WorldWideScience

Sample records for profiler pcr array

  1. Pathway-focused PCR array profiling of enriched populations of laser capture microdissected hippocampal cells after traumatic brain injury.

    Directory of Open Access Journals (Sweden)

    Deborah R Boone

    Full Text Available Cognitive deficits in survivors of traumatic brain injury (TBI are associated with irreversible neurodegeneration in brain regions such as the hippocampus. Comparative gene expression analysis of dying and surviving neurons could provide insight into potential therapeutic targets. We used two pathway-specific PCR arrays (RT2 Profiler Apoptosis and Neurotrophins & Receptors PCR arrays to identify and validate TBI-induced gene expression in dying (Fluoro-Jade-positive or surviving (Fluoro-Jade-negative pyramidal neurons obtained by laser capture microdissection (LCM. In the Apoptosis PCR array, dying neurons showed significant increases in expression of genes associated with cell death, inflammation, and endoplasmic reticulum (ER stress compared with adjacent, surviving neurons. Pro-survival genes with pleiotropic functions were also significantly increased in dying neurons compared to surviving neurons, suggesting that even irreversibly injured neurons are able to mount a protective response. In the Neurotrophins & Receptors PCR array, which consists of genes that are normally expected to be expressed in both groups of hippocampal neurons, only a few genes were expressed at significantly different levels between dying and surviving neurons. Immunohistochemical analysis of selected, differentially expressed proteins supported the gene expression data. This is the first demonstration of pathway-focused PCR array profiling of identified populations of dying and surviving neurons in the brain after TBI. Combining precise laser microdissection of identifiable cells with pathway-focused PCR array analysis is a practical, low-cost alternative to microarrays that provided insight into neuroprotective signals that could be therapeutically targeted to ameliorate TBI-induced neurodegeneration.

  2. Mathematical analysis of the real time array PCR (RTA PCR) process

    NARCIS (Netherlands)

    Dijksman, Johan Frederik; Pierik, A.

    2012-01-01

    Real time array PCR (RTA PCR) is a recently developed biochemical technique that measures amplification curves (like with quantitative real time Polymerase Chain Reaction (qRT PCR)) of a multitude of different templates in a sample. It combines two different methods in order to profit from the

  3. Real-time PCR gene expression profiling

    Czech Academy of Sciences Publication Activity Database

    Kubista, Mikael; Sjögreen, B.; Forootan, A.; Šindelka, Radek; Jonák, Jiří; Andrade, J.M.

    2007-01-01

    Roč. 1, - (2007), s. 56-60 ISSN 1360-8606 R&D Projects: GA AV ČR KJB500520601 Institutional research plan: CEZ:AV0Z50520514 Keywords : real - time PCR, * expression profiling * statistical analysis Subject RIV: EB - Genetics ; Molecular Biology

  4. Antibody repertoire profiling with mimotope arrays

    OpenAIRE

    Pashova, Shina; Schneider, Christoph; von Gunten, Stephan; Pashov, Anastas

    2016-01-01

    Large-scale profiling and monitoring of antibody repertoires is possible through next generation sequencing (NGS), phage display libraries and microarrays. These methods can be combined in a pipeline, which ultimately maps the antibody reactivities onto defined arrays of structures - peptides or carbohydrates. The arrays can help analyze the individual specificities or can be used as complex patterns. In any case, the targets recognized should formally be considered mimotopes unless they are ...

  5. Typing DNA profiles from previously enhanced fingerprints using direct PCR.

    Science.gov (United States)

    Templeton, Jennifer E L; Taylor, Duncan; Handt, Oliva; Linacre, Adrian

    2017-07-01

    Fingermarks are a source of human identification both through the ridge patterns and DNA profiling. Typing nuclear STR DNA markers from previously enhanced fingermarks provides an alternative method of utilising the limited fingermark deposit that can be left behind during a criminal act. Dusting with fingerprint powders is a standard method used in classical fingermark enhancement and can affect DNA data. The ability to generate informative DNA profiles from powdered fingerprints using direct PCR swabs was investigated. Direct PCR was used as the opportunity to generate usable DNA profiles after performing any of the standard DNA extraction processes is minimal. Omitting the extraction step will, for many samples, be the key to success if there is limited sample DNA. DNA profiles were generated by direct PCR from 160 fingermarks after treatment with one of the following dactyloscopic fingerprint powders: white hadonite; silver aluminium; HiFi Volcano silk black; or black magnetic fingerprint powder. This was achieved by a combination of an optimised double-swabbing technique and swab media, omission of the extraction step to minimise loss of critical low-template DNA, and additional AmpliTaq Gold ® DNA polymerase to boost the PCR. Ninety eight out of 160 samples (61%) were considered 'up-loadable' to the Australian National Criminal Investigation DNA Database (NCIDD). The method described required a minimum of working steps, equipment and reagents, and was completed within 4h. Direct PCR allows the generation of DNA profiles from enhanced prints without the need to increase PCR cycle numbers beyond manufacturer's recommendations. Particular emphasis was placed on preventing contamination by applying strict protocols and avoiding the use of previously used fingerprint brushes. Based on this extensive survey, the data provided indicate minimal effects of any of these four powders on the chance of obtaining DNA profiles from enhanced fingermarks. Copyright © 2017

  6. PCR melting profile (PCR MP - a new tool for differentiation of Candida albicans strains

    Directory of Open Access Journals (Sweden)

    Nowak Magdalena

    2009-11-01

    Full Text Available Abstract Background We have previously reported the use of PCR Melting Profile (PCR MP technique based on using low denaturation temperatures during ligation mediated PCR (LM PCR for bacterial strain differentiation. The aim of the current study was to evaluate this method for intra-species differentiation of Candida albicans strains. Methods In total 123 Candida albicans strains (including 7 reference, 11 clinical unrelated, and 105 isolates from patients of two hospitals in Poland were examined using three genotyping methods: PCR MP, macrorestriction analysis of the chromosomal DNA by pulsed-field gel electrophoresis (REA-PFGE and RAPD techniques. Results The genotyping results of the PCR MP were compared with results from REA-PFGE and RAPD techniques giving 27, 26 and 25 unique types, respectively. The results showed that the PCR MP technique has at least the same discriminatory power as REA-PFGE and RAPD. Conclusion Data presented here show for the first time the evaluation of PCR MP technique for candidial strains differentiation and we propose that this can be used as a relatively simple and cheap technique for epidemiological studies in short period of time in hospital.

  7. DNA Array-Based Gene Profiling

    Science.gov (United States)

    Mocellin, Simone; Provenzano, Maurizio; Rossi, Carlo Riccardo; Pilati, Pierluigi; Nitti, Donato; Lise, Mario

    2005-01-01

    Cancer is a heterogeneous disease in most respects, including its cellularity, different genetic alterations, and diverse clinical behaviors. Traditional molecular analyses are reductionist, assessing only 1 or a few genes at a time, thus working with a biologic model too specific and limited to confront a process whose clinical outcome is likely to be governed by the combined influence of many genes. The potential of functional genomics is enormous, because for each experiment, thousands of relevant observations can be made simultaneously. Accordingly, DNA array, like other high-throughput technologies, might catalyze and ultimately accelerate the development of knowledge in tumor cell biology. Although in its infancy, the implementation of DNA array technology in cancer research has already provided investigators with novel data and intriguing new hypotheses on the molecular cascade leading to carcinogenesis, tumor aggressiveness, and sensitivity to antiblastic agents. Given the revolutionary implications that the use of this technology might have in the clinical management of patients with cancer, principles of DNA array-based tumor gene profiling need to be clearly understood for the data to be correctly interpreted and appreciated. In the present work, we discuss the technical features characterizing this powerful laboratory tool and review the applications so far described in the field of oncology. PMID:15621987

  8. Cross-platform comparison of SYBR® Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC study

    Directory of Open Access Journals (Sweden)

