Showing papers by "Applied Biosystems published in 2003"
TL;DR: The development of standardized protocols for RQ-PCR analysis of FG transcripts provides a milestone for molecular determination of MRD levels and is likely to prove invaluable to the management of patients entered into multicenter therapeutic trials.
Abstract: Detection of minimal residual disease (MRD) has proven to provide independent prognostic information for treatment stratification in several types of leukemias such as childhood acute lymphoblastic leukemia (ALL), chronic myeloid leukemia (CML) and acute promyelocytc leukemia. This report focuses on the accurate quantitative measurement of fusion gene (FG) transcripts as can be applied in 35-45% of ALL and acute myeloid leukemia, and in more than 90% of CML. A total of 26 European university laboratories from 10 countries have collaborated to establish a standardized protocol for TaqMan-based real-time quantitative PCR (RQ-PCR) analysis of the main leukemia-associated FGs within the Europe Against Cancer EAC) program. Four phases were scheduled: (1) training, (2) optimization, (3) sensitivity testing and (4) patient sample testing. During our program, three quality control rounds on a large series of coded RNA samples were performed including a balanced randomized assay, which enabled final validation of the EAC primer and probe sets. The expression level of the nine major FG transcripts in a large series of stored diagnostic leukemia samples (n = 278) was evaluated. After normalization, no statistically significant difference in expression level was observed between bone marrow and peripheral blood on paired samples at diagnosis. However, RQ-PCR revealed marked differences in FG expression between transcripts in leukemic samples at diagnosis that could account for differential assay sensitivity. The development of standardized protocols for RQ-PCR analysis of FG transcripts provides a milestone for molecular determination of MRD levels. This is likely to prove invaluable to the management of patients entered into multicenter therapeutic trials.
1,450 citations
TL;DR: The ABL gene is proposed to be used as CG for RQ-PCR-based diagnosis and MRD detection in leukemic patients and these data are not only eligible for quantifying of fusion gene transcripts, but also for the quantification of aberrantly expressed genes.
Abstract: Real-time quantitative RT-PCR (RQ-PCR) is a sensitive tool to monitor minimal residual disease (MRD) in leukemic patients through the amplification of a fusion gene (FG) transcript. In order to correct variations in RNA quality and quantity and to calculate the sensitivity of each measurement, a control gene (CG) transcript should be amplified in parallel to the FG transcript. To identify suitable CGs, a study group within the Europe Against Cancer (EAC) program initially focused on 14 potential CGs using a standardized RQ-PCR protocol. Based on the absence of pseudogenes and the level and stability of the CG expression, three genes were finally selected: Abelson (ABL), beta-2-microglobulin (B2M), and beta-glucuronidase (GUS). A multicenter prospective study on normal (n=126) and diagnostic leukemic (n=184) samples processed the same day has established reference values for the CG expression. A multicenter retrospective study on over 250 acute and chronic leukemia samples obtained at diagnosis and with an identified FG transcript confirmed that the three CGs had a stable expression in the different types of samples. However, only ABL gene transcript expression did not differ significantly between normal and leukemic samples at diagnosis. We therefore propose to use the ABL gene as CG for RQ-PCR-based diagnosis and MRD detection in leukemic patients. Overall, these data are not only eligible for quantification of fusion gene transcripts, but also for the quantification of aberrantly expressed genes.
894 citations
TL;DR: Partitions of genes into inferred biological classes identified accelerated evolution in several functional classes, including olfaction and nuclear transport and human-accelerated genes are significantly more likely to underlie major known Mendelian disorders.
