proteolytic sensitivity of the peptide, resulting in a change of a detectable property of the composition. Panel assays for determining substrates or modulators of kinase, phosphatase or other protein post-translational modification activity are also described. | 04-05-2012 |
| 20120082980 | PNA Probes, Probe Sets, Methods and Kits Pertaining to the Detection of Candida - This invention is related to novel PNA probes, probe sets, methods and kits pertaining to the detection of one or more species of | 04-05-2012 |
| 20120082979 | COMPOSITIONS, METHODS, AND KITS FOR (MIS)LIGATING OLIGONUCLEOTIDES - Methods, reagents, and kits for (mis)ligating oligonucleotide probes or for identifying at least one target nucleotide are disclosed. One can enhance the generation of misligation product using a ligase under reaction conditions and with reagents where that particular ligase is prone to misligation. Alternatively, one can decrease or avoid generating misligation products using a particular ligase under reaction conditions and using reagents where that ligase is at least less prone to misligation. In certain embodiments, the recombinant ligase from | 04-05-2012 |
| 20120080610 | OPTICAL CAMERA ALIGNMENT - 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. | 04-05-2012 |
| 20120077706 | METHOD FOR ASSAYING PROTEIN-PROTEIN INTERACTION - The invention relates to a method for determining if a test compound, or a mix of compounds, modulates the interaction between two proteins of interest. The determination is made possible via the use of two recombinant molecules, one of which contains the first protein a cleavage site for a proteolytic molecules, and an activator of a gene. The second recombinant molecule includes the second protein and the proteolytic molecule. If the test compound binds to the first protein, a reaction is initiated whereby the activator is cleaved, and activates a reporter gene. | 03-29-2012 |
| 20120077702 | METHODS AND KITS FOR DETECTING PROSTATE CANCER BIOMARKERS - Provided herein are novel autoantibody biomarkers, and panels for detecting autoantibody biomarkers for prostate cancer, and methods and kits for detecting these biomarkers in the serum of individuals suspected of having prostate cancer. | 03-29-2012 |
| 20120077256 | MATCHED PAIR TRANSISTOR CIRCUITS - 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. | 03-29-2012 |
| 20120077211 | STABLE COMPOSITIONS COMPRISING CHROMOGENIC COMPOUNDS AND METHODS OF USE - Compositions, assays, methods, and kits are disclosed for use in applications that utilize oxidation of a chromogenic electron donor such as diaminobenzidine (DAB) to generate a signal. Applications include, but are not limited to, immunohistochemistry, chromogenic in situ hybridization, Western blots, Northern blots, Southern blots, ELISA assays, and microarray detection. The compositions, assays, methods, and kits disclosed herein make use of a novel, stabilized formulation of DAB and a novel, stabilized formulation of hydrogen peroxide. | 03-29-2012 |
| 20120077199 | IDENTIFICATION, MONITORING AND TREATMENT OF DISEASE AND CHARACTERIZATION OF BIOLOGICAL CONDITION USING GENE EXPRESSION PROFILES - A method provides an index that is indicative of the state of a subject, as to a biological condition, based on a sample from the subject. An embodiment of this method includes: deriving from the sample a profile data set, the profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables evaluation of the biological condition; and in deriving the profile data set, achieving such measure for each constituent under measurement conditions that are substantially repeatable; and applying values from the profile data set to an index function that provides a mapping from an instance of a profile data set into a single-valued measure of biological condition, so as to produce an index pertinent to the biological condition of the subject. | 03-29-2012 |
| 20120074956 | METHOD AND SYSTEM FOR DELTA DOUBLE SAMPLING - 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. | 03-29-2012 |
| 20120074165 | FLUIDICS SYSTEM FOR SEQUENTIAL DELIVERY OF REAGENTS - The invention provides a passive fluidics circuit for directing different fluids to a common volume, such as a reaction chamber or flow cell, without intermixing or cross contamination. The direction and rate of flow through junctions, nodes and passages of the fluidics circuit are controlled by the states of upstream valves (e.g. opened or closed), differential fluid pressures at circuit inlets or upstream reservoirs, flow path resistances, and the like. Free diffusion or leakage of fluids from unselected inlets into the common outlet or other inlets at junctions or nodes is prevented by the flow of the selected inlet fluid, a portion of which sweeps by the inlets of unselected fluids and exits the fluidics circuit by waste ports, thereby creating a barrier against undesired intermixing with the outlet flow through leakage or diffusion. | 03-29-2012 |
| 20120073667 | FLUIDICS SYSTEM FOR SEQUENTIAL DELIVERY OF REAGENTS - The invention provides a passive fluidics circuit for directing different fluids to a common volume, such as a reaction chamber or flow cell, without intermixing or cross contamination. The direction and rate of flow through junctions, nodes and passages of the fluidics circuit are controlled by the states of upstream valves (e.g. opened or closed), differential fluid pressures at circuit inlets or upstream reservoirs, flow path resistances, and the like. Free diffusion or leakage of fluids from unselected inlets into the common outlet or other inlets at junctions or nodes is prevented by the flow of the selected inlet fluid, a portion of which sweeps by the inlets of unselected fluids and exits the fluidics circuit by waste ports, thereby creating a barrier against undesired intermixing with the outlet flow through leakage or diffusion. The invention is particularly advantageous in apparatus for performing sensitive multistep reactions, such as pH-based DNA sequencing reactions. | 03-29-2012 |
| 20120072120 | AUTOMATIC THRESHOLD SETTING AND BASELINE DETERMINATION FOR REAL-TIME PCR - The invention discloses a system and methods for quantitating the presence of nucleic acid sequences by evaluation of amplification data generated using real-time PCR. In one aspect, the methods may be adapted to identify a threshold and threshold cycle for one or more reactions based upon evaluation of exponential and baseline regions for each amplification reaction. The methodology used in the analysis may be readily automated such that subjective user interpretation of the data is substantially reduced or eliminated. | 03-22-2012 |
| 20120071363 | METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 03-22-2012 |
| 20120071354 | NORMALIZED NUCLEIC ACID LIBRARIES AND METHODS OF PRODUCTION THEREOF - The present invention relates generally to methods for producing normalized nucleic acid libraries in which each member of the library can be isolated with approximately equivalent probability. In particular, the present methods comprise subtractive hybridization of a nucleic acid library with haptenylated (e.g., biotinylated, avidinated or streptavidinated) nucleic acid molecules that are complementary to one or more of the nucleic acid molecules of the library, such that the variation in the abundances of the individual nucleic acid molecules in the library is reduced. The invention also relates to production of normalized nucleic acid libraries (particularly cDNA libraries) in which contaminating nucleic acid molecules have been reduced or eliminated, and to normalized nucleic acid libraries produced by such methods. | 03-22-2012 |
| 20120070838 | Polymerase Assay with a FRET Substrate - This specification generally relates to non-radioactive methods of detecting nucleic acid polymerase activity and methods of detecting compounds that modulate nucleic acid polymerase activity. The activity may be measured in real-time using a real-time PCR instrument. | 03-22-2012 |
| 20120070832 | SE33 MUTATIONS IMPACTING GENOTYPE CONCORDANCE - Disclosed are primer set compositions, methods and kits for human identification using the highly complex sequence locus, SE33 (ACTBP2) in single and multiplex PCR reactions. Additionally, disclosed are three newly discovered single nucleotide polymorphisms (SNPs) within the SE33 locus that can cause discordance seen as mobility shift or allelic dropout. Also disclosed are kits useful in human identification. | 03-22-2012 |
| 20120070821 | Interference Control Panel for Evaluation of Analytical Assays For Samples Derived from Blood - The invention relates to quality control of analytical assays, particularly NAT assays of blood samples containing nucleic acids. A control panel containing quantified amounts of substances known to interfere with an analytical assay is used and compared with a reference sample in the analytical assay. A comparison of the assay results interference panel validates the assay and can serve as a periodic quality control check for the analytical assay as well as related methods and protocols. The use of the control panel of the invention can also determine whether interfering substances are present and establish under what conditions the analytical assay reliable. | 03-22-2012 |
| 20120067723 | Temperature Control of Chemical Detection System - An apparatus for detecting chemical reactions may be provided. The apparatus may comprise a chemical detection device. The chemical detection device may include a chemical sensor, which may be mounted on the chemical detection device. The apparatus may further comprise a valve block. The valve block may fluidly couple a plurality of reagent containers to the chemical detection device. The apparatus may further comprise a heat exchanger and a controller. The controller may control a fluid connection between the valve block and the chemical detection device. The controller may be also configured to adjust a temperature of a selected reagent from the plurality of reagent containers via the heat exchanger. The temperature of the selected reagent may be adjusted prior to the reagent entering the chemical detection device. | 03-22-2012 |
| 20120065105 | Chimeric Oligonucleotides for Ligation-Enhanced Nucleic Acid Detection, Methods and Compositions Therefor - Ligation-enhanced nucleic acid detection assay embodiments for detection of RNA or DNA are described. The assay embodiments rely on ligation of chimeric oligonucleotide probes to generate a template for amplification and detection. The assay embodiments are substantially independent of the fidelity of a polymerase for copying compromised nucleic acid. Very little background amplification is observed and as few as 1000 copies of target nucleic acid can be detected. Method embodiments are particularly adept for detection of RNA from compromised samples such as formalin-fixed and paraffin-embedded samples. Heavily degraded and cross-linked nucleic acids of compromised samples, in which classic quantitative real time PCR assays typically fail to adequately amplify signal, can be reliably detected and quantified. | 03-15-2012 |
| 20120065093 | Methods and Apparatus for Detecting Molecular Interactions Using FET Arrays - Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. | 03-15-2012 |
| 20120065090 | QUANTUM DOT-ENCODED BEAD SET FOR CALIBRATION AND QUANTIFICATION OF MULTIPLEXED ASSAYS, AND METHODS FOR THEIR USE - Control beads are disclosed that allow for improved quantitation of analytes in multiplexed bead assays. The control beads have a range of concentrations of calibration moieties that provide for the preparation of a titration curve. The titration curve can be used to quantify the concentration of the analytes. The titration curve can be used to correlate the signal obtained from a bead with the concentration (or absolute number of molecules) of the analyte bound to the bead. | 03-15-2012 |