    Dial Stacey L

    2008-07-01

    Full Text Available Abstract Background The MicroArray Quality Control (MAQC project evaluated the inter- and intra-platform reproducibility of seven microarray platforms and three quantitative gene expression assays in profiling the expression of two commercially available Reference RNA samples (Nat Biotechnol 24:1115-22, 2006. The tested microarrays were the platforms from Affymetrix, Agilent Technologies, Applied Biosystems, GE Healthcare, Illumina, Eppendorf and the National Cancer Institute, and quantitative gene expression assays included TaqMan® Gene Expression PCR Assay, Standardized (Sta RT-PCR™ and QuantiGene®. The data showed great consistency in gene expression measurements across different microarray platforms, different technologies and test sites. However, SYBR® Green real-time PCR, another common technique utilized by half of all real-time PCR users for gene expression measurement, was not addressed in the MAQC study. In the present study, we compared the performance of SYBR Green PCR with TaqMan PCR, microarrays and other quantitative technologies using the same two Reference RNA samples as the MAQC project. We assessed SYBR Green real-time PCR using commercially available RT2 Profiler™ PCR Arrays from SuperArray, containing primer pairs that have been experimentally validated to ensure gene-specificity and high amplification efficiency. Results The SYBR Green PCR Arrays exhibit good reproducibility among different users, PCR instruments and test sites. In addition, the SYBR Green PCR Arrays have the highest concordance with TaqMan PCR, and a high level of concordance with other quantitative methods and microarrays that were evaluated in this study in terms of fold-change correlation and overlap of lists of differentially expressed genes. Conclusion These data demonstrate that SYBR Green real-time PCR delivers highly comparable results in gene expression measurement with TaqMan PCR and other high-density microarrays.

  9. Direct-to-PCR tissue preservation for DNA profiling.

    Science.gov (United States)

    Sorensen, Amy; Berry, Clare; Bruce, David; Gahan, Michelle Elizabeth; Hughes-Stamm, Sheree; McNevin, Dennis

    2016-05-01

    Disaster victim identification (DVI) often occurs in remote locations with extremes of temperatures and humidities. Access to mortuary facilities and refrigeration are not always available. An effective and robust DNA sampling and preservation procedure would increase the probability of successful DNA profiling and allow faster repatriation of bodies and body parts. If the act of tissue preservation also released DNA into solution, ready for polymerase chain reaction (PCR), the DVI process could be further streamlined. In this study, we explored the possibility of obtaining DNA profiles without DNA extraction, by adding aliquots of preservative solutions surrounding fresh human muscle and decomposing human muscle and skin tissue samples directly to PCR. The preservatives consisted of two custom preparations and two proprietary solutions. The custom preparations were a salt-saturated solution of dimethyl sulfoxide (DMSO) with ethylenediaminetetraacetic (EDTA) and TENT buffer (Tris, EDTA, NaCl, Tween 20). The proprietary preservatives were DNAgard (Biomatrica(®)) and Tissue Stabilising Kit (DNA Genotek). We obtained full PowerPlex(®) 21 (Promega) and GlobalFiler(®) (Life Technologies) DNA profiles from fresh and decomposed tissue preserved at 35 °C for up to 28 days for all four preservatives. The preservative aliquots removed from the fresh muscle tissue samples had been stored at -80 °C for 4 years, indicating that long-term archival does not diminish the probability of successful DNA typing. Rather, storage at -80 °C seems to reduce PCR inhibition.

  10. Tumour metastasis-associated gene profiling using one-dimensional microfluidic beads array

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Great efforts have been made on the early diagnosis and molecular mechanism research of tumour metastasis in recent years. In this paper, based on the one-dimensional microfluidic beads array, a novel platform for tumour metastasis-associated genes profiling has been developed by depositing nucleic acids functional beads in the microchannel. This platform is sensitive (limit of detection: 0.02 nmol/L) and can perform mRNAs analysis without PCR. Two human colon cancer cell lines (primary and metastatic) from the same patient were used as a model, and transcriptional expression profiling of multiple tumour metastasis-associated genes in these two cell lines was successfully achieved. Furthermore, the results obtained on the beads array were validated by RT-PCR. This novel beads array has advantages of high sensitivity, little sample consumption, short assay time, low cost and high throughput capability. It holds the potential in early diagnosis and mechanism research of tumour metastasis.

  11. A rapid method for screening arrayed plasmid cDNA library by PCR

    International Nuclear Information System (INIS)

    Hu Yingchun; Zhang Kaitai; Wu Dechang; Li Gang; Xiang Xiaoqiong

    1999-01-01

    Objective: To develop a PCR-based method for rapid and effective screening of arrayed plasmid cDNA library. Methods: The plasmid cDNA library was arrayed and screened by PCR with a particular set of primers. Results: Four positive clones were obtained through about one week. Conclusion: This method can be applied to screening not only normal cDNA clones, but also cDNA clones-containing small size fragments. This method offers significant advantages over traditional screening method in terms of sensitivity, specificity and efficiency

  12. Customizable PCR-microplate array for differential identification of multiple pathogens.

    Science.gov (United States)

    Woubit, Abdela; Yehualaeshet, Teshome; Roberts, Sherrelle; Graham, Martha; Kim, Moonil; Samuel, Temesgen

    2013-11-01

    Customizable PCR-microplate arrays were developed for the rapid identification of Salmonella Typhimurium, Salmonella Saintpaul, Salmonella Typhi, Shigella dysenteriae, Escherichia coli O157:H7, Francisella tularensis subsp. tularensis, Francisella tularensis subsp. novicida, Vibrio cholerae, Vibrio parahaemolyticus, Yersinia pestis, and Yersinia pseudotuberculosis. Previously, we identified highly specific primers targeting each of these pathogens. Here, we report the development of customizable PCR-microplate arrays for simultaneous identification of the pathogens using the primers identified. A mixed aliquot of genomic DNA from 38 strains was used to validate three PCR-microplate array formats. Identical PCR conditions were used to run all the samples on the three formats. Specific amplifications were obtained on all three custom plates. In preliminary tests performed to evaluate the sensitivity of these assays in samples inoculated in the laboratory with Salmonella Typhimurium, amplifications were obtained from 1 g of beef hot dog inoculated at as low as 9 CFU/ml or from milk inoculated at as low as 78 CFU/ml. Such microplate arrays could be valuable tools for initial identification or secondary confirmation of contamination by these pathogens.

  13. The potential of TaqMan Array Cards for detection of multiple biological agents by real-time PCR.

    Directory of Open Access Journals (Sweden)

    Phillip A Rachwal

    Full Text Available The TaqMan Array Card architecture, normally used for gene expression studies, was evaluated for its potential to detect multiple bacterial agents by real-time PCR. Ten PCR assays targeting five biological agents (Bacillus anthracis, Burkholderia mallei, Burkholderia pseudomallei, Francisella tularensis, and Yersinia pestis were incorporated onto Array Cards. A comparison of PCR performance of each PCR in Array Card and singleplex format was conducted using DNA extracted from pure bacterial cultures. When 100 fg of agent DNA was added to Array Card channels the following levels of agent detection (where at least one agent PCR replicate returned a positive result were observed: Y. pestis 100%, B. mallei & F. tularensis 93%; B. anthracis 71%; B. pseudomallei 43%. For B. mallei & pseudomallei detection the BPM2 PCR, which detects both species, outperformed PCR assays specific to each organism indicating identification of the respective species would not be reproducible at the 100 fg level. Near 100% levels of detection were observed when 100 fg of DNA was added to each PCR in singleplex format with singleplex PCRs also returning sporadic positives at the 10 fg per PCR level. Before evaluating the use of Array Cards for the testing of environmental and clinical sample types, with potential levels of background DNA and PCR inhibitors, users would therefore have to accept a 10-fold reduction in sensitivity of PCR assays on the Array Card format, in order to benefit for the capacity to test multiple samples for multiple agents. A two PCR per agent strategy would allow the testing of 7 samples for the presence of 11 biological agents or 3 samples for 23 biological agents per card (with negative control channels.

