Showing papers by "Stratagene published in 2006"
Food and Drug Administration1, GE Healthcare2, Thermo Fisher Scientific3, Illumina4, Agilent Technologies5, National Institutes of Health6, Applied Biosystems7, University of Toledo8, Stratagene9, United States Environmental Protection Agency10, University of Massachusetts Boston11, Clinical Data, Inc12, University of California, Los Angeles13, SAS Institute14, Biogen Idec15, Yale University16, Cold Spring Harbor Laboratory17, Discovery Institute18, Stanford University19, Harvard University20, Vanderbilt University21, University of Texas at Dallas22, University of Oslo23, Novartis24, University of Texas MD Anderson Cancer Center25, Luminex Corporation26, Wake Forest University27, University of Illinois at Urbana–Champaign28
TL;DR: This study describes the experimental design and probe mapping efforts behind the MicroArray Quality Control project and shows intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed.
Abstract: Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.
1,987 citations
TL;DR: RNA titration samples may be regarded as a valuable tool, not only for assessing microarray platform performance and different analysis methods, but also for determining some underlying biological features of the samples.
Abstract: We have assessed the utility of RNA titration samples for evaluating microarray platform performance and the impact of different normalization methods on the results obtained. As part of the MicroArray Quality Control project, we investigated the performance of five commercial microarray platforms using two independent RNA samples and two titration mixtures of these samples. Focusing on 12,091 genes common across all platforms, we determined the ability of each platform to detect the correct titration response across the samples. Global deviations from the response predicted by the titration ratios were observed. These differences could be explained by variations in relative amounts of messenger RNA as a fraction of total RNA between the two independent samples. Overall, both the qualitative and quantitative correspondence across platforms was high. In summary, titration samples may be regarded as a valuable tool, not only for assessing microarray platform performance and different analysis methods, but also for determining some underlying biological features of the samples.
178 citations
TL;DR: It is demonstrated that Msh3 but not Msh6 plays also a key role in the formation of expansions over successive generation, indicating that MSh3 is rate-limiting in this process.
Abstract: The CTG repeat involved in myotonic dystrophy is one of the most unstable trinucleotide repeats. However, the molecular mechanisms underlying this particular form of genetic instability-biased towards expansions-have not yet been completely elucidated. We previously showed, with highly unstable CTG repeat arrays in DM1 transgenic mice, that Msh2 is required for the formation of intergenerational and somatic expansions. To identify the partners of Msh2 in the formation of intergenerational CTG repeat expansions, we investigated the involvement of Msh3 and Msh6, partners of Msh2 in mismatch repair. Transgenic mice with CTG expansions were crossed with Msh3- or Msh6-deficient mice and CTG repeats were analysed after maternal and paternal transmissions. We demonstrated that Msh3 but not Msh6 plays also a key role in the formation of expansions over successive generation. Furthermore, the absence of one Msh3 allele was sufficient to decrease the formation of expansions, indicating that Msh3 is rate-limiting in this process. In the absence of Msh6, the frequency of expansions decreased only in maternal transmissions. However, the significantly lower levels of Msh2 and Msh3 proteins in Msh6 -/- ovaries suggest that the absence of Msh6 may have an indirect effect.
137 citations
TL;DR: A differential pattern of expression of genes encoding cell cycle regulators and extracellular matrix components was identified that correlated with the development of irreversible post‐denervation changes, suggesting different signaling networks are recruited over time to induce and maintain muscle atrophy.
Abstract: Skeletal muscle function and viability are dependent upon intact innervation. Peripheral nerve injury and muscle denervation cause muscle atrophy. Time to re-innervation is one of the most important determinants of functional outcome. While short-term denervation can result in nearly fully reversible changes in muscle mass, prolonged denervation leads to irreversible muscle impairment from profound atrophy, myocyte death and fibrosis. We performed transcriptional profiling to identify genes that were altered in expression in short-term (1 month) and long-term (3 month) denervated muscle and validated the microarray data by RT-PCR and Western blotting. Genes controlling cell death, metabolism, proteolysis, stress responses and protein synthesis/translation were altered in expression in the denervated muscle. A differential pattern of expression of genes encoding cell cycle regulators and extracellular matrix components was identified that correlated with the development of irreversible post-denervation changes. Genes encoding mediators of protein degradation were differentially expressed between 1 and 3 month denervated muscle suggesting different signaling networks are recruited over time to induce and maintain muscle atrophy. Understanding of the timing and type of pathological processes that are triggered by denervation may allow the design of interventions that delay or protect muscle from loss of nerve function.