Abstract: Even though human and chimpanzee gene sequences are nearly 99% identical, sequence comparisons can nevertheless be highly informative in identifying biologically important changes that have occurred since our ancestral lineages diverged. We analyzed alignments of 7645 chimpanzee gene sequences to their human and mouse orthologs. These three-species sequence alignments allowed us to identify genes undergoing natural selection along the human and chimp lineage by fitting models that include parameters specifying rates of synonymous and nonsynonymous nucleotide substitution. This evolutionary approach revealed an informative set of genes with significantly different patterns of substitution on the human lineage compared with the chimpanzee and mouse lineages. Partitions of genes into inferred biological classes identified accelerated evolution in several functional classes, including olfaction and nuclear transport. In addition to suggesting adaptive physiological differences between chimps and humans, human-accelerated genes are significantly more likely to underlie major known Mendelian disorders.
648 citations
TL;DR: In this paper, NADA was identified as an endogenous ligand for the vanilloid type 1 receptor (VR1) in the human embryonic kidney (HEK) 293 cells or paw withdrawal latency from a radiant heat source.
341 citations
TL;DR: Attenuated total reflection-Fourier transform infrared spectroscopy spectra suggested that beta-sheet content of the Abeta mutants correlates with their aggregation, however, beta-turn is also a critical secondary structure because residues at positions 22 and 23 that preferably form two-residue beta- turn significantly enhanced the aggregative ability.
224 citations
TL;DR: By means of reverse pharmacology screening using a peptide library generated from human hemofiltrate, TIG2 is isolated and identified as the natural ligand of ChemR23 and report the specific molecular form of the bioactive, circulating Tig2, representing the amino‐acid residues 21 to 154 of the 163 amino acid‐containing prepropeptide.
196 citations
TL;DR: The high resolution furnished by MalDI-TOF/TOF allowed determination of certain ions that were commonly overlooked by MALDI-toF or MAL DI-magnetic sector instruments as a result of their lower resolution.
Abstract: Extensive cross-ring fragmentation ions, which are very informative of the linkages of the monosaccharide residues constituting these molecules, were readily observed in the MALDI-TOF/TOF/MS/MS spectra of oligosaccharides. These ions, in some cases, were more intense than the commonly observed Y and B ions. The A-type ions observed for the simple oligosaccharides allowed the distinction between α(1−4)- and α(1−6)-linked isobaric structures. The distinction was based not merely on the differences in the type of ions formed, but also on the ion intensities. For example, both α(1−4)- and α(1−6)-linked isobaric structures produce ions resulting from the loss of ∼120 m/z units, but with different intensities, as a result of the fact that they correspond to two different ions (i.e., 0,4A- and 2,4A-ions), requiring different energies to be formed. Abundant A- and X-type ions were also observed for high-mannose N-glycans, allowing the determination of linkages. In addition, the high resolution furnished by MALDI-...
186 citations
TL;DR: These studies are the first to systematically evaluate the embryonic globins in the zebrafish and will ultimately be useful in evaluating zebra fish mutants with defects in hemoglobin production and switching.
159 citations
TL;DR: It is suggested that for further lymphoma studies based on the real-time RT-PCR quantification of gene expression, that RNA input in each reaction be equalized between the specimens by spectrophotometric OD260 measurements.
Abstract: Optimization of quantitative real-time RT-PCR parameters for the study of lymphoid malignancies
153 citations
Patent•
14 Nov 2003TL;DR: In this paper, the authors present methods and compositions involving the production or generation of siRNA mixtures or pools capable of triggering RNA-mediated interference (RNAi) in a cell.
Abstract: The present invention concerns methods and compositions involving the production or generation of siRNA mixtures or pools capable of triggering RNA-mediated interference (RNAi) in a cell. Compositions of the invention include kits that include reagents for producing or generating siRNA pools. The present invention further concerns methods using polypeptides with RNase III activity for generating siRNA mixtures or pools that effect RNAi, including the generation of a number of RNA molecules to the same target gene.
151 citations
TL;DR: The unique scanning capabilities of a hybrid linear ion trap (Q TRAP) mass spectrometer are described with an emphasis on proteomics applications, allowing rapid identification of peptides at low concentrations derived from post‐translationally modified proteins on chromatographic time scales.