  14. PCR

    African Journals Online (AJOL)

    Elham

    2013-07-03

    Jul 3, 2013 ... was constructed with competitive strategy by PCR-cloning technique and the limitation range was determined. The PCR products of MTB and IAC were 245 and 660 bp, respectively on .... products' differentiation was easy.

  15. Accurate confidence aware clustering of array CGH tumor profiles.

    NARCIS (Netherlands)

    van Houte, B.P.P.; Heringa, J.

    2010-01-01

    Motivation: Chromosomal aberrations tend to be characteristic for given (sub)types of cancer. Such aberrations can be detected with array comparative genomic hybridization (aCGH). Clustering aCGH tumor profiles aids in identifying chromosomal regions of interest and provides useful diagnostic

  16. Kinome profiling of Arabidopsis using arrays of kinase consensus substrates

    Directory of Open Access Journals (Sweden)

    Pieterse Corné MJ

    2007-02-01

    Full Text Available Abstract Background Kinome profiling aims at the parallel analysis of kinase activities in a cell. Novel developed arrays containing consensus substrates for kinases are used to assess those kinase activities. The arrays described in this paper were already used to determine kinase activities in mammalian systems, but since substrates from many organisms are present we decided to test these arrays for the determination of kinase activities in the model plant species Arabidopsis thaliana. Results Kinome profiling using Arabidopsis cell extracts resulted in the labelling of many consensus peptides by kinases from the plant, indicating the usefulness of this kinome profiling tool for plants. Method development showed that fresh and frozen plant material could be used to make cell lysates containing active kinases. Dilution of the plant extract increased the signal to noise ratio and non-radioactive ATP enhances full development of spot intensities. Upon infection of Arabidopsis with an avirulent strain of the bacterial pathogen Pseudomonas syringae pv. tomato, we could detect differential kinase activities by measuring phosphorylation of consensus peptides. Conclusion We show that kinome profiling on arrays with consensus substrates can be used to monitor kinase activities in plants. In a case study we show that upon infection with avirulent P. syringae differential kinase activities can be found. The PepChip can for example be used to purify (unknown kinases that play a role in P. syringae infection. This paper shows that kinome profiling using arrays of consensus peptides is a valuable new tool to study signal-transduction in plants. It complements the available methods for genomics and proteomics research.

  17. PCR/LDR/universal array platforms for the diagnosis of infectious disease.

    Science.gov (United States)

    Pingle, Maneesh; Rundell, Mark; Das, Sanchita; Golightly, Linnie M; Barany, Francis

    2010-01-01

    Infectious diseases account for between 14 and 17 million deaths worldwide each year. Accurate and rapid diagnosis of bacterial, fungal, viral, and parasitic infections is therefore essential to reduce the morbidity and mortality associated with these diseases. Classical microbiological and serological methods have long served as the gold standard for diagnosis but are increasingly being replaced by molecular diagnostic methods that demonstrate increased sensitivity and specificity and provide an identification of the etiologic agent in a shorter period of time. PCR/LDR coupled with universal array detection provides a highly sensitive and specific platform for the detection and identification of bacterial and viral infections.

  18. Low profile conformal antenna arrays on high impedance substrate

    CERN Document Server

    Singh, Hema; Jha, Rakesh Mohan

    2016-01-01

    This book presents electromagnetic (EM) design and analysis of dipole antenna array over high impedance substrate (HIS). HIS is a preferred substrate for low-profile antenna design, owing to its unique boundary conditions. Such substrates permit radiating elements to be printed on them without any disturbance in the radiation characteristics. Moreover HIS provides improved impedance matching, enhanced bandwidth, and increased broadside directivity owing to total reflection from the reactive surface and high input impedance. This book considers different configurations of HIS for array design on planar and non-planar high-impedance surfaces. Results are presented for cylindrical dipole, printed dipole, and folded dipole over single- and double-layered square-patch-based HIS and dogbone-based HIS. The performance of antenna arrays is analyzed in terms of performance parameters such as return loss and radiation pattern. The design presented shows acceptable return loss and mainlobe gain of radiation pattern. Thi...

  19. Evaluation of methods for oligonucleotide array data via quantitative real-time PCR.

    Science.gov (United States)

    Qin, Li-Xuan; Beyer, Richard P; Hudson, Francesca N; Linford, Nancy J; Morris, Daryl E; Kerr, Kathleen F

    2006-01-17

    There are currently many different methods for processing and summarizing probe-level data from Affymetrix oligonucleotide arrays. It is of great interest to validate these methods and identify those that are most effective. There is no single best way to do this validation, and a variety of approaches is needed. Moreover, gene expression data are collected to answer a variety of scientific questions, and the same method may not be best for all questions. Only a handful of validation studies have been done so far, most of which rely on spike-in datasets and focus on the question of detecting differential expression. Here we seek methods that excel at estimating relative expression. We evaluate methods by identifying those that give the strongest linear association between expression measurements by array and the "gold-standard" assay. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) is generally considered the "gold-standard" assay for measuring gene expression by biologists and is often used to confirm findings from microarray data. Here we use qRT-PCR measurements to validate methods for the components of processing oligo array data: background adjustment, normalization, mismatch adjustment, and probeset summary. An advantage of our approach over spike-in studies is that methods are validated on a real dataset that was collected to address a scientific question. We initially identify three of six popular methods that consistently produced the best agreement between oligo array and RT-PCR data for medium- and high-intensity genes. The three methods are generally known as MAS5, gcRMA, and the dChip mismatch mode. For medium- and high-intensity genes, we identified use of data from mismatch probes (as in MAS5 and dChip mismatch) and a sequence-based method of background adjustment (as in gcRMA) as the most important factors in methods' performances. However, we found poor reliability for methods using mismatch probes for low-intensity genes

  20. Evaluation of methods for oligonucleotide array data via quantitative real-time PCR

    Directory of Open Access Journals (Sweden)

    Morris Daryl E

    2006-01-01

    Full Text Available Abstract Background There are currently many different methods for processing and summarizing probe-level data from Affymetrix oligonucleotide arrays. It is of great interest to validate these methods and identify those that are most effective. There is no single best way to do this validation, and a variety of approaches is needed. Moreover, gene expression data are collected to answer a variety of scientific questions, and the same method may not be best for all questions. Only a handful of validation studies have been done so far, most of which rely on spike-in datasets and focus on the question of detecting differential expression. Here we seek methods that excel at estimating relative expression. We evaluate methods by identifying those that give the strongest linear association between expression measurements by array and the "gold-standard" assay. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR is generally considered the "gold-standard" assay for measuring gene expression by biologists and is often used to confirm findings from microarray data. Here we use qRT-PCR measurements to validate methods for the components of processing oligo array data: background adjustment, normalization, mismatch adjustment, and probeset summary. An advantage of our approach over spike-in studies is that methods are validated on a real dataset that was collected to address a scientific question. Results We initially identify three of six popular methods that consistently produced the best agreement between oligo array and RT-PCR data for medium- and high-intensity genes. The three methods are generally known as MAS5, gcRMA, and the dChip mismatch mode. For medium- and high-intensity genes, we identified use of data from mismatch probes (as in MAS5 and dChip mismatch and a sequence-based method of background adjustment (as in gcRMA as the most important factors in methods' performances. However, we found poor reliability for methods

  1. 1-Million droplet array with wide-field fluorescence imaging for digital PCR.