119 citations
Patent•
07 Aug 2006TL;DR: In this article, the authors proposed a nucleic acid synthesis dependent, flap-mediated amplification method for sequentially producing detectable, released flaps to detect a target nucleic acids.
Abstract: The invention relates to nucleic acid, flap-mediated, sequential amplification methods which permit detection of a nucleic acid target in a nucleic acid sample. The invention provides for nucleic acid synthesis dependent, flap-mediated amplification methods for sequentially producing detectable, released flaps to detect a target nucleic acid. The invention provides for both linear, and exponential nucleic acid synthesis dependent, flap-mediated, sequential amplification methods.
60 citations
TL;DR: This chapter will briefly review the current understanding of CoV assembly, highlighting some recent results from the laboratory in the context of work that has been done by numerous other groups in this field.
Abstract: A number of approaches have been taken to elucidate the network of interactions, among the canonical structural proteins S, M, E, and N, and the genomic RNA, that lead to assembly of virions. The earliest efforts employed the fractionation and reassociation of components of purified virions. These studies were followed by molecular genetic and co-immunoprecipitation analyses of expressed proteins or proteins from virus-infected cells. More recently, reverse-genetic techniques have become available. This chapter will briefly review the current understanding of CoV assembly, highlighting some recent results from our laboratory in the context of work that has been done by numerous other groups in this field. From a large body of work extending over two decades, the main principle that has emerged is that M is the central organizer of CoV assembly. The M protein (~25 kDa)
28 citations
Patent•
09 Feb 2006TL;DR: In this article, a hairpin structure was proposed for detection of nucleic acid sequences in the absence of the target nucleic acids sequence in the form of a pair of moieties that produce a detectable signal when the probe hybridizes to the target sequence.
Abstract: The invention relates to compositions and methods for detection of nucleic acid sequences. The invention further relates to kit format of said compositions for detection of nucleic acid sequences. Oligonucleotide probes of the invention comprise a target binding sequence and a sequence at least partially complementary thereto, joined by an optional linker to form a hairpin structure in the absence of the target nucleic acid sequence. The probes of the invention comprise a pair of moieties that produce a detectable signal when the probe hybridizes to the target sequence.
24 citations
Patent•
15 Jun 2006TL;DR: In this article, the authors present compositions, methods, and kits for lysing cells, storing nucleic acids, amplifying nucleic acid, and analyzing nucleic amino acid sequences.
Abstract: The present invention provides compositions, methods, and kits for lysing cells, storing nucleic acids, amplifying nucleic acids, and analyzing nucleic acids. Among other things, the compositions, methods, and kits are suitable for one-step lysis and amplification of nucleic acid sequences of interest, hi general, the compositions comprise TCEP and a non-ionic surfactant, such as Triton X-100.
22 citations
Patent•
12 Jun 2006TL;DR: In this article, a system and method for fluorescence excitation and detection having distinct optical paths is described, which includes a light source (40) that emits an excitation light (48) into an illumination tube (44); a plurality of collection optics (39) located around an aperture (47) in the illumination tube for collecting fluorescence; and a detector (53) for determining the amount of fluorescence.
Abstract: A system and method for fluorescence excitation and detection having distinct optical paths is disclosed. A system for detecting fluorescence comprises a light source(40) that emits an excitation light (48) into an illumination tube (44); a plurality of collection optics (39) located around an aperture (47) in the illumination tube for collecting fluorescence; and a detector (53) for determining the amount of fluorescence. A method for detecting fluorescence comprises emitting an excitation light (48) from a light source (40) into an illumination tube (44); directing the excitation light to an excitation filter (62); illuminating a sample with the excitation light (48) to generate an emission light; and detecting the optical characteristics of the emission light using a plurality of collection optics (39) located around the illumination tube (44).