| 20120064530 | SEQUENCE AMPLIFICATION WITH LOOPABLE PRIMERS - The present disclosure relates to the amplification of target nucleic acid sequences. This can be accomplished via the use of various primers. The use of these primers, as described herein, results in nucleic acid structures that can reduce the amplification of nonspecific hybridization events (such as primer dimerization) while allowing the amplification of the target nucleic acid sequences. | 03-15-2012 |
| 20120064012 | Uniform Fluorescent Microspheres with Hydrophobic Surfaces - Fluorescent microspheres for the measurement of blood flow are provided. The microspheres are substantially uniform in diameter and have a hydrophobic surface, which allows them to circulate more freely throughout bloodstream, while reducing immunogenicity, particle aggregation and bioaccumulation. The hydrophobic surface on each microsphere is generally comprised of polymeric material having a limited surface charge. | 03-15-2012 |
| 20120061733 | METHODS AND APPARATUS FOR DETECTING MOLECULAR INTERACTIONS USING FET ARRAYS - Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. | 03-15-2012 |
| 20120061256 | Methods and Apparatus for Detecting Molecular Interactions Using FET Arrays - Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. | 03-15-2012 |
| 20120061255 | Methods and Apparatus for Detecting Molecular Interactions Using FET Arrays - Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. | 03-15-2012 |
| 20120058566 | DETECTION OF IMMOBILIZED NUCLEIC ACID - The present invention provides methods for determining the presence of immobilized nucleic acid employing unsymmetrical cyanine dyes that are derivatives of thiazole orange, a staining solution and select fluorogenic compounds that are characterized as being essentially non-genotoxic. The methods comprise immobilizing nucleic acid, single or double stranded DNA, RNA or a combination thereof, on a solid or semi solid support, contacting the immobilized nucleic acid with an unsymmetrical cyanine dye compound and then illuminating the immobilized nucleic acid with an appropriate wavelength whereby the presence of the nucleic acid is determined. The cyanine dye compounds are typically present in an aqueous staining solution comprising the dye compound and a tris acetate or tris borate buffer wherein the solution facilitates the contact of the dye compound and the immobilized nucleic acid. Typically the solid or semi-solid support is selected from the group consisting of a polymeric gel, a membrane, an array, a glass bead, a glass slide, and a polymeric microparticle. Preferably, the polymeric gel is agarose or polyacrylamide. The methods employing the non-genotoxic compounds represent an improvement over commonly used methods employing ethidium bromide wherein the present methods retain the advantages of ethidium bromide, ease of use and low cost, but without the disadvantageous, known mutagen requiring special handling and waste procedures. | 03-08-2012 |
| 20120058481 | Quantitative Real Time PCR Assay Using FRET Dual-Labeled Primers - This specification generally relates to non-radioactive methods of non-radioactive real-time PCR using FRET dual-labeled primers. | 03-08-2012 |
| 20120056248 | ONE-TRANSISTOR PIXEL ARRAY - To reduce the pixel size to the smallest dimensions and simplest form of operation, a pixel may be formed by using only one ion sensitive field-effect transistor (ISFET). This one-transistor, or 1T, pixel can provide gain by converting the drain current to voltage in the column. Configurable pixels can be created to allow both common source read out as well as source follower read out. A plurality of the 1T pixels may form an array, having a number of rows and a number of columns and a column readout circuit in each column. | 03-08-2012 |
| 20120055813 | Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 03-08-2012 |
| 20120055811 | Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 03-08-2012 |
| 20120046877 | SYSTEMS AND METHODS TO DETECT COPY NUMBER VARIATION - In one aspect, a system for implementing a copy number variation analysis method, is disclosed. The system can include a nucleic acid sequencer and a computing device in communications with the nucleic acid sequencer. The nucleic acid sequencer can be configured to interrogate a sample to produce a nucleic acid sequence data file containing a plurality of nucleic acid sequence reads. In various embodiments, the computing device can be a workstation, mainframe computer, personal computer, mobile device, etc. | 02-23-2012 |
| 20120045848 | PYRENYLOXYSULFONIC ACID FLUORESCENT AGENTS - The invention provides a novel class of reactive fluorescent agents that are based on a pyrene sulfonic acid nucleus. The agents are readily incorporated into conjugates with other species by reacting the reactive group with a group of complementary reactivity on the other species of the conjugate. Also provided are methods of using the compounds of the invention to detect and/or quantify an analyte in a sample. In an exemplary embodiment, the invention provides multi-color assays incorporating the compounds of the invention. | 02-23-2012 |
| 20120045844 | METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 02-23-2012 |
| 20120045767 | MAGNETIC BEADS HAVING SURFACE GLYCOCONJUGATES AND USE THEREOF - Magnetic beads that include polyvalent ligands comprising various carbohydrates are described. Methods for fabricating such magnetic beads are also provided as well as methods of their use to capture and enrich pathogen cell population for subsequent culture, lysis and identification. | 02-23-2012 |
| 20120045368 | Chemical Coating of Microwell for Electrochemical Detection Device - The described embodiments may provide a method of fabricating a chemical detection device. The method may comprise forming a microwell above a CMOS device. The microwell may comprise a bottom surface and sidewalls. The method may further comprise applying a first chemical to be selectively attached to the bottom surface of the microwell, forming a metal oxide layer on the sidewalls of the microwell, and applying a second chemical to be selectively attached to the sidewalls of the microwell. The second chemical may lack an affinity to the first chemical. | 02-23-2012 |
| 20120041687 | IDENTIFICATION, MONITORING AND TREATMENT OF INFECTIOUS DISEASE AND CHARACTERIZATION OF INFLAMMATORY CONDITIONS RELATED TO INFECTIOUS DISEASE USING GENE EXPRESSION PROFILES - A method is provided in various embodiments for determining a profile data set for a subject with infectious disease or inflammatory conditions related to infectious disease based on a sample from the subject, wherein the sample provides a source of RNAs. The method includes using amplification for measuring the amount of RNA corresponding to at least 2 constituents from Table 1. The profile data set comprises the measure of each constituent, and amplification is performed under measurement conditions that are substantially repeatable. | 02-16-2012 |
| 20120040844 | Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 02-16-2012 |
| 20120040380 | OPTICALLY-DETECTABLE ENZYME SUBSTRATES AND THEIR METHOD OF USE - The present invention relates to compounds that are substrates for an enzyme, and upon reaction with the enzyme provide a detectable response, such as an optically detectable response. In particular, the compounds have utility in detecting the presence of a β-lactamase in a sample. In addition to the compounds, methods are disclosed for analyzing a sample for the presence of a β-lactmase, for example, as an indicator of expression of a nucleic acid sequence including a sequence coding for a β-lactmase. Kits are disclosed that include the disclosed compounds and additional components, for example, cells, antibodies, a β-lactmase or instructions for using the components in an assay. | 02-16-2012 |
| 20120037961 | Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 02-16-2012 |
| 20120035082 | Synthesis of Oligomers in Arrays - Systems, including apparatus and methods, for synthesis of oligomers in arrays. | 02-09-2012 |
| 20120035062 | ALTERNATIVE NUCLEOTIDE FLOWS IN SEQUENCING-BY-SYNTHESIS METHODS - A method for sequencing a polynucleotide strand by using sequencing-by-synthesis techniques. To address the problem of incomplete extension (IE) and/or carry forward (CF) errors that can occur in sequencing-by-synthesis reactions, an alternative flow ordering of dNTPs is used. In contrast to conventional flow orderings, the dNTPs are flowed in an ordering that is not a continuous repeat of an ordering of the four different dNTPs. This alternate flow ordering may reduce the loss of phasic synchrony in the population of template polynucleotide strands that result from IE and/or CF errors. | 02-09-2012 |
| 20120034622 | ACTIVATION AND MONITORING OF CELLULAR TRANSMEMBRANE POTENTIALS - The use of nanostructures to monitor or modulate changes in cellular membrane potentials is disclosed. | 02-09-2012 |
| 20120034607 | Methods and apparatus for measuring analytes using large scale fet arrays - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 02-09-2012 |
| 20120034606 | DETECTION OF SALMONELLA ENTERICA SUBSPECIES ENTERICA SEROVAR ENTERITIDIS IN FOOD AND ENVIRONMENTAL SAMPLES, METHODS AND COMPOSITIONS THEREFOR - Embodiments of the disclosure relate to compositions of isolated nucleic acid sequences, methods, workflows and kits of use thereof for detection of | 02-09-2012 |
| 20120030618 | SYSTEMS AND METHODS FOR ASSIGNING ATTRIBUTES TO A PLURALITY OF SAMPLES - Systems and methods for assigning attributes to a plurality of samples are provided. An exemplary system includes an instrument configured to perform an experiment on a plurality of samples in a multi-sample support device and to produce a plurality of measured values. The system further includes a computer system in communication with the instrument. The computer system is configured to receive the plurality of measured values from the instrument, store the plurality of measured values in a memory configured as a grid of cells representing the grid of the multi-sample support device, display the grid of cells in a graphical user interface, receive a selected cell from the graphical user interface, receive two or more attribute values for the selected cell from the graphical user interface, and store the two or more assigned attribute values along with a measured value of the selected cell in the memory configured as a grid of cells. | 02-02-2012 |
| 20120028335 | ANTI-VIRAL AZIDE-CONTAINING COMPOUNDS - Methods of using azide-modified biomolecules, such as fatty acids, carbohydrates and lipids, to treat a plant or an animal infected with a virus or to inhibit infectivity of a virus, such as the human immunodeficiency virus, are provided. Also provided are methods of labeling a human immunodeficiency virus with an azide-modified biomolecule, such as a fatty acid, a carbohydrate, or an isoprenoid lipid. The azide-modified biomolecules may be combined with a pharmaceutically acceptable excipient to produce a pharmaceutical composition, optionally containing another anti-viral agent and/or a delivery agent, such as a liposome. | 02-02-2012 |
| 20120028312 | METHODS AND COMPOSITIONS RELATING TO POLYPEPTIDES WITH RNASE III DOMAINS THAT MEDIATE RNA INTERFERENCE - The present invention concerns methods and compositions involving RNase III and polypeptides containing RNase III domains to generate RNA capable of triggering RNA-mediated interference (RNAi) in a cell. In some embodiments, the RNase III is from a prokaryote. RNase III activity will cleave a double-stranded RNA molecule into short RNA molecules that may trigger or mediate RNAi (siRNA). Compositions of the invention include kits that include an RNase III domain-containing polypeptide. The present invention further concerns methods using polypeptides with RNase III activity for generating RNA molecules that effect RNAi, including the generation of a number of RNA molecules to the same target. | 02-02-2012 |