    Science.gov (United States)

    Hatch, Andrew C; Fisher, Jeffrey S; Tovar, Armando R; Hsieh, Albert T; Lin, Robert; Pentoney, Stephen L; Yang, David L; Lee, Abraham P

    2011-11-21

    Digital droplet reactors are useful as chemical and biological containers to discretize reagents into picolitre or nanolitre volumes for analysis of single cells, organisms, or molecules. However, most DNA based assays require processing of samples on the order of tens of microlitres and contain as few as one to as many as millions of fragments to be detected. Presented in this work is a droplet microfluidic platform and fluorescence imaging setup designed to better meet the needs of the high-throughput and high-dynamic-range by integrating multiple high-throughput droplet processing schemes on the chip. The design is capable of generating over 1-million, monodisperse, 50 picolitre droplets in 2-7 minutes that then self-assemble into high density 3-dimensional sphere packing configurations in a large viewing chamber for visualization and analysis. This device then undergoes on-chip polymerase chain reaction (PCR) amplification and fluorescence detection to digitally quantify the sample's nucleic acid contents. Wide-field fluorescence images are captured using a low cost 21-megapixel digital camera and macro-lens with an 8-12 cm(2) field-of-view at 1× to 0.85× magnification, respectively. We demonstrate both end-point and real-time imaging ability to perform on-chip quantitative digital PCR analysis of the entire droplet array. Compared to previous work, this highly integrated design yields a 100-fold increase in the number of on-chip digitized reactors with simultaneous fluorescence imaging for digital PCR based assays.

  2. Characterization of some Brucella species from Zimbabwe by biochemical profiling and AMOS-PCR

    Directory of Open Access Journals (Sweden)

    Skjerve Eystein

    2009-12-01

    Full Text Available Abstract Background Bovine brucellosis caused by Brucella abortus is endemic in most large commercial and smallholder cattle farms of Zimbabwe, while brucellosis in other domestic animals is rare. The diagnosis of brucellosis is mainly accomplished using serological tests. However, some Brucella spp. have been isolated from clinical cases in the field and kept in culture collection but their biochemical profiles were not documented. We report biochemical profiling and AMOS-PCR characterization of some of these field isolates of Brucella originating from both commercial and smallholder cattle farming sectors of Zimbabwe. Findings Fourteen isolates of Brucella from culture collection were typed using biochemical profiles, agglutination by monospecific antisera, susceptibility to Brucella-specific bacteriophages and by AMOS-PCR that amplifies species- specific IS711. The results of the biochemical profiles for B. abortus biovar 1 (11 isolates and biovar 2 (2 isolates were consistent with those of reference strains. A single isolate from a goat originating from a smallholder mixed animal farm was identified as B. melitensis biovar 1. The AMOS-PCR produced DNA products of sizes 498 bp and 731 bp for B. abortus (biovar 1 and 2 and B. melitensis biovar 1, respectively. Conclusion We concluded that the biochemical profiles and AMOS-PCR characterization were consistent with their respective species and biovars. B. abortus biovar 1 is likely to be the predominant cause of brucellosis in both commercial and smallholder cattle farms in Zimbabwe.

  3. Identification of Multiple Bacteriocins in Enterococcus spp. Using an Enterococcus-Specific Bacteriocin PCR Array

    Directory of Open Access Journals (Sweden)

    Chris Henning

    2015-02-01

    Full Text Available Twenty-two bacteriocin-producing Enterococcus isolates obtained from food and animal sources, and demonstrating activity against Listeria monocytogenes, were screened for bacteriocin-related genes using a bacteriocin PCR array based on known enterococcal bacteriocin gene sequences in the NCBI GenBank database. The 22 bacteriocin-positive (Bac+ enterococci included En. durans (1, En. faecalis (4, En. faecium (12, En. hirae (3, and En. thailandicus (2. Enterocin A (entA, enterocins mr10A and mr10B (mr10AB, and bacteriocin T8 (bacA were the most commonly found structural genes in order of decreasing prevalence. Forty-five bacteriocin genes were identified within the 22 Bac+ isolates, each containing at least one of the screened structural genes. Of the 22 Bac+ isolates, 15 possessed two bacteriocin genes, seven isolates contained three different bacteriocins, and three isolates contained as many as four different bacteriocin genes. These results may explain the high degree of bactericidal activity observed with various Bac+ Enterococcus spp. Antimicrobial activity against wild-type L. monocytogenes and a bacteriocin-resistant variant demonstrated bacteriocins having different modes-of-action. Mixtures of bacteriocins, especially those with different modes-of-action and having activity against foodborne pathogens, such as L. monocytogenes, may play a promising role in the preservation of food.

  4. Riems influenza a typing array (RITA): An RT-qPCR-based low density array for subtyping avian and mammalian influenza a viruses.

    Science.gov (United States)

    Hoffmann, Bernd; Hoffmann, Donata; Henritzi, Dinah; Beer, Martin; Harder, Timm C

    2016-06-03

    Rapid and sensitive diagnostic approaches are of the utmost importance for the detection of humans and animals infected by specific influenza virus subtype(s). Cascade-like diagnostics starting with the use of pan-influenza assays and subsequent subtyping devices are normally used. Here, we demonstrated a novel low density array combining 32 TaqMan(®) real-time RT-PCR systems in parallel for the specific detection of the haemagglutinin (HA) and neuraminidase (NA) subtypes of avian and porcine hosts. The sensitivity of the newly developed system was compared with that of the pan-influenza assay, and the specificity of all RT-qPCRs was examined using a broad panel of 404 different influenza A virus isolates representing 45 different subtypes. Furthermore, we analysed the performance of the RT-qPCR assays with diagnostic samples obtained from wild birds and swine. Due to the open format of the array, adaptations to detect newly emerging influenza A virus strains can easily be integrated. The RITA array represents a competitive, fast and sensitive subtyping tool that requires neither new machinery nor additional training of staff in a lab where RT-qPCR is already established.

  5. DNA profiling of spermatozoa by laser capture microdissection and low volume-PCR.

    Directory of Open Access Journals (Sweden)

    Cai-xia Li

    Full Text Available Genetic profiling of sperm from complex biological mixtures such as sexual assault casework samples requires isolation of a pure sperm population and the ability to analyze low abundant samples. Current standard procedure for sperm isolation includes preferential lysis of epithelial contaminants followed by collection of intact sperm by centrifugation. While effective for samples where sperm are abundant, this method is less effective when samples contain few spermatozoa. Laser capture microdissection (LCM is a proven method for the isolation of cells biological mixtures, even when found in low abundance. Here, we demonstrate the efficacy of LCM coupled with on-chip low volume PCR (LV-PCR for the isolation and genotyping of low abundance sperm samples. Our results indicate that this method can obtain complete profiles (13-16 loci from as few as 15 sperm cells with 80% reproducibility, whereas at least 40 sperm cells are required to profile 13-16 loci by standard 'in-tube' PCR. Further, LCM and LV-PCR of a sexual assault casework sample generated a DNA genotype that was consistent with that of the suspect. This method was unable, however, to analyze a casework sample from a gang rape case in which two or more sperm contributors were in a mixed population. The results indicate that LCM and LV-PCR is sensitive and effective for genotyping sperm from sperm/epithelial cell mixtures when epithelial lysis may be insufficient due to low abundance of sperm; LCM and LV-PCR, however, failed in a casework sample when spermatozoa from multiple donors was present, indicating that further study is necessitated.

  6. Biogeochemical sensor performance in the SOCCOM profiling float array

    Science.gov (United States)

    Johnson, Kenneth S.; Plant, Joshua N.; Coletti, Luke J.; Jannasch, Hans W.; Sakamoto, Carole M.; Riser, Stephen C.; Swift, Dana D.; Williams, Nancy L.; Boss, Emmanuel; Haëntjens, Nils; Talley, Lynne D.; Sarmiento, Jorge L.