17 citations
Patent•
02 May 2006TL;DR: A system and method for a pulsed light source (40) used in detecting fluorescence from a plurality of samples (94) of biological material discretely, continuously or intermittently during thermal cycling of DNA to accomplish a polymerase chain reaction (PCR) is described in this article.
Abstract: A system and method for a pulsed light source (40) used in detecting fluorescence from a plurality of samples (94) of biological material discretely, continuously or intermittently during thermal cycling of DNA to accomplish a polymerase chain reaction (PCR). An apparatus for sampling at least one sample (94) of a biological material comprises a light source (40) that emits a pulsed excitation light (42) that interacts with the sample (94) and a detector (50) sensitive to fluorescence emitted from the sample (94). A method of sampling at least one sample (94) to detect fluorescence comprises generating a pulsed excitation light (42) with a pulsed light source (40); directing the pulsed excitation light (42) into the sample (94); illuminating a sample (94) with the pulsed excitation light (42) to generate an emission light; and detecting the optical characteristics of the emission light.
17 citations
Patent•
15 Jun 2006TL;DR: In this article, an oligonucleotide primer, compositions, methods, and kits for determining the amount of gDNA or the number of cells from which a cell lysate originated are provided.
Abstract: The present invention provides oligonucleotide primers, compositions, methods, and kits for determining the amount of gDNA or the number of cells from which a cell lysate originated. The invention relies on detection and amplification of unique genomic sequences within the genome of an organism of interest to determine the amount of genomic nucleic acid in a sample. The invention can be used to normalize samples from particular cells, cell types, or organism, and provide an accurate basis for comparison of expression of genes across the samples.
Patent•
10 Aug 2006TL;DR: In this paper, the generation and characterization of stable MMLV reverse transcriptase mutants is discussed. But the authors do not discuss the methods of using stable mutants in the real world.
Abstract: The invention relates to the generation and characterization of stable MMLV reverse transcriptase mutants. The invention also discloses methods of using stable MMLV reverse transcriptase mutants.
Patent•
04 Jan 2006TL;DR: In this article, a thermally inactivated blocking polymerase protein is used to prevent access to a thermostable nucleic acid polymerase, thereby preventing the denature of the blocking polymerases.
Abstract: The invention relates to compositions, methods, and kits for hot start polynucleotide synthesis, including extension of primed polynucleotide templates and polymerase chain reaction (PCR). Hot start is provided by a thermally inactivated blocking polymerase protein that binds primed polynucleotide templates and prevents their access to a thermostable nucleic acid polymerase. High temperatures employed in the synthesis reaction cause the blocking polymerase to denature, thereby permitting the action of a thermostable processive polymerase. Compositions of the invention include a specific blocking polymerase protein which is a mutant of the Klenow fragment of E. coli DNA polymerase. The mutant is essentially devoid of polymerase activity, processivity, and 3' to 5' exonuclease activity. Use of the thermally inactivated blocking polymerase together with a thermostable polymerase reduces non-specific priming and accumulation of unwanted amplification products, increasing the specificity and sensitivity of the synthesis reaction.
Patent•
25 May 2006TL;DR: In this article, the authors propose compositions for generating a signal indicative of the presence of a target nucleic acid in a sample, where the compositions include an RNA polymerase, a FEN nuclease, and a probe.
Abstract: The invention relates to compositions for generating a signal indicative of the presence of a target nucleic acid in a sample, where the compositions include an RNA polymerase, a FEN nuclease, and a probe.
Patent•
01 May 2006TL;DR: In this paper, a labeled oligonucleotide pair was proposed for detecting a target nucleic acid and methods, kits and compositions containing the pair were described, including methods, compositions and methods.
Abstract: The invention is related to a labeled oligonucleotide pair for detecting a target nucleic acid and methods, kits and compositions containing the labeled oligonucleotide pair. The labeled oligonucleotide pair forms a complex comprising a nucleic acid primer and a nucleic acid probe.
Journal Article•
TL;DR: The performance characteristics of the Hycor Turbo-MP quantitative radioimmunoassay for food-specific IgE were assessed and this method's comparability to another assay, the Pharmacia ImmunoCAP fluorescence enzyme immunoassays (FEIA), was determined.