| 20120028249 | ANTHRAQUINONE BASED NEAR IR EMITTING COMPOUNDS AND USES THEREOF - Disclosed are near IR emitting fluorescent compounds; methods of making and kits containing the described compounds; and their use in fluorescence-based detection of biological materials. | 02-02-2012 |
| 20120028244 | Anti-Viral Azide Containing Compounds - Methods of using azide-modified biomolecules, such as fatty acids, carbohydrates and lipids, to treat a plant, an insect or an animal infected with a virus or to inhibit infectivity of a virus, such as the human immunodeficiency virus, are provided. Also provided are methods of labeling a virus, such as human immunodeficiency virus, with an azide-modified biomolecule, such as a fatty acid, a carbohydrate, or an isoprenoid lipid. Also, provided are methods of tracking a virus in vivo, with an azide-modified biomolecule, such as a fatty acid, a carbohydrate, or an isoprenoid lipid. The azide-modified biomolecules may be combined with a pharmaceutically acceptable excipient to produce a pharmaceutical composition, optionally containing another anti-viral agent and/or a delivery agent, such as a liposome. | 02-02-2012 |
| 20120027846 | ANTI-VIRAL AZIDE CONTAINING COMPOUNDS - Methods of using azide-modified biomolecules, such as fatty acids, carbohydrates and lipids, to treat a plant, an insect or an animal infected with a virus or to inhibit infectivity of a virus, such as the human immunodeficiency virus, are provided. Also provided are methods of labeling a virus, such as human immunodeficiency virus, with an azide-modified biomolecule, such as a fatty acid, a carbohydrate, or an isoprenoid lipid. Also, provided are methods of tracking a virus in vivo, with an azide-modified biomolecule, such as a fatty acid, a carbohydrate, or an isoprenoid lipid. The azide-modified biomolecules may be combined with a pharmaceutically acceptable excipient to produce a pharmaceutical composition, optionally containing another anti-viral agent and/or a delivery agent, such as a liposome. | 02-02-2012 |
| 20120022966 | METHOD AND SYSTEM FOR PROVIDING A CUSTOM BIOPOLYMER TO A CUSTOMER - The present invention relates to a method and a system for providing a customer biopolymer to a customer. The sequence of a customer biopolymer is transferred to a production control system of a biopolymer service provider, synthesized on a production machine of the service provider and delivered to the customer, wherein no human action is necessary to initiate or control the synthesis process. | 01-26-2012 |
| 20120022795 | ARRAY CONFIGURATION AND READOUT SCHEME - The described embodiments may provide a chemical detection circuit that may comprise a plurality of first output circuits at a first side and a plurality of second output circuits at a second side of the chemical detection circuit. The chemical detection circuit may further comprise a plurality of tiles of pixels each placed between respective pairs of first and second output circuits. Each tile may include four quadrants of pixels. Each quadrant may have columns with designated first columns interleaved with second columns. Each first column may be coupled to a respective first output circuit in first and second quadrants, and to a respective second output circuit in third and fourth quadrants. Each second column may be coupled to a respective second output circuit in first and second quadrants, and to a respective first output circuit in third and fourth quadrants. | 01-26-2012 |
| 20120021951 | Apparatus for Assay, Synthesis and Storage, and Methods of Manufacture, Use, and Manipulation Thereof - The invention features methods of making devices, or “platens”, having a high-density array of through-holes, as well as methods of cleaning and refurbishing the surfaces of the platens. The invention further features methods of making high-density arrays of chemical, biochemical, and biological compounds, having many advantages over conventional, lower-density arrays. The invention includes methods by which many physical, chemical or biological transformations can be implemented in serial or in parallel within each addressable through-hole of the devices. Additionally, the invention includes methods of analyzing the contents of the array, including assaying of physical properties of the samples. | 01-26-2012 |
| 20120021464 | THERMOSTABLE REVERSE TRANSCRIPTASES AND USES THEREOF - The present invention is in the fields of molecular and cellular biology. The invention is generally related to reverse transcriptase enzymes and methods for the reverse transcription of nucleic acid molecules, especially messenger RNA molecules. Specifically, the invention relates to reverse transcriptase enzymes which have been mutated or modified to increase thermostability, decrease terminal deoxynucleotidyl transferase activity, and/or increase fidelity, and to methods of producing, amplifying or sequencing nucleic acid molecules (particularly cDNA molecules) using these reverse transcriptase enzymes or compositions. The invention also relates to nucleic acid molecules produced by these methods and to the use of such nucleic acid molecules to produce desired polypeptides. The invention also concerns kits comprising such enzymes or compositions. | 01-26-2012 |
| 20120021424 | Device and Method for Thermal Cycling - A thermal cycling device for performing nucleic acid amplification on a plurality of biological samples positioned in a sample well tray. The thermal cycling device includes a sample block assembly, an optical detection system, and a sample well tray holder configured to hold the sample well tray. The sample block assembly is adapted for translation between a first position permitting the movement of the sample well tray into alignment with sample block assembly, and a second position, upward relative to the first position, where the sample block assembly contacts the sample well tray. A method of performing nucleic acid amplification on a plurality of biological samples positioned in a sample well tray in a thermal cycling device is also provided. | 01-26-2012 |
| 20120015821 | Methods of Generating Gene Specific Libraries - The invention provides compositions and methods for generating a target enriched, sequencing ready library for resequencing at least one target region of interest from a nucleic acid containing sample. | 01-19-2012 |
| 20120015426 | BACTERIA FOR HIGH EFFICIENCY CLONING - Disclosed are novel bacterial hosts that are capable of high efficiency transformation with methylated and/or unmethylated nucleic acids, and that are bacteriophage resistant. Such bacteria contain: (1) an F′ episome that confers high efficiency transformability; (2) one or more mutations that allow transformation of methylated nucleic acids; (3) one or more mutations that allow transformation with unmethylated nucleic acids; and/or (4) one or more mutations that confer resistance to bacteriophage infection. Also disclosed are methods for transforming such bacteria, and kits that contain such bacteria (e.g., that have been made competent for transformation). | 01-19-2012 |
| 20120013392 | METHODS AND APPARATUS FOR MEASURING ANALYTES - Methods and apparatus relating to FET arrays including large 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. | 01-19-2012 |
| 20120011086 | SYSTEMS AND METHODS FOR SEQUENCE DATA ALIGNMENT QUALITY ASSESSMENT - A computer-implemented method for classifying alignments of paired nucleic acid sequence reads is disclosed. A plurality of paired nucleic acid sequence reads is received, wherein each read is comprised of a first tag and a second tag separated by an insert region. Potential alignments for the first and second tags of each read to a reference sequence is determined, wherein the potential alignments satisfies a minimum threshold mismatch constraint. Potential paired alignments of the first and second tags of each read are identified, wherein a distance between the first and second tags of each potential paired alignment is within an estimated insert size range. An alignment score is calculated for each potential paired alignment based on a distance between the first and second tags and a total number of mismatches for each tag. | 01-12-2012 |
| 20120009683 | Fluorescent Metal Ion Indicators with Large Stokes Shifts - The present invention provides fluorogenic compounds for the detection of target metal ions wherein the compounds exhibit a Stokes shift greater than 50 nm and the detectable signal is modulated by photoinduced electron transfer (PET). The present compounds consist of three functional elements, the ion sensing moiety (chelating moiety), the reporter moiety (fluorophore or fluorescent protein) and spacer or linker between the sensing and reporter moieties of the present compound that allows for PET upon binding of a metal ion and excitation by an appropriate wavelength. | 01-12-2012 |
| 20120009575 | INDUCIBLE NUCLEIC ACID TARGETS FOR DETECTION OF PATHOGENS, METHODS AND COMPOSITIONS THEREOF - The present application describes compositions, methods and kits for rapid detection and identification of various microorganisms using inducible RNA. Methods for rapidly detecting microorganisms by detecting expression of inducible RNA of target genes following induction of a target gene using an inducer are described. Some embodiments describe methods and workflows for rapidly detecting microbes such as, but not limited to, | 01-12-2012 |
| 20120009574 | DETECTION OF LISTERIA SPECIES IN FOOD AND ENVIRONMENTAL SAMPLES, METHODS AND COMPOSITIONS THEREOF - Embodiments of the disclosure relate to isolated nucleic acid sequences, methods of use thereof, and workflows for detection of several | 01-12-2012 |
| 20120004397 | VIOLET LASER EXCITABLE DYES AND THEIR METHOD OF USE - The present invention provides dye compounds optimally excited at about 400 nm and have a Stokes shift of at least about 80 nm. These dyes find use in detection of analyte in a sample and the preparation of dye-conjugates. | 01-05-2012 |
| 20120004138 | ELECTROPHORESIS APPARATUS FOR SIMULTANEOUS LOADING OF MULTIPLE SAMPLES - The present invention includes apparatus for simultaneous loading of multiple samples for molecular separation, including a separation area with walls wherein at least one of the walls has apertures having loading sites, a gel located within the separation area, and a plurality of wells within the gel. The apertures are connected to the plurality of wells by channels structurally configured to convey samples from the apertures to the wells. | 01-05-2012 |
| 20120004131 | MICROARRAYS AND USES THEREFOR - Methods of using microarrays to simplify analysis and characterization of genes and their function are provided. Such methods can be used to identify and characterize antibodies having binding affinity for a specific target antigen. A method of determining gene expression at the protein level by contacting an array of characterized or uncharacterized antibodies on a solid surface with one or more proteins and identifying the antibodies to which said protein(s) binds also is provided. This method can be used to compare the protein expression in two different populations of cells, such as normal cells and cancer cells or resting cells and stimulated cells. In addition, a method of determining gene expression at the protein level by contacting a microarray of nucleic acid samples derived from a variety of different sources with one or more nucleic acid probes then identifying the sample or samples to which the probe binds is provided. | 01-05-2012 |