    2017-08-01

    The Southern Ocean Carbon and Climate Observations and Modeling (SOCCOM) program has begun deploying a large array of biogeochemical sensors on profiling floats in the Southern Ocean. As of February 2016, 86 floats have been deployed. Here the focus is on 56 floats with quality-controlled and adjusted data that have been in the water at least 6 months. The floats carry oxygen, nitrate, pH, chlorophyll fluorescence, and optical backscatter sensors. The raw data generated by these sensors can suffer from inaccurate initial calibrations and from sensor drift over time. Procedures to correct the data are defined. The initial accuracy of the adjusted concentrations is assessed by comparing the corrected data to laboratory measurements made on samples collected by a hydrographic cast with a rosette sampler at the float deployment station. The long-term accuracy of the corrected data is compared to the GLODAPv2 data set whenever a float made a profile within 20 km of a GLODAPv2 station. Based on these assessments, the fleet average oxygen data are accurate to 1 ± 1%, nitrate to within 0.5 ± 0.5 µmol kg-1, and pH to 0.005 ± 0.007, where the error limit is 1 standard deviation of the fleet data. The bio-optical measurements of chlorophyll fluorescence and optical backscatter are used to estimate chlorophyll a and particulate organic carbon concentration. The particulate organic carbon concentrations inferred from optical backscatter appear accurate to with 35 mg C m-3 or 20%, whichever is larger. Factors affecting the accuracy of the estimated chlorophyll a concentrations are evaluated.Plain Language SummaryThe ocean science community must move toward greater use of autonomous platforms and sensors if we are to extend our knowledge of the effects of climate driven change within the ocean. Essential to this shift in observing strategies is an understanding of the performance that can be obtained from biogeochemical sensors on platforms deployed for years and the

  7. Identification of circulating miRNA biomarkers based on global quantitative real-time PCR profiling

    Directory of Open Access Journals (Sweden)

    Kang Kang

    2012-02-01

    Full Text Available Abstract MicroRNAs (miRNAs are small noncoding RNAs (18-25 nucleotides that regulate gene expression at the post-transcriptional level. Recent studies have demonstrated the presence of miRNAs in the blood circulation. Deregulation of miRNAs in serum or plasma has been associated with many diseases including cancers and cardiovascular diseases, suggesting the possible use of miRNAs as diagnostic biomarkers. However, the detection of the small amount of miRNAs found in serum or plasma requires a method with high sensitivity and accuracy. Therefore, the current study describes polymerase chain reaction (PCR-based methods for measuring circulating miRNAs. Briefly, the procedure involves four major steps: (1 sample collection and preparation; (2 global miRNAs profiling using quantitative real-time PCR (qRT-PCR; (3 data normalization and analysis; and (4 selection and validation of miRNA biomarkers. In conclusion, qRT-PCR is a promising method for profiling of circulating miRNAs as biomarkers.

  8. The workflow of single-cell expression profiling using quantitative real-time PCR

    Czech Academy of Sciences Publication Activity Database

    Stahlberg, A.; Kubista, Mikael

    2014-01-01

    Roč. 14, č. 3 (2014), s. 323-331 ISSN 1473-7159 R&D Projects: GA ČR GA13-02154S; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:86652036 Keywords : single-cell workflow * gene expression profiling * RT-qPCR Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.516, year: 2014

  9. Genetic profiles of gastroesophageal cancer: combined analysis using expression array and tiling array--comparative genomic hybridization

    DEFF Research Database (Denmark)

    Isinger-Ekstrand, Anna; Johansson, Jan; Ohlsson, Mattias

    2010-01-01

    15, 13q34, and 12q13, whereas different profiles with gains at 5p15, 7p22, 2q35, and 13q34 characterized gastric cancers. CDK6 and EGFR were identified as putative target genes in cancers of the esophagus and the gastroesophageal junction, with upregulation in one quarter of the tumors. Gains......We aimed to characterize the genomic profiles of adenocarcinomas in the gastroesophageal junction in relation to cancers in the esophagus and the stomach. Profiles of gains/losses as well as gene expression profiles were obtained from 27 gastroesophageal adenocarcinomas by means of 32k high......-resolution array-based comparative genomic hybridization and 27k oligo gene expression arrays, and putative target genes were validated in an extended series. Adenocarcinomas in the distal esophagus and the gastroesophageal junction showed strong similarities with the most common gains at 20q13, 8q24, 1q21-23, 5p...

  10. A Novel Pressure Indicator for Continuous Flow PCR Chip Using Micro Molded PDMS Pillar Arrays

    National Research Council Canada - National Science Library

    Zhao, Yi; Zhang, Xin

    2005-01-01

    .... Continuous flow PCR chip releases biologists from their laborious exercises. The use of such chip is, however, hindered by costly expense of the syringe pump, which is used to maintain a constant flow rate...

  11. Rice1265 Array: PCR check - RMOS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available rophoresis were applied. Data analysis method Upper and Lower primer (refer to the ...cale cDNA analysis in RGP (rice genome research program). To check the clone uniqueness, PCR and gel-elect

  12. Digital quantification of gene methylation in stool DNA by emulsion-PCR coupled with hydrogel immobilized bead-array.

    Science.gov (United States)

    Liu, Yunlong; Wu, Haiping; Zhou, Qiang; Song, Qinxin; Rui, Jianzhong; Zou, Bingjie; Zhou, Guohua

    2017-06-15

    Aberrations of gene methylation in stool DNA (sDNA) is an effective biomarker for non-invasive colorectal cancer diagnosis. However, it is challenging to accurately quantitate the gene methylation levels in sDNA due to the low abundance and degradation of sDNA. In this study, a digital quantification strategy was proposed by combining emulsion PCR (emPCR) with hydrogel immobilized bead-array. The assay includes following steps: bisulfite conversion of sDNA, pre-amplification by PCR with specific primers containing 5' universal sequences, emPCR of pre-amplicons with beaded primers to achieve single-molecular amplification and identification of hydrogel embedding beads coated with amplicons. The sensitivity and the specificity of the method are high enough to pick up 0.05% methylated targets from unmethylated DNA background. The successful detection of hypermethylated vimentin gene in clinical stool samples suggests that the proposed method should be a potential tool for non-invasive colorectal cancer screening. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. High Throughput Sample Preparation and Analysis for DNA Sequencing, PCR and Combinatorial Screening of Catalysis Based on Capillary Array Technique

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yonghua [Iowa State Univ., Ames, IA (United States)

    2000-01-01

    Sample preparation has been one of the major bottlenecks for many high throughput analyses. The purpose of this research was to develop new sample preparation and integration approach for DNA sequencing, PCR based DNA analysis and combinatorial screening of homogeneous catalysis based on multiplexed capillary electrophoresis with laser induced fluorescence or imaging UV absorption detection. The author first introduced a method to integrate the front-end tasks to DNA capillary-array sequencers. protocols for directly sequencing the plasmids from a single bacterial colony in fused-silica capillaries were developed. After the colony was picked, lysis was accomplished in situ in the plastic sample tube using either a thermocycler or heating block. Upon heating, the plasmids were released while chromsomal DNA and membrane proteins were denatured and precipitated to the bottom of the tube. After adding enzyme and Sanger reagents, the resulting solution was aspirated into the reaction capillaries by a syringe pump, and cycle sequencing was initiated. No deleterious effect upon the reaction efficiency, the on-line purification system, or the capillary electrophoresis separation was observed, even though the crude lysate was used as the template. Multiplexed on-line DNA sequencing data from 8 parallel channels allowed base calling up to 620 bp with an accuracy of 98%. The entire system can be automatically regenerated for repeated operation. For PCR based DNA analysis, they demonstrated that capillary electrophoresis with UV detection can be used for DNA analysis starting from clinical sample without purification. After PCR reaction using cheek cell, blood or HIV-1 gag DNA, the reaction mixtures was injected into the capillary either on-line or off-line by base stacking. The protocol was also applied to capillary array electrophoresis. The use of cheaper detection, and the elimination of purification of DNA sample before or after PCR reaction, will make this approach an

  14. A novel lab-on-chip platform with integrated solid phase PCR and Supercritical Angle Fluorescence (SAF) microlens array for highly sensitive and multiplexed pathogen detection

    DEFF Research Database (Denmark)

    Hung, Tran Quang; Chin, Wai Hoe; Sun, Yi

    2016-01-01

    technology. In this paper, we addressed this challenge by combining the SP-PCR with super critical angle fluorescence (SAF) microlens array embedded in a microchip. We fabricated miniaturized SAF microlens array as part of a microfluidic chamber in thermoplastic material and performed multiplexed SP...