Abstract: It has been reported that in vitro measurement of food-specific IgE can be used to accurately predict food allergy and reduce the risk associated with double-blinded placebo-controlled food challenges (DBPCFC). Our objective was to assess the performance characteristics of the Hycor Turbo-MP quantitative radioimmunoassay for food-specific IgE and to determine this method's comparability to another assay, the Pharmacia ImmunoCAP fluorescence enzyme immunoassay (FEIA). The dynamic range of the Turbo-MP assay is 0.05 to 100 IU/ml, compared to 0.35 to 100 IU/ml for the FEIA. Performance characteristics of the Turbo-MP assay (ie, reproducibility of the calibration curve, within-run precision, total precision, parallelism, and linearity) were determined using samples from the Hycor serum bank. The precision (CV) of IgE calibrator replicates was <10%. The total precision (CV) of the Turbo-MP assay ranged from 8.8% to 18.4% for specific IgE concentrations between 0.28 to 31.4 IU/ml. Testing of serial dilutions of sera with IgE specificities for egg white, cow's milk, codfish, wheat, peanut, and soybean showed that the assay is linear over the entire dynamic range. Serial dilution data (slopes of 1.01 to 1.10) showed parallelism to serial dilutions of the IgE calibrator (slope of 0.96). The Turbo-MP and FEIA methods were both used for quantitative assays of food-specific IgE in 457 serum samples obtained from a clinical reference laboratory. Comparison of specific IgE results by the Turbo-MP and FEIA methods for 6 major food allergens exhibited a slope of 0.99 (0.92 to 1.03) with a correlation coefficient of 0.81.
Patent•
10 May 2006TL;DR: The Snapback oligonucleotide probes of the invention as discussed by the authors contain a target binding sequence, a hairpin forming sequence, and a reporter binding sequence and can be used to detect specific nucleic acid sequences during an amplification reaction.
Abstract: The invention relates to compositions and methods for detection of specific nucleic acid sequences during an amplification reaction. The invention further relates to a kit format of said compositions for detection of nucleic acid sequences. The Snapback oligonucleotide probes of the invention comprise a target binding sequence, a hairpin forming sequence, and a reporter binding sequence. The action of a nucleic acid polymerase or a flap endonuclease cleaves off a 'snapback segment' of the probe containing the hairpin forming sequence and reporter binding sequence, causing the probe to 'snap back' and form a hairpin structure. The further action of a nucleic acid polymerase or a flap endonuclease cleaves off a label moiety from a reporter oligonucleotide hybridized to the reporter binding sequence, resulting in a detectable signal.
Patent•
11 Oct 2006TL;DR: In this article, the authors present methods, compositions and kits for detecting a target nucleic acid, which can be produced by a cleavage reaction in an assay for detection of biological samples.
Abstract: Provided herein are methods, compositions and kits for detecting a target nucleic acid. A target nucleic acid can be produced, for example, by a cleavage reaction in an assay for detection of biological samples. In one aspect, a described method comprises the following steps: hybridizing the target nucleic acid having a 5' end and a 3' end to a probe to form a circular hybridization complex; forming a covalent circular target nucleic acid using the probe as a template for nucleic acid synthesis; and detecting the covalent circular target nucleic acid.
Patent•
29 Nov 2006TL;DR: In this paper, the present invention is directed compositions having a Fen nuclease consisting of a 5′ to 3′ exonuclease and one or more dNTPs.
Abstract: The present invention is directed compositions having a Fen nuclease consisting of a 5′ to 3′ exonuclease and/or endonuclease activity and one or more dNTPs.
Patent•
18 Aug 2006TL;DR: In this paper, the authors present compositions and methods of generating a signal indicative of the presence of a target nucleic acid in a sample, where the method includes forming a cleavage structure by incubating a sample comprising a target nucleus with a probe.
Abstract: The invention relates to compositions and methods of generating a signal indicative of the presence of a target nucleic acid in a sample, where the method includes forming a cleavage structure by incubating a sample comprising a target nucleic acid with a probe. The invention also includes the steps of cleaving the cleavage structure with a nuclease to release a nucleic acid fragment to generate a signal, wherein generation of the signal is indicative of the presence of a target nucleic acid in a sample.