| 20120003740 | ELECTROPORATION APPARATUS AND METHODS - This document discloses electroporation vessels, electrocompetent cells that have been aliquoted and frozen in electroporation vessels, and a number of other apparatuses, kits, and methods for electroporation. Some embodiments of electroporation vessels described herein may include a pair of opposing walls that are downwardly angled toward one another in a gap between two electrode surfaces. Further embodiments of devices and methods described herein may eliminate the need for an end user to transfer competent cells from a capped tube to electroporation cuvette, thereby saving time and producing less waste. | 01-05-2012 |
| 20120003698 | LINEAR AMPLIFICATION OF SHORT NUCLEIC ACIDS - 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. | 01-05-2012 |
| 20120003656 | SAMPLE PREPARATION FOR IN SITU NUCLEIC ACID ANALYSIS, METHODS AND COMPOSITIONS THEREFOR - Sample preparation processes for in situ RNA or DNA analysis, methods and compositions therefor are provided. Processes provided herein allow DNA or RNA analysis to be carried out in the same tube or on an aliquot of the prepared sample without centrifugation or extraction. The preparation process can be carried out at room temperature in as little as seven minutes and is amenable to high throughput processing using manual or robotic platforms. | 01-05-2012 |
| 20120003645 | Compositions, Methods and Kits for Nucleic Acid Synthesis and Amplification - The present invention is directed to compositions, methods and kits useful for the synthesis of nucleic acid molecules. More specifically, compositions, methods and kits are provided for the amplification of nucleic acid molecules in a one-step RT-PCR procedure comprising one or more agents used to increase tolerance to PCR inhibitors. | 01-05-2012 |
| 20120001779 | SERIALIZER CIRCUIT - The described embodiments may provide a chemical detection circuit. The chemical detection circuit may comprise a pixel array, a pair of analog-to-digital converter (ADC) circuit blocks, a pair of input/output (I/O) circuit blocks coupled to the pair of ADC circuit blocks respectively, and a plurality of serial link terminals coupled to the pair of IO circuit blocks. The pixel array may comprise a plurality of chemically-sensitive pixels formed in columns and rows. Each chemically-sensitive pixel may comprise: a chemically-sensitive transistor, and a row selection device. | 01-05-2012 |
| 20120001685 | CAPACITIVE CHARGE PUMP - One or more charge pumps may be used to amplify the output voltage from a chemically-sensitive pixel that comprises one or more transistors. A charge pump may include a number of track stage switches, a number of boost phase switches and a number of capacitors. The capacitors are in parallel during the track phase and in series during the boost phase, and the total capacitance is divided during the boost phase while the total charge remains fixed. Consequently, the output voltage is pushed up. | 01-05-2012 |
| 20120001646 | METHODS AND APPARATUS FOR TESTING ISFET ARRAYS - The invention provides testing of a chemically-sensitive transistor device, such as an ISFET device, without exposing the device to liquids. In one embodiment, the invention performs a first test to calculate a resistance of the transistor. Based on the resistance, the invention performs a second test to transition the testing transistor among a plurality of modes. Based on corresponding measurements, a floating gate voltage is then calculated with little or no circuitry overhead. In another embodiment, the parasitic capacitance of at least either the source or drain is used to bias the floating gate of an ISFET. A driving voltage and biasing current are applied to exploit the parasitic capacitance to test the functionality of the transistor. | 01-05-2012 |
| 20120001616 | COLUMN ADC - The described embodiments may provide a chemical detection circuit. The chemical detection circuit may comprise a column of chemically-sensitive pixels. Each chemically-sensitive pixel may comprise a chemically-sensitive transistor, and a row selection device. The chemical detection circuit may further comprise a column interface circuit coupled to the column of chemically-sensitive pixels and an analog-to-digital converter (ADC) coupled to the column interface circuit. Each column interface circuit and column-level ADC may be arrayed with other identical circuits and share critical resources such as biasing and voltage references, thereby saving area and power. | 01-05-2012 |
| 20120001615 | ARRAY COLUMN INTEGRATOR - The described embodiments may provide a chemical detection circuit with an improved signal-to-noise ration. The chemical detection circuit may include a current source, a chemical detection pixel, an amplifier and a capacitor. The chemical detection pixel may comprise a chemical-sensitive transistor that may have a first and second terminals and a row-select switch coupled between the current source and chemically-sensitive transistor. The amplifier may have a first input and a second input, with the first input coupled to an output of the chemically-sensitive transistor via a switch and the second input coupled to an offset voltage line. The capacitor may be coupled between an output of the amplifier and the first input of the amplifier. The capacitor and amplifier may form an integrator and may be shared by a column of chemical detection pixels. | 01-05-2012 |
| 20120001237 | TWO-TRANSISTOR PIXEL ARRAY - A two-transistor (2T) pixel comprises a chemically-sensitive transistor (ChemFET) and a selection device which is a non-chemically sensitive transistor. A plurality of the 2T pixels may form an array, having a number of rows and a number of columns. The ChemFET can be configured in a source follower or common source readout mode. Both the ChemFET and the non-chemically sensitive transistor can be NMOS or PMOS device. | 01-05-2012 |
| 20120001236 | ONE-TRANSISTOR PIXEL ARRAY WITH CASCODED COLUMN CIRCUIT - To reduce the pixel size to the smallest dimensions and simplest form of operation, a pixel may be formed by using only one ion sensitive field-effect transistor (ISFET). This one-transistor, or | 01-05-2012 |
| 20120001235 | CHEMICALLY SENSITIVE SENSOR WITH LIGHTLY DOPED DRAINS - A chemically sensitive sensor with a lightly doped region that affects an overlap capacitance between a gate and an electrode of the chemical sensitive sensor. The lightly doped region extends beneath and adjacent to a gate region of the chemical sensitive sensor. Modifying the gain of the chemically sensitive sensor is achieved by manipulating the lightly doped region under the electrodes. | 01-05-2012 |
| 20120001056 | CCD-BASED MULTI-TRANSISTOR ACTIVE PIXEL SENSOR ARRAY - A floating electrode is used to detect ions in close proximity to the electrode. The electrode is charge coupled to other electrodes and to other transistors to form a pixel that can be placed into an array for addressable readout. It is possible to obtain gain by accumulating charge into another electrode or onto a floating diffusion (FD) node or directly onto the column line. It is desirable to achieve both a reduction in pixel size as well as increase in signal level. To reduce pixel size, ancillary transistors may be eliminated and a charge storage node with certain activation and deactivation sequences may be used. | 01-05-2012 |
| 20120000274 | ION-SENSING CHARGE-ACCUMULATION CIRCUITS AND METHODS - An ion-sensitive circuit can include a charge accumulation device, to accumulate a plurality of charge packets as a function of an ion concentration of a fluid, and at least one control and readout transistor, to generate an output signal as a function of the accumulated plurality of charge packets, the output signal representing the ion concentration of the solution. The charge accumulation device can include a first charge control electrode above a first electrode semiconductor region, an electrically floating gate structure above a gate semiconductor region and below an ion-sensitive passivation surface, a second charge control electrode above a second electrode semiconductor region, and a drain diffusion region. The first control electrode can control entry of charge into a gate semiconductor region in response to a first control signal. The ion-sensitive passivation surface can be configured to receive the fluid. The second charge control electrode can control transmission of the plurality of charge packets out of the gate semiconductor region and into the drain diffusion region in response to a second control signal. The drain diffusion region can receive the plurality of charge packets from the gate semiconductor region via the second electrode semiconductor region. | 01-05-2012 |
| 20110318820 | Immobilized Buffer Particles and Uses Thereof - The disclosure relates to novel particle compositions and methods of making said compositions having applications in nucleic acid analysis, as well as apparatuses and systems for the same. | 12-29-2011 |
| 20110318813 | CHIMERIC PESTIVIRUS WITH INSERTION IN 3' NONTRANSLATED REGION (3' NTR) WITH STABLE REPLICATION AND RNASE RESISTANCE - 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. | 12-29-2011 |
| 20110318748 | Modified Proteins and Methods of Making and Using Same - Methods, compositions, systems, apparatuses and kits comprising modified proteins, particularly modified nucleic acid-binding proteins with altered buffering properties are provided. For example, in some embodiments, methods of forming modified proteins including one or more amino acid modifications to achieve desired pKa values are described. Furthermore, the invention provides methods for using such modified proteins in ion-producing reactions, such as ion-based nucleic acid sequencing reactions. | 12-29-2011 |
| 20110318743 | METHODS, WORKFLOWS, KITS, APPARATUSES, AND COMPUTER PROGRAM MEDIA FOR NUCLEIC ACID SAMPLE PREPARATION FOR NUCLEIC ACID SEQUENCING - A method for preparing a nucleic acid sample for nucleic acid sequencing includes amplifying a nucleic acid target sequence using a primer bound to a first capture substrate; capturing an amplified nucleic acid product by the first capture substrate; generating at least one sequencing ladder from the amplified nucleic acid product using at least one sequencing primer; capturing the at least one sequencing ladder by hybridizing the at least one sequencing ladder to a complementary capture compound on a second capture substrate; and removing the at least one sequencing ladder from the second capture substrate. The first and/or second capture substrate may include a magnetic particle. Other methods, workflows, kits, and computer program media for nucleic acid sample preparation are also disclosed. | 12-29-2011 |
| 20110318740 | Reduced Interference from Single Strand Binding Proteins - Disclosed, for example, are methods for detecting at least one target polynucleotide comprising cleaving a flap from a polynucleotide probe that is hybridized to a complementary target polynucleotide, and hybridizing the cleaved flap to a complementary capture probe immobilized on a surface, wherein said cleaving and/or hybridizing occurs in the presence of a single strand binding protein that is capable of binding single-stranded DNA, but that can bind neither the flap nor the capture probe. The cleaved flap and the complementary capture probe may each comprise PNA, RNA, LNA, L-DNA or other modified nucleotides or chimeras thereof that do not significantly bind to the single strand binding protein. | 12-29-2011 |