Abstract: The unique scanning capabilities of a hybrid linear ion trap (Q TRAP) mass spectrometer are described with an emphasis on proteomics applications. The combination of the very selective triple quadrupole based tandem mass spectrometry (MS/MS) scans with the very sensitive ion trap product ion scans allows rapid identification of peptides at low concentrations derived from post-translationally modified proteins on chromatographic time scales. The Q TRAP instrument also offers the opportunity to conduct a variety of ion processing steps prior to performing a mass scan. For example, the enhancement of the multiple-charge ion contents of the ion trap can be performed resulting in a survey mass spectrum dominated by double- and triple-charge peptides. This facilitates the identification of relevant biological species in both separated and unseparated peptide mixtures for further MS/MS experiments.
TL;DR: This technique is proposed as a suitable candidate method for the identification and quantitation of bile acids in routine analysis based on high performance liquid chromatography separation coupled to an electrospray triple-quadrupole mass spectrometer.
Abstract: Bile acids play a pivotal role in the metabolism of cholesterol and lipids. Their blood concentrations are important prognostic and diagnostic indicators of hepatobiliary and intestinal dysfunction. This class of molecules comprises a heterogeneous group of compounds with a common cholesterol scaffold. Recently, the introduction of liquid chromatography coupled to tandem mass spectrometry methods has revealed an innovative path in the quantisation of specific bile acids in biological specimens. A robust and sensitive method has been developed based on high performance liquid chromatography separation coupled to an electrospray triple-quadrupole mass spectrometer. Human plasma samples were analysed on a C18 reverse-phase column. The elution profiles were monitored in multiple reaction-monitoring mode, quantifying and identifying each analyte by its own unique precursor to product patterns. A linear correlation over a broad range of bile acid concentrations (0.1-100 microM) was observed. The average recovery period for all of the analysed bile acids was 98 +/- 3%. Intra-day and inter-day precision averages were 2% and 5.4%, respectively. The determination was achieved within a single chromatographic run for all unconjugated, glycine- and taurine-conjugated isomeric forms of bile acids. As a proof of principle this method has been validated on a small subset of cholestatic patients (n = 7) and compared to appropriate clinical controls (n = 10). Based upon our encouraging experimental results, the described HPLC separation coupled to tandem mass spectrometry method for the analysis of bile acids in biological samples is deemed a robust and accurate procedure. Consequently, we propose this technique as a suitable candidate method for the identification and quantitation of bile acids in routine analysis.
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18 Jul 2003TL;DR: In this paper, the authors present assembly and control systems for microfluidic devices, assemblies, and systems, as well as methods of manipulating micro-sized samples of fluids.
Abstract: Microfluidic devices, assemblies, and systems are provided, as are methods of manipulating micro-sized samples of fluids. Microfluidic devices having a plurality of specialized processing features are also provided.
TL;DR: A new type of quadrupole linear ion trap mass spectrometer, Q TRAP trade mark LC/MS/MS system, was evaluated for its performance in two studies: firstly, the in vitro metabolism of gemfibrozil in human liver microsomes, and the quantification of propranolol in rat plasma.
Abstract: A new type of quadrupole linear ion trap mass spectrometer, Q TRAP™ LC/MS/MS system (Q TRAP™), was evaluated for its performance in two studies: firstly, the in vitro metabolism of gemfibrozil in human liver microsomes, and, secondly, the quantification of propranolol in rat plasma. With the built-in information-dependent-acquisition (IDA) software, the instrument utilizes full scan MS in the ion trap mode and/or constant neutral loss scans as survey scans to trigger product ion scan (MS2) and MS3 experiments to obtain structural information of drug metabolites ‘on-the-fly’. Using this approach, five metabolites of gemfibrozil were detected in a single injection. This instrument combines some of the unique features of a triple quadrupole mass spectrometer, such as constant neutral loss scan, precursor ion scan and multiple reaction monitoring (MRM), together with the capability of a three-dimensional ion trap. Therefore, it becomes a powerful instrument for metabolite identification. The fast duty cycle in the ion trap mode allows the use of full product ion scan for quantification. For the quantification of propranolol, both MRM mode and full product ion scan in the ion trap mode were employed. Similar sensitivity, reproducibility and linearity values were established using these two approaches. The use of the product ion scan mode for quantification provided a convenient tool in selecting transitions for improving selectivity during the method development stage. Copyright © 2003 John Wiley & Sons, Ltd.