  15. Absorption and emission profiles of unresolved arrays near local thermodynamic equilibrium

    Energy Technology Data Exchange (ETDEWEB)

    Busquet, M.; Klapisch, M. E-mail: klapisch@this.nrl.navy.mil; Bar-Shalom, A

    2003-11-01

    The absorption and emission arrays in the unresolved transition array (UTA) and super transition array (STA) models are usually assumed to have the same Gaussian spectral shape. It is shown, starting from a Boltzmann population distribution, that the assumption of profile identity for both absorption and emission is inconsistent with Kirchhoff's law. A correcting formula is established. It is extended to the cases where one or two effective population temperatures are involved. Examples are shown where the effect is noticeable.

  16. Absorption and emission profiles of unresolved arrays near local thermodynamic equilibrium

    International Nuclear Information System (INIS)

    Busquet, M.; Klapisch, M.; Bar-Shalom, A.

    2003-01-01

    The absorption and emission arrays in the unresolved transition array (UTA) and super transition array (STA) models are usually assumed to have the same Gaussian spectral shape. It is shown, starting from a Boltzmann population distribution, that the assumption of profile identity for both absorption and emission is inconsistent with Kirchhoff's law. A correcting formula is established. It is extended to the cases where one or two effective population temperatures are involved. Examples are shown where the effect is noticeable

  17. Compression dynamics of quasi-spherical wire arrays with different linear mass profiles

    International Nuclear Information System (INIS)

    Mitrofanov, K. N.; Aleksandrov, V. V.; Gritsuk, A. N.; Grabovski, E. V.; Frolov, I. N.; Laukhin, Ya. N.; Oleinik, G. M.; Ol’khovskaya, O. G.

    2016-01-01

    Results of experimental studies of the implosion of quasi-spherical wire (or metalized fiber) arrays are presented. The goal of the experiments was to achieve synchronous three-dimensional compression of the plasma produced in different regions of a quasi-spherical array into its geometrical center. To search for optimal synchronization conditions, quasi-spherical arrays with different initial profiles of the linear mass were used. The following dependences of the linear mass on the poloidal angle were used: m_l(θ) ∝ sin"–"1θ and m_l(θ) ∝ sin"–"2θ. The compression dynamics of such arrays was compared with that of quasi-spherical arrays without linear mass profiling, m_l(θ) = const. To verify the experimental data, the spatiotemporal dynamics of plasma compression in quasi-spherical arrays was studied using various diagnostics. The experiments on three-dimensional implosion of quasi-spherical arrays made it possible to study how the frozen-in magnetic field of the discharge current penetrates into the array. By measuring the magnetic field in the plasma of a quasi-spherical array, information is obtained on the processes of plasma production and formation of plasma flows from the wire/fiber regions with and without an additionally deposited mass. It is found that penetration of the magnetic flux depends on the initial linear mass profile m_l(θ) of the quasi-spherical array. From space-resolved spectral measurements and frame imaging of plasma X-ray emission, information is obtained on the dimensions and shape of the X-ray source formed during the implosion of a quasi-spherical array. The intensity of this source is estimated and compared with that of the Z-pinch formed during the implosion of a cylindrical array.

  18. Two-dimensional beam-profile monitor using the Reticon MC510A array camera

    International Nuclear Information System (INIS)

    Gottschalk, B.

    1981-08-01

    A quantitative two-dimensional beam profile may be obtained from a scintillator viewed by a Reticon camera which uses a 32 x 32 array of photodiodes as its sensing element. In this note, CAMAC-oriented data acquisition electronics which allow one either to transmit the profile to a computer, or to use the monitor in a stand-alone mode are described

  19. Molecular characterization of Salmonella enterica serotype Enteritidis isolates from food and human samples by serotyping, antimicrobial resistance, plasmid profiling, (GTG5-PCR and ERIC-PCR

    Directory of Open Access Journals (Sweden)

    F. Fardsanei

    2016-11-01

    Full Text Available In recent years, Salmonella enterica serovar Enteritidis has been a primary cause of human salmonellosis in many countries. The major objective of this study was to investigate genetic diversity among Salmonella Enteritidis strains from different origins (food and human by Enterobacterial Repetitive Intergenic Consensus (ERIC -PCR, as well as to assess their plasmid profiling and antimicrobial resistance. A total of 30 Salmonella Enteritidis isolates, 15 from food samples (chicken, lamb, beef and duck meats and 15 from clinical samples were collected in Tehran. Identification of isolates as Salmonella was confirmed by using conventional standard biochemical and serological tests. Multiplex-PCR was used for serotyping of isolates to identify Salmonella Enteritidis. Antimicrobial susceptibility testing to 16 agents founds drug resistance patterns among Salmonella Enteritidis isolates. No resistance was observed to cephalexin, ceftriaxone, ceftazidime and cefotaxime, ciprofloxacin, imipenem or meropenem, chloramphenicol and gentamicin. The highest resistance (96.7% was observed to nitrofurantoin. Seven plasmid profiles (P1–P7 were detected, and a 68-kb plasmid was found in all isolates. Two different primers; ERIC and (GTG5 were used for genotyping, which each produced four profiles. The majority of clinical and food isolates fell into two separate common types (CTs with a similar percentage of 95% by ERIC-PCR. Using primer (GTG5, 29 isolates incorporated in three CTs with 70% of isolates showing a single banding pattern. Limited genetic diversity among human and food isolates of Salmonella Enteritidis may indicate that contaminated foods were possibly the source of human salmonellosis. These results confirmed that ERIC-PCR genotyping has limited discriminatory power for Salmonella Enteritidis of different origin.

  20. Breast Carcinoma Cells in Primary Tumors and Effusions Have Different Gene Array Profiles

    Directory of Open Access Journals (Sweden)

    Sophya Konstantinovsky

    2010-01-01

    Full Text Available The detection of breast carcinoma cells in effusions is associated with rapidly fatal outcome, but these cells are poorly characterized at the molecular level. This study compared the gene array signatures of breast carcinoma cells in primary carcinomas and effusions. The genetic signature of 10 primary tumors and 10 effusions was analyzed using the Array-Ready Oligo set for the Human Genome platform. Results for selected genes were validated using PCR, Western blotting, and immunohistochemistry. Array analysis identified 255 significantly downregulated and 96 upregulated genes in the effusion samples. The majority of differentially expressed genes were part of pathways involved in focal adhesion, extracellular matrix-cell interaction, and the regulation of the actin cytoskeleton. Genes that were upregulated in effusions included KRT8, BCAR1, CLDN4, VIL2, while DCN, CLDN19, ITGA7, and ITGA5 were downregulated at this anatomic site. PCR, Western blotting, and immunohistochemistry confirmed the array findings for BCAR1, CLDN4, VIL2, and DCN. Our data show that breast carcinoma cells in primary carcinomas and effusions have different gene expression signatures, and differentially express a large number of molecules related to adhesion, motility, and metastasis. These differences may have a critical role in designing therapy and in prognostication for patients with metastatic disease localized to the serosal cavities.

  1. Real-time PCR array as a universal platform for the detection of genetically modified crops and its application in identifying unapproved genetically modified crops in Japan.

    Science.gov (United States)

    Mano, Junichi; Shigemitsu, Natsuki; Futo, Satoshi; Akiyama, Hiroshi; Teshima, Reiko; Hino, Akihiro; Furui, Satoshi; Kitta, Kazumi

    2009-01-14

    We developed a novel type of real-time polymerase chain reaction (PCR) array with TaqMan chemistry as a platform for the comprehensive and semiquantitative detection of genetically modified (GM) crops. Thirty primer-probe sets for the specific detection of GM lines, recombinant DNA (r-DNA) segments, endogenous reference genes, and donor organisms were synthesized, and a 96-well PCR plate was prepared with a different primer-probe in each well as the real-time PCR array. The specificity and sensitivity of the array were evaluated. A comparative analysis with the data and publicly available information on GM crops approved in Japan allowed us to assume the possibility of unapproved GM crop contamination. Furthermore, we designed a Microsoft Excel spreadsheet application, Unapproved GMO Checker version 2.01, which helps process all the data of real-time PCR arrays for the easy assumption of unapproved GM crop contamination. The spreadsheet is available free of charge at http://cse.naro.affrc.go.jp/jmano/index.html .