| 20110318241 | SYSTEMS AND METHODS FOR TRANSFER OF LIQUID SAMPLES - A system for preparing biological sample contains a body including a proximal side and a distal side, a plurality of mandrels, a plurality of resilient elements, a plurality of fluid dispensers, and one or more samples. The mandrels are moveably positioned within the body, where each resilient element engages a respective one of the mandrels. Each of the fluid dispensers is configured to engage a distal end of a corresponding one of the mandrels. Each sample comprises a solution containing one or more nucleic acid sequences contained within at least one of the fluid dispensers. | 12-29-2011 |
| 20110315930 | Compositions and methods for analyzing biomolecules using mass spectroscopy - Compositions and methods for mass spectroscopy are disclosed. The compositions and methods relate to the analysis of proteins and other biopolymers using mass spectroscopy, particularly matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS). | 12-29-2011 |
| 20110315927 | METHODS FOR PREPARATION OF NANOCRYSTALS USING A WEAK ELECTRON TRANSFER AGENT AND MISMATCHED SHELL PRECURSORS - Methods for preparing core/shell nanocrystals are provided, using mismatched shell precursors and an electron transfer agent to control the nucleation and growth phases of particle formation. | 12-29-2011 |
| 20110313143 | NUCLEIC ACID PURIFICATION APPARATUS AND METHOD - Provided herein is a clarification/binding device for the isolation of at least one target molecule from a sample. The clarification/binding device can comprise an clarification column and a binding column. The clarification column can be configured to receive the sample. Further, the clarification column can comprise a filter configured to filter at least one non-target molecule from the sample. The binding column can be configured to receive the filtered sample from the clarification column. The binding column can comprise a binding material for binding at least one target molecule. The clarification/binding device can be configured to filter the sample and bind at least one target molecule under negative pressure. Further provided herein is an apparatus for the isolation of a target molecule from a sample. The apparatus can comprise a top plate and a vacuum manifold comprising a first chamber and a second chamber. The top plate can be configured to be used with one or both of the first vacuum chamber and the second chamber of the vacuum manifold. Further provided herein are methods of use of the clarification/binding device and the vacuum apparatus and kits comprising the clarification/binding device and vacuum apparatus. | 12-22-2011 |
| 20110313129 | LARGE STOKES SHIFT DYES - Provided herein are heptamethine cyanine dyes having a large Stokes shift, and the salts and conjugates thereof. Also provided are methods of using and making such large Stokes shift dyes as fluorescence resonance energy transfer (FRET) acceptors or donors. | 12-22-2011 |
| 20110311963 | Method and Apparatus for Addressable Flow Cells in Single Molecule Sequencing - A method of sequencing a plurality of template nucleotide sequences includes immobilizing the plurality of template nucleotide sequences on a substrate. A first subset of the plurality of template nucleotide sequences is immobilized in a first field of view and a second subset of the plurality of template nucleotide sequences is immobilized in a second field of view. The first and second subsets are hybridized to a caged primer. The caged primer includes a caging group. The method further includes lysing the caging group from the caged primer in the first field of view and observing the first field of view to detect sequencing of the first subset of the plurality of template nucleotide sequences. | 12-22-2011 |
| 20110306520 | Methods, Kits and Compositions Pertaining to the Suppression of the Detectable Probe Binding to Randomly Distributed Repeat Sequences Genomic Nucleic Acid - This invention is directed to methods, kits, non-nucleotide probes as well as other compositions pertaining to the suppression of binding of detectable nucleic acid probes to undesired nucleotide sequences of genomic nucleic acid in assays designed to determine target genomic nucleic acid. | 12-15-2011 |
| 20110306505 | X-STR multiplex PCR amplification system - The methods and compositions provided herein relate to the discovery of several new STR alleles and a 20-plex multiplex assay for markers found on the human X chromosome. These X-STR markers have been found when used in a multiplex reaction to provide higher discriminatory power when compared to existing X-STR assay kits available commercially. Embodiments of the present teachings include methods for allelic determination of X-STR markers, amplification primers for the analysis of X-STR markers in a multiplex reaction, allelic ladders for analysis of X-STR markers, and kits for the analysis of X-STR markers. | 12-15-2011 |
| 20110306082 | "BENZOXAZOLE-BASED FLUORESCENT METAL ION INDICATORS" - Disclosed are benzoxazole-based compounds, kits, and methods of producing and using the described compounds in fluorescence-based detection of analytes (e.g., metal ions). Also disclosed are uses of benzoxazole-based compounds as ratiometric metal ion indicators. | 12-15-2011 |
| 20110301343 | METHODS AND COMPOSITIONS FOR DEPLETING ABUNDANT RNA TRANSCRIPTS - The present invention concerns a system for isolating, depleting, and/or preventing the amplification of a targeted nucleic acid, such as mRNA or rRNA, from a sample comprising targeted and nontargeted nucleic acids. | 12-08-2011 |
| 20110301041 | Modified Proteins and Methods of Making and Using Same - Methods, compositions, systems, apparatuses and kits comprising modified proteins, particularly modified nucleic acid-binding proteins with altered buffering properties are provided. For example, in some embodiments, methods of forming modified proteins including one or more amino acid modifications to achieve desired pKa values are described. Furthermore, the invention provides methods for using such modified proteins in ion-producing reactions, such as ion-based nucleic acid sequencing reactions. | 12-08-2011 |
| 20110300622 | Apparatus and Method for Transporting Sample Well Trays - An apparatus for transporting sample well trays with respect to a heating device is provided. The apparatus includes a sample well tray holder, a rotational actuator, and a biasing mechanism. The sample well tray holder includes a plate in which a sample well tray may be positioned. The sample well tray holder is configured to rotate about a first rotational axis. The rotational actuator is configured to rotate the sample well tray holder about the first rotational axis. The biasing mechanism is configured to urge the sample well tray holder in a generally upward direction along the first rotational axis. | 12-08-2011 |
| 20110300610 | Thermally Conductive Microplate - Embodiments according to the present teachings of a microplate comprising a main body portion having a first surface and an opposing second surface are disclosed. A plurality of wells are formed in the first surface, each of the plurality of wells being sized to receive an assay therein. A backing is coupled to the opposing second surface of the main body portion. | 12-08-2011 |
| 20110300076 | METHODS FOR PREPARATION OF ZnTe NANOCRYSTALS - Nanocrystals having a ZnTe core and methods for making and using them to construct core-shell nanocrystals are described. These core-shell nanocrystals are highly stable and provide quantum yields and stability suitable for applications such as flow cytometry, cellular imaging, and protein blotting, medical imaging, and other applications where cadmium toxicity is an issue. | 12-08-2011 |
| 20110300038 | Devices for Improving the Flatness of High-Density Microplates - The present teachings are methods and apparatuses for improving the flatness of high density microwell plates. The flattening devices impart a level of flatness that is equal to or better than a predetermined value thereby enabling the microwells to be precisely located and easily accessed. | 12-08-2011 |
| 20110300037 | Multi-Material Microplate and Method - A microplate assembly for performing an analytical method on an assay, comprising a microplate base structure having a plurality of apertures formed therethrough, and a plurality of well inserts coupled to the microplate base structure adjacent the apertures. Each of the plurality of well inserts has an open top portion and is adapted to receive an assay. The microplate base structure and the plurality of well inserts can comprise different materials. Methods of manufacturing the microplate assembly are also provided. | 12-08-2011 |
| 20110295514 | Computational Methods For Translating A Sequence Of Multi-Base Color Calls To A Sequence Of Bases - Disclosed are systems and methods for resequencing using color calls. A DNA sample is encoded and sequenced according to a multi-base code producing a string of read color calls for a fragment of the sample. A reference sequence is obtained. The string of read color calls is mapped to the reference sequence. A base sequence is extracted from the reference sequence. The base sequence is encoded as a string of reference color codes according to the multi-base code. The string of read color calls is aligned with the string of reference color codes and mismatches in the alignment are detected. One or more mismatches of the string of read color calls are annotated as inconsistent. The one or more inconsistent mismatches of the string of read color calls are corrected. The string of corrected read color calls is decoded to bases producing a read sequence. | 12-01-2011 |
| 20110294701 | Nucleic acid amplification using non-random primers - The present invention provides methods for selectively amplifying a target population of nucleic acid molecules (e.g., all mRNA molecules expressed in a cell type except for the most highly expressed mRNA species). The present invention also provides populations of oligonucleotides including the nucleic acid sequences set forth in SEQ ID NOS:1-933. These oligonucleotides can be used, for example, to prime the synthesis of cDNA molecules complementary to mRNA molecules isolated from mammalian blood without priming the synthesis of cDNA molecules complementary to globin mRNA, or ribosomal RNA molecules. | 12-01-2011 |
| 20110294122 | Synthesis of 2', 3'-Dideoxynucleosides for Automated DNA Synthesis and Pyrophosphorolysis Activated Polymerization - Methods for preparation of 2′,3′-dideoxynucleotides support structures, such as 2′,3′-dideoxyguanosine, 2′,3′-dideoxyadenosine, and 3′-deoxythymidine support structures are disclosed. Various methods of using such structures are also provided, such as their use for automated DNA synthesis and pyrophosphorolysis activated polymerization. | 12-01-2011 |
| 20110288781 | SYSTEMS AND METHODS FOR CHARACTERIZING A BIOLOGICAL CONDITION OR AGENT USING SELECTED GENE EXPRESSION PROFILES - Methods are provided for evaluating a biological condition of a subject using a calibrated profile data set derived from a data set having a plurality of members, each member being a quantitative measure of the amount of a subject's RNA or protein as distinct constituents in a panel of constituents. The biological condition may be a naturally occurring physiological state or may be responsive to treatment of the subject with one or more agents. Calibrated profile data sets may be used as a descriptive record for an agent. | 11-24-2011 |
| 20110287945 | Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 11-24-2011 |
| 20110287489 | RECOMBINATIONAL CLONING USING ENGINEERED RECOMBINATION SITES - Recombinational cloning is provided by the use of nucleic acids, vectors and methods, in vitro and in vivo, for moving or exchanging segments of DNA molecules using engineered recombination sites and recombination proteins to provide chimeric DNA molecules that have the desired characteristic(s) and/or DNA segment(s). | 11-24-2011 |