Patent•
19 May 2003
TL;DR: In this article, an apparatus and method for differentiating multiple detectable signals by excitation wavelength is provided 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.
Abstract: 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.
TL;DR: FISH performs well with commonly used continuously monitoring blood culture systems and is performed on smears made directly from positive blood culture bottles with gram-positive cocci in clusters from three different manufacturers.
Abstract: Fluorescence in situ hybridization (FISH) using peptide nucleic acid (PNA) probes targeting Staphylococcus aureus 16S rRNA is a novel method for direct identification of S. aureus from positive blood culture bottles. The test (S. aureus PNA FISH) is performed on smears made directly from positive blood culture bottles with gram-positive cocci in clusters (GPCC) and provides results within 2.5 h. A blinded comparison of S. aureus PNA FISH with standard identification methods was performed in collaboration with eight clinical microbiology laboratories. A total of 564 routine blood culture bottles positive for GPCC recovered from both aerobic and anaerobic media from three different manufacturers (ESP, BACTEC, and BacT/Alert) were included in the study. The sensitivity and specificity of S. aureus PNA FISH were 100% (57 of 57) and 99.2% (116 of 117), respectively, with 174 GPCC-positive ESP blood culture bottles, 98.5% (67 of 68) and 98.5% (129 of 131), respectively, with 200 GPCC-positive BACTEC blood culture bottles, and 100% (74 of 74) and 99.1% (115 of 116), respectively, with 190 GPCC-positive BacT/Alert blood culture bottles. It is concluded that S. aureus PNA FISH performs well with commonly used continuously monitoring blood culture systems.
TL;DR: A population study of Chamorros and Filipinos using short tandem repeat (STR) loci amplified with the AmpFlSTR Profiler Plus PCR amplification kit demonstrated an excess of observed homozygosity at the D8S1179 locus.
TL;DR: It is proposed that AFLP, REP-PCR, Box- PCR and ribotyping techniques can all be used for discriminating O157:H7 isolates and are preferred for large-scale screening because of the speed and ease of the methods.
TL;DR: Preliminary results show that the sensitivity and mass structural information brought by this new LC-QqQlinear ion-trap instrument may help design an efficient toxicological GUS procedure.
10 Apr 2003
TL;DR: In this article, the authors compared two methods for reducing the complexity of SNP variation: haplotype tagging, i.e., typing a subset of SNPs to identify segments of the genome that appear to be nearly unrecombined (haplotype blocks), and a new block-free model that they developed in this report.
Abstract: It is widely hoped that variation in the human genome will provide a means of predicting risk of a variety of complex, chronic diseases. A major stumbling block to the successful identification of association between human DNA polymorphisms (SNPs) and variability in risk of complex diseases is the enormous number of SNPs in the human genome (4,9). The large number of SNPs results in unacceptably high costs for exhaustive genotyping, and so there is a broad effort to determine ways to select SNPs so as to maximize the informativeness of a subset.In this paper we contrast two methods for reducing the complexity of SNP variation: haplotype tagging, i.e. typing a subset of SNPs to identify segments of the genome that appear to be nearly unrecombined (haplotype blocks), and a new block-free model that we develop in this report. We present a statistic for comparing haplotype blocks and show that while the concept of haplotype blocks is reasonably robust there is substantial variability among block partitions. We develop a measure for selecting an informative subset of SNPs in a block free model. We show that the general version of this problem is NP-hard and give efficient algorithms for two important special cases of this problem.