  2. Use of a custom RT-PCR array to analyze toxicity pathways at different life stages in Brown Norway Rat Brain following acute Toluene exposure.

    Science.gov (United States)

    To investigate the contribution of different life stages on response to toxicants, we utilized a custom designed RT-PCR array to examine the effects of acute exposure by oral gavage of the volatile organic solvent toluene (0.00, 0.65 or 1.0 glkg) in the brains of ma1e Brown Norwa...

  3. Diagnostic evaluation of a multiplexed RT-PCR microsphere array assay for the detection of foot-and-mouth disease virus and look-alike disease viruses

    Energy Technology Data Exchange (ETDEWEB)

    Hindson, B J; Reid, S M; Baker, B R; Ebert, K; Ferris, N P; Bentley Tammero, L F; Lenhoff, R J; Naraghi-Arani, P; Vitalis, E A; Slezak, T R; Hullinger, P J; King, D P

    2007-07-26

    A high-throughput multiplexed assay was developed for the differential laboratory diagnosis of foot-and-mouth disease virus (FMDV) from viruses which cause clinically similar diseases of livestock. This assay simultaneously screens for five RNA and two DNA viruses using multiplexed reverse transcription PCR (mRT-PCR) amplification coupled with a microsphere hybridization array and flow-cytometric detection. Two of the seventeen primer-probe sets included in this multiplex assay were adopted from previously characterized real-time RT-PCR (rRT-PCR) assays for FMDV. The diagnostic accuracy of the mRT-PCR was evaluated using 287 field samples, including 248 (true positive n= 213, true negative n=34) from suspect cases of foot-and-mouth disease collected from 65 countries between 1965 and 2006 and 39 true negative samples collected from healthy animals. The mRT-PCR assay results were compared with two singleplex rRT-PCR assays, using virus isolation with antigen-ELISA as the reference method. The diagnostic sensitivity of the mRT-PCR assay for FMDV was 93.9% [95% C.I. 89.8-96.4%], compared to 98.1% [95% C.I. 95.3-99.3%] for the two singleplex rRT-PCR assays used in combination. In addition, the assay could reliably differentiate between FMDV and other vesicular viruses such as swine vesicular disease virus and vesicular exanthema of swine virus. Interestingly, the mRT-PCR detected parapoxvirus (n=2) and bovine viral diarrhea virus (n=2) in clinical samples, demonstrating the screening potential of this mRT-PCR assay to identify viruses in FMDV-negative material not previously recognized using focused single-target rRT-PCR assays.

  4. Visualisation of air–water bubbly column flow using array Ultrasonic Velocity Profiler

    Directory of Open Access Journals (Sweden)

    Munkhbat Batsaikhan

    2017-11-01

    Full Text Available In the present work, an experimental study of bubbly two-phase flow in a rectangular bubble column was performed using two ultrasonic array sensors, which can measure the instantaneous velocity of gas bubbles on multiple measurement lines. After the sound pressure distribution of sensors had been evaluated with a needle hydrophone technique, the array sensors were applied to two-phase bubble column. To assess the accuracy of the measurement system with array sensors for one and two-dimensional velocity, a simultaneous measurement was performed with an optical measurement technique called particle image velocimetry (PIV. Experimental results showed that accuracy of the measurement system with array sensors is under 10% for one-dimensional velocity profile measurement compared with PIV technique. The accuracy of the system was estimated to be under 20% along the mean flow direction in the case of two-dimensional vector mapping.

  5. The reproducibility of RAPD profiles: Effects of PCR components on RAPD analysis of four centaurium species

    Directory of Open Access Journals (Sweden)

    Skorić Marijana

    2012-01-01

    Full Text Available Random amplified polymorphic DNA (RAPD analysis is a simple and reliable method used to detect DNA polymorphism. Several factors can affect the amplification profiles, thereby causing false bands and non-reproducibility of the assay. In this study, we analyzed the effects of different concentrations of primer, magnesium chloride, template DNA and Taq DNA polymerase to develop and standardize a RAPD protocol for Centaurium species. The optimized PCR reaction mixture included: 50 ng of DNA extracted using a CTbased protocol, 2.5 mM MgCl2, 7.5 pmol primer and 2 U of Taq polymerase in a final volume of 25 μl. Each of the five primers used in experiments (OPB11, OPB15, OPB18, OPF05 and OPH02 generated reproducible and distinguishable fingerprinting patterns of four Centaurium species. The obtained optimized RAPD protocol and the selected primers are useful for our further work in the genetic diversity studies of Centaurium species.

  6. Detailed profiling of CNTs arrays along the growth window in a floating catalyst reactor

    International Nuclear Information System (INIS)

    Maghrebi, Morteza; Khodadadi, Abbas Ali; Mortazavi, Yadollah; Mhaisalkar, Subodh

    2009-01-01

    We report a detailed longitudinal and depth profiles of multi-wall carbon nanotubes (CNTs) arrays synthesized using xylene and ferrocene in a floating catalyst reactor. Point to point analyses of the CNTs grown in a 'growth window' with CNTs arrays longer than 0.5 mm were performed using optical microscopy, Raman spectroscopy, FESEM, high-resolution TGA/DTA, and TEM techniques. The heights of the CNTs arrays show a maximum at a mid point of the growth window, while a reverse trend of minimum is observed for iron-to-CNTs atomic ratios. The ratio of amorphous carbon to CNTs sharply increases along the growth window and from the bottom to top of CNTs arrays. The CNTs diameter also increases along the growth window, due to deposition of the amorphous carbon, which can be almost removed by temperature programmed oxidation up to around 500 deg. C. A base growth mechanism, the variations of catalyst content, residence time and temperature profile along the growth window, the adsorption and decomposition of polycyclic aromatic hydrocarbons to amorphous carbon, and a limited diffusion of hydrocarbon species through the arrays covered by excessive amorphous carbon may explain the results.

  7. Fabrication of Faraday Cup Array for the Measurement of 2-Dimensional Proton Beam Profile

    International Nuclear Information System (INIS)

    Jung, Myunghwan; Kim, Bom Sok; Kim, Kyeryung

    2014-01-01

    It has an advantage of easy-to-use and possible to visually check, immediately; on the other hand, the measurement range is very limited. Another method is using the CCD camera-scintillator device such as p43 phosphor screen or chromox. A variety of faraday cup detectors have been recently introduced. The faraday cup is one of the powerful and popular tools for the measurement of beam current. By using several faraday cups in array geometry, it is possible to observe current distribution. In this study, we developed an external faraday cup array for the measure the beam current and profile at a KOMAC (Korea Multi-purpose Accelerator Complex) beam utilization facility. To measure the beam profile, before fabrication of faraday cup array, we use gafchromic film. By making the faraday cup array we were able to reduce the consumption of Gafchromic film and a more accurate diagnosis of the proton beam is possible. The use of faraday cup array, experiment using the proton beam is more reliable and confident

  8. Flatness of two-dimensional beam profile measured with an ionization chamber array

    International Nuclear Information System (INIS)

    Stefanovski, Z.