| 20110287447 | APPARATUS FOR AND METHOD OF AUTOMATED PROCESSING OF BIOLOGICAL SAMPLES - Provided herein is a bioprocessing device, bioprocessing card, and fluidics cartridge for performing automated bioprocessing of a sample. The bioprocessing card may include a plurality of pipette tips; and at least one pump in fluid communication with the plurality of pipette tips. In some embodiments, the pumps and the pipette tips are in fluid communication through a processing channel which may be a microscale channel. Also provided herein is an automated bioprocessing device comprising: at least one bioprocessing card; at least one fluidic cartridge; and an automated control system configured to control automated bioprocessing of a sample. Further provided herein are methods of use of the device, card, and cartridge. | 11-24-2011 |
| 20110287431 | MODIFIED OLIGONUCLEOTIDES AND APPLICATIONS THEREOF - Disclosed, among other things, are primers containing certain modified nucleobases in the 3′ terminal region of the primers that provide reduced formation of primer-dimers during amplification reactions, and various methods of use thereof. | 11-24-2011 |
| 20110287424 | METHYLATION-SPECIFIC COMPETITIVE ALLELE-SPECIFIC TAQMAN POLYMERASE CHAIN REACTION (CAST-PCR) - In some embodiments, the present inventions relates generally to compositions, methods and kits for use in discriminating between different methylated and/or unmethylated nucleic acid loci. In certain embodiments, the inventions provides for detecting or quantitating undifferentiated embryonic stem cells in a population of differentiated cells. The invention is also useful for discriminating between fetal versus maternal cells, or healthy versus infected cells, or normal versus cancerous cells, or detecting reduction in viral load or measuring therapeutic efficiency in a patient, and more. | 11-24-2011 |
| 20110281767 | COMPOSITIONS AND METHODS FOR MOLECULAR BIOLOGY - The present invention provides materials and methods for the utilization of the specific interaction of replication termination sequences with their binding proteins in molecular biology applications. | 11-17-2011 |
| 20110281755 | Karyotyping Assay - This disclosure relates to methods and kits for karyotyping in which chromosomes are interrogated by amplifying loci that are not within copy number variable regions thereof. | 11-17-2011 |
| 20110281741 | Method and Apparatus for Rapid Nucleic Acid Sequencing - Methods and apparatus relating to FET arrays including large 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. | 11-17-2011 |
| 20110281737 | Method and Apparatus for Rapid Nucleic Acid Sequencing - Methods and apparatus relating to FET arrays including large 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. | 11-17-2011 |
| 20110281276 | NUCLEIC ACID-FREE THERMOSTABLE ENZYMES AND METHODS OF PRODUCTION THEREOF - The present invention provides thermostable enzymes, such as DNA polymerases and restriction endonucleases, that are substantially free from contamination with nucleic acids. The invention also provides methods for the production of these enzymes, and kits comprising these enzymes which may be used in amplifying or sequencing nucleic acid molecules, including through use of the polymerase chain reaction (PCR). | 11-17-2011 |
| 20110281266 | Identification of Nucleic Acids - This disclosure relates to methods for identifying target nucleic acids in a sample by detecting an amplified sequence corresponding to the target using a detectable probe and by monitoring its melting temperature (T | 11-17-2011 |
| 20110276317 | SYSTEMS AND METHODS FOR MODEL-BASED qPCR - A method for determining a cycle threshold for a PCR amplification curve is provided. The method includes receiving a data set for a plurality of biological samples for a PCR amplification reaction. The data set includes a plurality of amplification curves, each amplification curve associated with a biological sample of the plurality of biological samples. The method further includes performing a nonlinear optimization comprising a fit of each amplification curve to a complementary modeled amplification curve to determine a best-fit set of parameters for a modeled efficiency curve and associated amplification curve. The modeled amplification curve is based on a modeled efficiency curve. The method includes determining a cycle threshold value for each biological sample based on a complementary relationship of the modeled efficiency curve to the modeled amplification curve. In an embodiment, the nonlinear optimization is a constrained nonlinear optimization. | 11-10-2011 |
| 20110275522 | Method and Apparatus for Rapid Nucleic Acid Sequencing - Methods and apparatus relating to FET arrays including large 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. | 11-10-2011 |
| 20110275125 | System and Method for Processing a Biological Sample - Systems and methods for processing a biological sample are provided herein. For example, the system can be configured to deaggregate/declump a sample before, during, and/or after sample preparation and/or sample analysis. For example, the system can include a deaggregation device/system in communication with, for example, a nucleic acid amplification process (e.g., an ePCR system). Various embodiments of the deaggregation device are provided herein. For example, in some embodiments, the deaggregation device can include a valve, a valve manifold, a conduit, a channel, or some combinations thereof. | 11-10-2011 |
| 20110275101 | METHOD FOR USING DIVISION ARRESTED CELLS IN SCREENING ASSAYS - Division arrested cells are used in screening assays to determine the effect of a substance of interest on the cells. The division arrested cells can be used in drug screening assays, signal transduction assays, and are especially useful in large scale, high throughput assays. | 11-10-2011 |
| 20110275071 | Methods and Reagents for Combined PCR Amplification - An oligonucleotide probe is disclosed, the probe including an oligonucleotide, a fluorescer molecule attached to a first end of the oligonucleotide and a quencher molecule attached to the opposite end of the oligonucleotide. The probe is rendered impervious to digestion by the 5′→3′ exonuclease activity of a polymerase and the 5′→3′ extension of by a polymerase. The invention also includes methods for performing combined PCR amplification and hybridization probing, one such method including the steps of contacting a target nucleic acid sequence with PCR reagents and an oligonucleotide probe as described above, and subjecting these reagents to thermal cycling. One preferred refinement of the above method further includes the addition of a strand displacer to facilitate amplification. Additional similar combined PCR hybridization methods are disclosed, such methods not requiring probes having their 5′ ends protected, wherein (i) the polymerase lacks 5′→3′ exonuclease activity, (ii) a 5′→3′ exonuclease inhibitor is included, and (iii) an exonuclease deactivation step is performed. | 11-10-2011 |
| 20110275055 | THERMAL UNIFORMITY FOR THERMAL CYCLER INSTRUMENTATION USING DYNAMIC CONTROL - A method for performing polymerase chain reactions (PCR) for improving thermal non-uniformity is provided. The method includes measuring a first temperature, by a first sensor, of a first sample block sector of a sample block and measuring a second temperature, by a second sensor, of a second sample block sector of the sample block that is adjacent to the first sample block sector. The method further includes calculating, by a thermoelectric controller, a difference in temperature between the first temperature and the second temperature and adjusting, by the thermoelectric controller, the first temperature of the first sample block sector based on the difference in temperature by using one or more thermoelectric coolers. The one or more thermoelectric coolers is configured to heat or cool the first sample block sector by adjusting power output from the thermoelectric controller. | 11-10-2011 |
| 20110270533 | SYSTEMS AND METHODS FOR ANALYZING NUCLEIC ACID SEQUENCES - Nucleic acid sequence mapping/assembly methods are disclosed. The methods initially map only a contiguous portion of each read to a reference sequence and then extends the mapping of the read at both ends of the mapped contiguous portion until the entire read is mapped (aligned). In various embodiments, a mapping score can be calculated for the read alignment using a scoring function, score (i, j)=M+mx, where M can be the number of matches in the extended alignment, x can be the number of mismatches in the alignment, and m can be a negative penalty for each mismatch. The mapping score can be utilized to rank or choose the best alignment for each read. | 11-03-2011 |
| 20110270532 | Systems And Methods For Identifying Exon Junctions From Single Reads - Systems and methods are used to identify an exon junction from a single read of a transcript. A transcript sample is interrogated and a read sequence is produced using a nucleic acid sequencer. A first exon sequence and a second exon sequence are obtained using the processor. The first exon sequence is mapped to a prefix of the read sequence using the processor. The second exon sequence is mapped to a suffix of the read sequence using the processor. A sum of a number of sequence elements of the first exon sequence that overlap the prefix of the read sequence, of a number of sequence elements of the second exon sequence that overlap the suffix of the read sequence, and of a constant is calculated using the processor. If the sum equals a length of the read sequence, a junction is identified in the read using the processor. | 11-03-2011 |
| 20110269120 | METHODS AND COMPOSITIONS FOR DETECTING PROMOTER ACTIVITY AND EXPRESSING FUSIONPROTEINS - The present invention provides nucleic acid molecules comprising one or more nucleic acid sequences encoding a polypeptide having a detectable activity. The present invention also provides methods of joining such nucleic acid molecules to nucleic acid molecules to be assayed for promoter activity. The present invention also relates to methods of preparing fusion proteins comprising a polypeptide of interest and a polypeptide having a detectable activity. | 11-03-2011 |
| 20110263463 | INTEGRATED SENSOR ARRAYS FOR BIOLOGICAL AND CHEMICAL ANALYSIS - 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 μm 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. In one embodiment, the characteristic of said chemical or biological sample is a concentration of a charged species and wherein each of said chemical field effect transistors is an ion-sensitive field effect transistor having a floating gate with a dielectric layer on a surface thereof, the dielectric layer contacting said sample fluid and being capable of accumulating charge in proportion to a concentration of the charged species in said sample fluid. In one embodiment such charged species is a hydrogen ion such that the sensors measure changes in pH of the sample fluid in or adjacent to the sample-retaining region thereof. Apparatus and chips of the invention may be adapted for large scale pH-based DNA sequencing and other bioscience and biomedical applications. | 10-27-2011 |
| 20110263005 | PIPETTE TIP FOR ELECTROPORATION DEVICE - Provided herein is a pipette tip ( | 10-27-2011 |
| 20110263001 | Compositions and Methods for Engineering Cells - The disclosure relates generally to genetic manipulation of stem and primary cells and to reprogramming of somatic cells, more specifically, human cells. In particular, compositions and methods are disclosed for the generation and maintenance of such engineered cells. | 10-27-2011 |