TL;DR: The effects of variations in reversed-phase mode HPLC conditions such as mobile-phase flow rate, solvent composition, organic modifier content, and nebulizer temperature on the photoionization efficiency of both clozapine and lonafarnib are summarized.
Abstract: A generic high-performance liquid chromatography (HPLC) system interfaced with an atmospheric pressure photoionization (APPI) source and a tandem mass spectrometer was developed for the quantitative determination of small molecules in plasma in support of exploratory in vivo pharmacokinetics. This report summarizes the effects of variations in reversed-phase mode HPLC conditions such as mobile-phase flow rate, solvent composition, organic modifier content, and nebulizer temperature on the photoionization efficiency of both clozapine and lonafarnib. The matrix ionization suppression effect on this method was investigated using the postcolumn infusion technique. The procedure was used to quantitate plasma levels following oral administration of 42 drug discovery compounds to rats. The pharmacokinetic results of 42 drug discovery compounds in rats evaluated by both APPI and atmospheric pressure chemical ionization interfaces were found to be well correlated.
TL;DR: This non- redundant array was used to measure changes in gene copy number in DNA from actively growing versus stationary Typhi and to reveal the transcriptional response of Typhi to peroxide, a stress similar to that experienced when they are phagocytosed by macrophages.
Abstract: A microarray with sequences from the annotated open reading frames (ORFs) in Salmonella enterica subspecies 1, serovar Typhimurium was supplemented with annotated chromosomal ORFs from serovar Typhi that are divergent from Typhimurium (>10% DNA sequence divergence). This non- redundant array was used to (i) measure changes in gene copy number in DNA from actively growing versus stationary Typhi and (ii) to reveal the transcriptional response of Typhi to peroxide, a stress similar to that experienced when they are phagocytosed by macrophages. In S.enterica subspecies 1, pairs of genomes differ in the presence or absence of approximately 10% of their genes. An array twice the size of that needed to cover all ORFs for one genome could carry close homologs of all the ORFs for 10 genomes. Non-redundant DNA arrays could be constructed for any group of closely related organisms that differ by the presence and absence of a few genes.
TL;DR: Results indicate that 12-O-tetradecanoylphorbol 13-acetate binds to C1A of DGKγ to cause its translocation and is associated with the irreversible translocation of whole rat-DGKγ and its C1B deletion mutant from the cytoplasm to the plasma membrane of CHO-K1 cells.
TL;DR: With this large data set, it is sought to reconstruct a phylogenetic history of the laboratory mouse using Wagner parsimony analysis and the results are largely congruent with the known history of inbred mouse strains.
Abstract: To identify highly informative markers for a large number of commonly employed murine crosses, we selected a subset of the extant mouse simple sequence length polymorphism (SSLP) marker set for further development. Primer pairs for 314 SSLP markers were designed and typed against 54 inbred mouse strains. We designed new PCR primer sequences for the markers selected for multiplexing using the fluorescent dyes FAM, VIC, NED, and ROX. The number of informative markers for C57BL/6J x DBA/2J is 217, with an average spacing of 6.8 centiMorgans (cM). For all other pairs of strains, the mean number of informative markers per cross is 197.0 (SD 37.8) with a mean distance between markers of 6.8 cM (SD 1.1). To confirm map positions of the 224 markers in our set that are polymorphic between Mus musculus and Mus spretus, we used The Jackson Laboratory (TJL) interspecific backcross mapping panel (TJL BSS); 168 (75%) of these markers had not been previously mapped in this cross by other investigators, adding new information to this community map resource. With this large data set, we sought to reconstruct a phylogenetic history of the laboratory mouse using Wagner parsimony analysis. Our results are largely congruent with the known history of inbred mouse strains.
TL;DR: A novel approach to quantitative proteomics is described, based on a highly accurate algorithm for the automated quantification of chromatographically fractionated, isotope-coded affinity-tagged peptides and MALDI quadrupole time-of-flight tandem mass spectrometry for their identification.