| 20110262965 | CELL CULTURE MEDIUM COMPRISING SMALL PEPTIDES - Cell culture media, concentrated media and feeds, methods of manufacturing cell culture media and feeds, and methods of culturing cells are provided. One or more small peptides, including dipeptides are added to the cell culture media to provide improved stability and improved conditions for culturing cells. | 10-27-2011 |
| 20110262947 | Isotopically-Labeled Proteome Standards - The invention provides methods for quantifying biomolecules, such as polypeptides in mass spectrometric analysis. The methods include use of a biomolecule standard having at least one atomic isotope different than that of the naturally occurring isotopes in the biomolecule of interest. Methods of the present invention also include methods for quantifying biomolecules where the copy biomolecule standard is made by expressing the biomolecule using a recombinant cell. Further included are the biomolecule standards themselves, method for making such standards, kits, systems, reagents, and engineered cells relating to the use of biomolecule standards in mass spectrometric analysis. | 10-27-2011 |
| 20110262903 | Modified Proteins and Methods of Making and Using Same - Methods, compositions, systems, apparatuses and kits comprising modified proteins, particularly modified nucleic acid-binding proteins with altered buffering properties are provided. For example, in some embodiments, methods of forming modified proteins including one or more amino acid modifications to achieve desired pKa values are described. Furthermore, the invention provides methods for using such modified proteins in ion-producing reactions, such as ion-based nucleic acid sequencing reactions. | 10-27-2011 |
| 20110257385 | METHODS FOR FLIP-STRAND IMMOBILIZING AND SEQUENCING NUCLEIC ACIDS - Provided herein are compositions, materials, methods and kits for immobilizing a template polynucleotide in a first orientation, and immobilizing a complementary sequence of the template polynucleotide in an orientation that is flipped compared to the orientation of the template polynucleotide. Provided herein are adaptive oligonucleotides that can be used in various nucleic acid manipulations to generate immobilized complement polynucleotides that are flipped in orientation compared to the orientation of the immobilized template polynucleotides. | 10-20-2011 |
| 20110257049 | Sample Block Apparatus and Method for Maintaining a Microcard on a Sample Block - A thermal cycling device for thermally cycling samples of biological material contained in a microcard having a top and bottom surface. The thermal cycling device can include a sample block having an upper surface configured for engaging the bottom surface of a microcard, a vacuum device, and a temperature control system operatively connected with the sample block. The upper surface of the sample block may include a plurality of channels, the channels defining spaces between the sample block and the bottom surface of a microcard that may be positioned thereon. The vacuum device may be in fluid communication with the sample block for drawing gas out of the spaces defined by the channels in the sample block. The vacuum device may be configured for substantially maintaining a vacuum between the sample block and microcard so that a retention force is imparted on the microcard to urge the microcard toward the sample block. Methods of maintaining a microcard on a sample block of a thermal cycling device are also provided. | 10-20-2011 |
| 20110257039 | REVERSE TRANSCRIPTION PRIMERS AND METHODS OF DESIGN - The present invention provides novel algorithms for designing oligonucleotides that do not substantially hybridize to a small group of unwanted transcripts, while hybridizing to most other transcripts. Such oligonucleotides are particularly useful as primers for reverse transcription. The invention also provides compositions containing oligonucleotides that do not substantially hybridize to a small group of unwanted transcripts, while hybridizing to most other transcripts. | 10-20-2011 |
| 20110257031 | Nucleic acid, biomolecule and polymer identifier codes - Provided herein are systems, compositions and methods for tracking, sorting and/or identifying sample polynucleotides using nucleic acid barcodes. The barcodes provided herein are oligonucleotides that are designed to be uniquely identifiable. The nucleic acid barcodes have properties that permit them to be sequenced with high accuracy and/or reduced error rates. In some embodiments, the nucleic acid barcodes are designed to have certain nucleotide sequences that make up overlapping dibase color positions (also called color positions). The order of the overlapping dibase color positions can be determined using fluorophore-encoded dibase probes in a fluorophore color calling scheme to give high fidelity reads. | 10-20-2011 |
| 20110257019 | Directed Enrichment of Genomic DNA for High-Throughput Sequencing - The present invention provides microarrays of oligonucleotide primer pairs, and in particular, microarrays of primers that comprise at least one cleavable linkage. Also provided are methods to capture oligonucleotide primer pairs from one or more microarrays, and methods to use the captured oligonucleotide primer pairs, such as for amplification of a target polynucleotide sequence. In addition, methods of using a microarray to isolate, purify and/or amplify a target polynucleotide are provided. | 10-20-2011 |
| 20110256616 | Cooling in a Thermal Cycler Using Heat Pipes - A device for amplifying a nucleic acid sample may include a sample holder configured to receive a nucleic acid sample, a heating system configured to raise the temperature of the sample, a cooling system configured to lower the temperature of the sample, and a controller configured to operably control the heating system and the cooling system to cycle the device through a desired time-temperature profile. The cooling system may include at least one heat pipe and a heat sink and the at least one heat pipe may include a first portion disposed proximate to the sample holder and a second portion disposed proximate to the heat sink. | 10-20-2011 |
| 20110254963 | Methods and Systems for In Situ Calibration of Imaging in Biological Analysis - Software, methods, and systems for calibrating photometric devices are provided. These involve using a non-uniform test illumination field to approximate a photon transfer curve by calculating stable pixel values and statistical dispersions on a pixel-by-pixel basis. | 10-20-2011 |
| 20110252353 | Visualization Tool for qPCR Genotyping Data - Systems and methods are used to display data obtained from a qPCR instrument. Each of two or more samples is probed with a first labeling probe and a second labeling probe. A first data set is received from a qPCR instrument at a first cycle number that includes for each sample a first labeling probe intensity, and a second labeling probe intensity. A second data set is received at a second cycle number that includes for each sample a first labeling probe intensity and a second labeling probe intensity. A first plot of first labeling probe intensity as a function of second labeling probe intensity is created using the first data set. A second plot of first labeling probe intensity as a function of second labeling probe intensity is created using the second data set. The first plot and the second plot are displayed in response to user defined input to provide dynamic and real-time analysis of genotyping data. | 10-13-2011 |
| 20110252051 | Systems and Methods for Genotyping by Angle Configuration Search - Methods and systems for the analysis of genotyping data are presented. According to various embodiments of methods and systems, an angle configuration search may be performed. In various embodiments, an exhaustive search over the entirety of an angle configuration space may be performed to provide a fit to a plurality of angles determined for a plurality of points in a data set generated from a plurality of biological samples. For various embodiments, the angle configuration space may be defined to ensure that a global fit may be determined. According to various methods and systems, a data base of possible angle configurations may be searched, in which each angle configuration may include three angles. According to various methods and systems, a data base of possible angle configurations may include for each angle configuration a probability that the angle configuration may occur. | 10-13-2011 |
| 20110251382 | ISOLATION OF NUCLEIC ACID - The present invention provides a method of isolating nucleic acid from a sample, said method comprising contacting said sample with a detergent and a solid support, whereby soluble nucleic acid in said sample is bound to the support, and separating said support with bound nucleic acid from the sample. Where the method of the invention is used to isolate DNA, it may conveniently be couple with a further step to isolate RNA from the same sample. | 10-13-2011 |
| 20110251261 | COMPOSITIONS AND METHODS FOR INHIBITION OF NUCLEIC ACIDS FUNCTION - The invention relates generally to compositions and methods for inhibiting the function of target nucleic acids by sequence specific binding. The compositions and methods can be used for inhibition of micro RNAs and other relatively short non-coding RNAs. | 10-13-2011 |
| 20110251110 | Methods for Sequencing Individual Nucleic Acids Under Tension - 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. | 10-13-2011 |
| 20110251109 | Fluidic methods for devices for parallel chemical reactions - Fluidic methods and devices for conducting parallel chemical reactions are disclosed. The methods are based on the use of in situ photogenerated reagents such as photogenerated acids, photogenerated bases, or any other suitable chemical compounds that produce active reagents upon light radiation. The present invention describes devices and methods for performing a large number of parallel chemical reactions without the use of a large number of valves, pumps, and other complicated fluidic components. The present invention provides microfluidic devices that contain a plurality of microscopic vessels for carrying out discrete chemical reactions. Other applications may include the preparation of microarrays of DNA and RNA oligonucleotides, peptides, oligosaccharides, phospholipids and other biopolymers on a substrate surface for assessing gene sequence information, screening for biological and chemical activities, identifying intermolecular complex formations, and determining structural features of molecular complexes. | 10-13-2011 |
| 20110251078 | Methods for Sequencing Individual Nucleic Acids Under Tension - 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. | 10-13-2011 |
| 20110250700 | Methods for Sequencing Individual Nucleic Acids Under Tension - 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. | 10-13-2011 |
| 20110250699 | Fluorescent Dye Compounds, Conjugates and Uses Thereof - The present teachings generally relate to fluorescent dyes, linkable forms of fluorescent dyes, energy transfer dyes, reagents labeled with fluorescent dyes and uses thereof. | 10-13-2011 |
| 20110250672 | MUTANT DNA POLYMERASES AND USES THEROF - The present invention relates to mutant DNA polymerases which incorporate dideoxynucleotides with about the same efficiency as deoxynucleotides. The present invention also related to mutant DNA polymerases which also have substantially reduced 5′-to-3′ exonuclease activity or 3′-to-5′ exonuclease activity. The invention also relates to DNA molecules coding for the mutant DNA polymerases, and hosts containing the DNA molecules. | 10-13-2011 |