Abstract: The goal of quantitative proteomics is to determine the identity and relative quantity of each protein present in two or more complex protein samples Here we describe a novel approach to quantitative proteomics It is based on a highly accurate algorithm for the automated quantification of chromatographically fractionated, isotope-coded affinity-tagged peptides and MALDI quadrupole time-of-flight tandem mass spectrometry for their identification The method is capable of detecting and selectively identifying those proteins within a complex mixture that show a difference in relative abundance We demonstrate the effectiveness and the versatility of this approach in the analysis of a standard protein mixture, protein expression profiling in a human prostate cancer cell line model, and identification of the specific components of the multiprotein transcriptional machinery in S cerevisiae
Patent•
26 Nov 2003TL;DR: In this article, the authors present methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion.
Abstract: The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.
TL;DR: Results support a model in which activation of Gpa2p relieves the inhibition exerted by Krh1p and Krh2p on components of the cAMP/PKA signaling pathway.
Abstract: The yeast G(alpha) subunit Gpa2p and its coupled receptor Gpr1p function in a signaling pathway that is required for the transition to pseudohyphal and invasive growth A two-hybrid screen using a constitutively active allele of GPA2 identified the KRH1 gene as encoding a potential binding partner of Gpa2p Strains containing deletions of KRH1 and its homolog KRH2 were hyper-invasive and displayed a high level of expression of FLO11, a gene involved in pseudohyphal and invasive growth Therefore, KRH1 and KRH2 encode negative regulators of the invasive growth pathway Cells containing krh1Delta krh2Delta mutations also displayed increased sensitivity to heat shock and decreased sporulation efficiency, indicating that Krh1p and Krh2p regulate multiple processes controlled by the cAMP/PKA pathway The krh1Delta krh2Delta mutations suppressed the effect of a gpa2Delta mutation on FLO11 expression and eliminated the effect of a constitutively active GPA2 allele on induction of FLO11 and heat shock sensitivity, suggesting that Krh1p and Krh2p act downstream of Gpa2p The Sch9p kinase was not required for the signal generated by deletion of KRH1 and KRH2; however, the cAMP-dependent kinase Tpk2p was required for generation of this signal These results support a model in which activation of Gpa2p relieves the inhibition exerted by Krh1p and Krh2p on components of the cAMP/PKA signaling pathway
TL;DR: A real-time RT-PCR method for the quantification of dissimilatory (bi)sulphite reductase (DSR) mRNA in Desulfobacterium autotrophicum cells and found the maximum DSR mRNA per-cell contents correlated with cell-specific sulphate reduction rates for all experiments.
Abstract: We developed a real-time RT-PCR method for the quantification of dissimilatory (bi)sulphite reductase (DSR) mRNA in Desulfobacterium autotrophicum cells. The amount of DSR mRNA was determined relative to the amount of 16S rRNA at different growth conditions during transition from exponential to stationary phase: sulphate respiration with lactate, thiosulphate respiration with lactate, sulphate respiration with H2 and pyruvate fermentation. The dsr gene was expressed constitutively, although DSR mRNA content per-cell varied under different growth conditions. The maximum DSR mRNA per-cell content was 2.0 to 4.1-fold higher during sulphate or thiosulphate respiration than during pyruvate fermentation. After transfer of a pyruvate-fermenting culture into sulphate-rich medium, upregulation of the DSR mRNA content was observed. Irrespective of the mode of metabolism the per-cell DSR mRNA content changed significantly during growth (up to 310-fold from the early to the late exponential phase during respiration with thiosulphate). The maximum DSR mRNA per-cell contents correlated with cell-specific sulphate reduction rates for all experiments. Environmental applications for the quantification of DSR mRNA are discussed.
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02 Jan 2003TL;DR: In this paper, methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures and collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet.
Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.