| 20110250603 | Methods for Sequencing Individual Nucleic Acids Under Tension - 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. | 10-13-2011 |
| 20110250596 | METHODS, KITS AND COMPOSITIONS PERTAINING TO LINEAR BEACONS - This invention is directed to methods for determining amplified nucleic acid using Linear Beacons | 10-13-2011 |
| 20110248320 | METHODS AND APPARATUS FOR MEASURING ANALYTES - Methods and apparatus relating to FET arrays including large 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. | 10-13-2011 |
| 20110248319 | METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 10-13-2011 |
| 20110247933 | METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 10-13-2011 |
| 20110245462 | Non-Fluorescent Quencher Compounds and Biomolecular Assays - Bis-diazo, triaryl and aryldiazo-N-arylphenazonium quencher moieties, substituted with electron-withdrawing and electron-donating substituents which induce polarity in the delocalized aryl/diazo ring systems, are useful as labels when attached to biomolecules such as polynucleotides, nucleosides, nucleotides and polypeptides. The quencher moieties are non-fluorescent and accept energy transfer from fluorescent reporter labels by any energy-transfer mechanism, such as FRET. | 10-06-2011 |
| 20110244548 | DNA Polymerases Having Improved Labeled Nucleotide Incorporation Properties - The present invention relates to mutant DNA polymerases that exhibit reduced discrimination against labeled nucleotides into polynucleotides. The DNA polymerases of the invention have at least one mutation in the nucleotide label interaction region of the enzyme such the mutation results in reduced discrimination against labeled nucleotides. The nucleotide label interaction regions is located at portions of the O-helix, (ii) the K helix, and (iii) the inter O-P helical loop of Taq DNA polymerase or analogous positions in other DNA polymerases. In addition to providing novel mutant DNA polymerases, the invention also provides polynucleotides encoding the subject mutant DNA polymerases. The polynucleotides provided may comprise expression vectors for the recombinant production of the mutant polymerases. The invention also provides host cells containing the subject polynucleotides. The invention also includes numerous methods of using the subject DNA polymerases, including uses for chain termination sequencing and PCR. Another aspect of the invention is to provide kits for synthesizing fluorescently labeled polynucleotides in accordance with the methods of the invention. Kits of the invention comprise a mutant DNA polymerase of the invention and a fluorescently labeled nucleotide that exhibits reduced discrimination with respect to the mutant DNA polymerase in the kit. | 10-06-2011 |
| 20110241081 | METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 10-06-2011 |
| 20110237444 | METHODS OF MAPPING GENOMIC METHYLATION PATTERNS - The invention relates to sample analysis work flows for increasing the efficiency of experiments. Compositions and methods are described for selectively increase the abundance of methylated nucleic acid over non-methylated nucleic acid, followed by analysis of the nucleic acid to identify methylation sites. | 09-29-2011 |
| 20110237443 | Amelogenin SNP on Chromosome X - Disclosed are methods for gender determination in the intron 1 region of the amelogenin locus and a newly discovered single nucleotide polymorphism (SNP) within the X chromosome of the amelogenin locus which can cause allelic dropout. Also disclosed are kits useful in gender determination. | 09-29-2011 |
| 20110236984 | DNA SEQUENCING METHODS AND DETECTORS AND SYSTEMS FOR CARRYING OUT THE SAME - In some embodiments, an analyte detection system is provided that includes a nanochannel, an electrode arrangement, and a plurality of nanoFET devices disposed in the nanochannel. A plurality of nucleic acid base detection components can be used that include a plurality of nanopores, a plurality of nanochannels, a plurality of hybridization probes, combinations thereof, and the like. According to other embodiments of the present teachings, different coded molecules are hybridized to a target DNA molecule and used to detect the presence of various sequences along the target molecule. A kit including mixtures of coded molecules is also provided. In some embodiments, devices including nanochannels, nanopores, and the like, are used for manipulating movement of DNA molecules, for example, in preparation for a DNA sequencing detection. Nanopore structures and methods of making the same are also provided as are methods of nucleic acid sequencing using the nanopore structures. Surface-modified nanopores are provided as are methods of making them. In some embodiments, surfaced-modified nanopores for slowing the translocation of single stranded DNA (ssDNA) through the nanopore are provided, as are nanopores configured to detect each of a plurality of different bases on an ssDNA strand. | 09-29-2011 |
| 20110236980 | Automated Synthesis or Sequencing Apparatus and Method for Making and Using Same - An apparatus and method based on the apparatus is disclosed for automated single molecule or molecular assemblage detection via light irradiation and detection of transient FRET between a donor or acceptor bound to an immobilized single molecule or molecular assemblage and a corresponding acceptor or donor associated with, covalently bonded to, a reagent, where the donor or acceptor associated with the reagent is transiently in FRET proximity to the acceptor or donor associated with the immobilized molecule or molecular assemblage. | 09-29-2011 |
| 20110236964 | DNA Sequencing System - An apparatus for detecting labeled beads is provided. The apparatus can include: one or more irradiation sources disposed for irradiating the one or more detection zones with radiation; at least one detector disposed for collecting charges corresponding to light signals emitted from labeled beads in the one or more detection zones, which have been excited by the radiation; and a system coupled to the at least one detector for effecting time delay integration of the charges by accumulating the charges before reading the charges at the output of the at least one detector. | 09-29-2011 |
| 20110232356 | Electrophoretic Analysis System Having In-Situ Calibration - An electrophoretic system having a plurality of separation lanes is provided with an automatic calibration feature in which each lane is separately calibrated. For each lane, the calibration coefficients map a spectrum of received channel intensities onto values reflective of the relative likelihood of each of a plurality of dyes being present. Individual peaks, reflective of the influence of a single dye, are isolated from among the various sets of detected light intensity spectra, and these can be used to both detect the number of dye components present, and also to establish exemplary vectors for the calibration coefficients which may then be clustered and further processed to arrive at a calibration matrix for the system. The system thus permits one to use different dye sets to tag DNA nucleotides in samples which migrate in separate lanes, and also allows for in-situ calibration with new, previously unused dye sets. | 09-29-2011 |
| 20110231758 | SYSTEMS AND METHODS FOR GENERATING AUTOMATED SOFTWARE WORKFLOWS FOR BIOLOGICAL TESTING - The workflow application integrates with a research software application associated with a laboratory instrument to provide a user with step-by-step instructions on how to follow the workflow steps of a laboratory experiment. The instructions are dynamically tailored, according to the nature of the workflow, the samples being experimented upon and/or the operating states of the instrument and/or the research software application. The workflow application significantly reduces the learning curve to operate sophisticated laboratory instruments. In a genetic testing instrument the workflow application can prescribe the need for control samples and can optimize the layout of samples within the instrument's sample receiving plate or fixture. | 09-22-2011 |
| 20110231277 | CIS-Regulatory Modules - A process for identifying a cis-regulatory module including aligning a target sequence with at least one sequence from a moderately distant species; determining a non-coding region of the target sequence, wherein the non-coding region comprises at least one of a high level of conservation and a suppression of indels; and identifying at least one cis-regulatory module in the target sequence is disclosed. Also disclosed is a method for providing assays to a consumer. | 09-22-2011 |
| 20110231132 | Systems And Methods For Baseline Correction Using Non-Linear Normalization - Systems and methods are provided for calibrating emission data or other information signals collected during a polymerase chain reaction (PCR), amplification reaction, assay, process, or other reaction. Calibration of multiple detectable materials can be achieved during a single cycle or run, or during a plurality of runs of the reaction. A reading from every well, container, or other support region of a sample support does not have to be taken. Interpolation can be used to determine values for emission data or other information signals that were not taken, or are unknown, using detected emission data, or other detected information signals. By calibrating the detected emission data and the interpolated data, a more accurate reading of emission data or information signal can be obtained. | 09-22-2011 |
| 20110230375 | METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 09-22-2011 |
| 20110229397 | PROCESS AND APPARATUS FOR CONTINUOUS FLOW SYNTHESIS OF NANOCRYSTALS - Novel reactor, systems and methods of preparing nanocrystals in a continuous flow-through process are provided. The novel reactor is highly configurable and can be modified to achieve desired reaction times of a flow through mixture. The reactor is designed to provide uniform, efficient heating of the reaction mixture. | 09-22-2011 |
| 20110226995 | COMPOSITIONS AND METHODS FOR FUNCTIONALIZING OR CROSSLINKING LIGANDS ON NANOPARTICLE SURFACES - This disclosure provides novel ways to modify/functionalize, including crosslink, ligands in the surface coating or molecules in other coatings on a nanoparticle, by using radical addition reactions to add a reactant group onto a ligand/molecule of a nanoparticle. Examples include using a functionalized benzophenone that can be attached or crosslinked to a ligand in the surface coating of a nanocrystal by photochemically-initiated radical addition. | 09-22-2011 |
| 20110226994 | Fluorescent Polymeric Materials Containing Lipid Soluble Rhodamine Dyes - Fluorescent polymeric materials are disclosed comprising a polymer and one or more lipid soluble rhodamine dyes. The materials are especially useful in the preparation of multicolored microparticles, especially multicolored polystyrene microparticle, for use in the multiplexed analysis of a plurality of analytes in a single sample. When excited by a light source, the materials give off a unique emission based on the nature, concentration and ratio of the dyes therein. Methods of preparing and using said materials are also disclosed. | 09-22-2011 |
| 20110226991 | STABLE NANOPARTICLES AND METHODS OF MAKING AND USING SUCH PARTICLES - A population of nanoparticles is disclosed. The population is comprised of a plurality of core/shell nanocrystals, each including: a semiconductor core, an intermediate semiconductor shell layer disposed over the semiconductor core, an external semiconductor shell layer disposed over the intermediate semiconductor shell layer, and a hydrophilic organic layer in direct contact with the external semi-conductor shell layer. The population of nanoparticles has a α | 09-22-2011 |