    2006-01-01

    Open beam profiles are basic dosimetric characteristics for the formation of the dose calculation algorithms parameters and for determination of beam quality. One characteristic of the beam profiles as a measure for the beam quality is the field flatness defined as ratio of the difference of maximum and minimum dose in central 80% of the field to the sum of these doses in the part of the field. The measurements, instead with an ordinary ionization chamber, were performed with a chamber array in two depths (1.6 cm and 10 cm) in water phantom. Nominal photon beam energy was 6 MV and field size was 25 cm x 25 cm on the water surface. Field flatness was in the range of 1-2 % which is in accordance with the data acquired during the acceptance testing and commissioning of the accelerators. with the array chamber the beam profiles can be performed quickly and preciously. These features recommend a chamber array as an excellent tool for periodic quality control of beam profiles. (Author)

  9. Inversion for Sound Speed Profile by Using a Bottom Mounted Horizontal Line Array in Shallow Water

    International Nuclear Information System (INIS)

    Feng-Hua, Li; Ren-He, Zhang

    2010-01-01

    Ocean acoustic tomography is an appealing technique for remote monitoring of the ocean environment. In shallow water, matched field processing (MFP) with a vertical line array is one of the widely used methods for inverting the sound speed profile (SSP) of water column. The approach adopted is to invert the SSP with a bottom mounted horizontal line array (HLA) based on MFP. Empirical orthonormal functions are used to express the SSP, and perturbation theory is used in the forward sound field calculation. This inversion method is applied to the data measured in a shallow water acoustic experiment performed in 2003. Successful results show that the bottom mounted HLA is able to estimate the SSP. One of the most important advantages of the inversion method with bottom mounted HLA is that the bottom mounted HLA can keep a stable array shape and is safe in a relatively long period. (fundamental areas of phenomenology (including applications))

  10. Characterization of canine osteosarcoma by array comparative genomic hybridization and RT-qPCR: signatures of genomic imbalance in canine osteosarcoma parallel the human counterpart.

    Science.gov (United States)

    Angstadt, Andrea Y; Motsinger-Reif, Alison; Thomas, Rachael; Kisseberth, William C; Guillermo Couto, C; Duval, Dawn L; Nielsen, Dahlia M; Modiano, Jaime F; Breen, Matthew

    2011-11-01

    Osteosarcoma (OS) is the most commonly diagnosed malignant bone tumor in humans and dogs, characterized in both species by extremely complex karyotypes exhibiting high frequencies of genomic imbalance. Evaluation of genomic signatures in human OS using array comparative genomic hybridization (aCGH) has assisted in uncovering genetic mechanisms that result in disease phenotype. Previous low-resolution (10-20 Mb) aCGH analysis of canine OS identified a wide range of recurrent DNA copy number aberrations, indicating extensive genomic instability. In this study, we profiled 123 canine OS tumors by 1 Mb-resolution aCGH to generate a dataset for direct comparison with current data for human OS, concluding that several high frequency aberrations in canine and human OS are orthologous. To ensure complete coverage of gene annotation, we identified the human refseq genes that map to these orthologous aberrant dog regions and found several candidate genes warranting evaluation for OS involvement. Specifically, subsequenct FISH and qRT-PCR analysis of RUNX2, TUSC3, and PTEN indicated that expression levels correlated with genomic copy number status, showcasing RUNX2 as an OS associated gene and TUSC3 as a possible tumor suppressor candidate. Together these data demonstrate the ability of genomic comparative oncology to identify genetic abberations which may be important for OS progression. Large scale screening of genomic imbalance in canine OS further validates the use of the dog as a suitable model for human cancers, supporting the idea that dysregulation discovered in canine cancers will provide an avenue for complementary study in human counterparts. Copyright © 2011 Wiley-Liss, Inc.

  11. Quantitative PCR Profiling of Escherichia coli in Livestock Feces Reveals Increased Population Resilience Relative to Culturable Counts under Temperature Extremes.

    Science.gov (United States)

    Oliver, David M; Bird, Clare; Burd, Emmy; Wyman, Michael

    2016-09-06

    The relationship between culturable counts (CFU) and quantitative PCR (qPCR) cell equivalent counts of Escherichia coli in dairy feces exposed to different environmental conditions and temperature extremes was investigated. Fecal samples were collected in summer and winter from dairy cowpats held under two treatments: field-exposed versus polytunnel-protected. A significant correlation in quantified E. coli was recorded between the qPCR and culture-based methods (r = 0.82). Evaluation of the persistence profiles of E. coli over time revealed no significant difference in the E. coli numbers determined as either CFU or gene copies during the summer for the field-exposed cowpats, whereas significantly higher counts were observed by qPCR for the polytunnel-protected cowpats, which were exposed to higher ambient temperatures. In winter, the qPCR returned significantly higher counts of E. coli for the field-exposed cowpats, thus representing a reversal of the findings from the summer sampling campaign. Results from this study suggest that with increasing time post-defecation and with the onset of challenging environmental conditions, such as extremes in temperature, culture-based counts begin to underestimate the true resilience of viable E. coli populations in livestock feces. This is important not only in the long term as the Earth changes in response to climate-change drivers but also in the short term during spells of extremely cold or hot weather.

  12. Monitoring pressure profiles across an airfoil with a fiber Bragg grating sensor array

    Science.gov (United States)

    Papageorgiou, Anthony W.; Parkinson, Luke A.; Karas, Andrew R.; Hansen, Kristy L.; Arkwright, John W.

    2018-02-01

    Fluid flow over an airfoil section creates a pressure difference across the upper and lower surfaces, thus generating lift. Successful wing design is a combination of engineering design and experience in the field, with subtleties in design and manufacture having significant impact on the amount of lift produced. Current methods of airfoil optimization and validation typically involve computational fluid dynamics (CFD) and extensive wind tunnel testing with pressure sensors embedded into the airfoil to measure the pressure over the wing. Monitoring pressure along an airfoil in a wind tunnel is typically achieved using surface pressure taps that consist of hollow tubes running from the surface of the airfoil to individual pressure sensors external to the tunnel. These pressure taps are complex to configure and not ideal for in-flight testing. Fiber Bragg grating (FBG) pressure sensing arrays provide a highly viable option for both wind tunnel and inflight pressure measurement. We present a fiber optic sensor array that can detect positive and negative pressure suitable for validating CFD models of airfoil profile sections. The sensing array presented here consists of 6 independent sensing elements, each capable of a pressure resolution of less than 10 Pa over the range of 70 kPa to 120 kPa. The device has been tested with the sensor array attached to a 90mm chord length airfoil section subjected to low velocity flow. Results show that the arrays are capable of accurately detecting variations of the pressure profile along the airfoil as the angle of attack is varied from zero to the point at which stall occurs.

  13. High Throughput qPCR Expression Profiling of Circulating MicroRNAs Reveals Minimal Sex- and Sample Timing-Related Variation in Plasma of Healthy Volunteers.

    Directory of Open Access Journals (Sweden)

    Catherine Mooney

    Full Text Available MicroRNAs are a class of small non-coding RNA that regulate gene expression at a post-transcriptional level. MicroRNAs have been identified in various body fluids under normal conditions and their stability as well as their dysregulation in disease opens up a new field for biomarker study. However, diurnal and day-to-day variation in plasma microRNA levels, and differential regulation between males and females, may affect biomarker stability. A QuantStudio 12K Flex Real-Time PCR System was used to profile plasma microRNA levels using OpenArray in male and female healthy volunteers, in the morning and afternoon, and at four time points over a one month period. Using this system we were able to run four OpenArray plates in a single run, the equivalent of 32 traditional 384-well qPCR plates or 12,000 data points. Up to 754 microRNAs can be identified in a single plasma sample in under two hours. 108 individual microRNAs were identified in at least 80% of all our samples which compares favourably with other reports of microRNA profiles in serum or plasma in healthy adults. Many of these microRNAs, including miR-16-5p, miR-17-5p, miR-19a-3p, miR-24-3p, miR-30c-5p, miR-191-5p, miR-223-3p and miR-451a are highly expressed and consistent with previous studies using other platforms. Overall, microRNA levels were very consistent between individuals, males and females, and time points and we did not detect significant differences in levels of microRNAs. These results suggest the suitability of this platform for microRNA profiling and biomarker discovery and suggest minimal confounding influence of sex or sample timing. However, the platform has not been subjected to rigorous validation which must be demonstrated in future biomarker studies where large differences may exist between disease and control samples.

  14. Profiling post-centrifugation delay of serum and plasma with antibody bead arrays.

    Science.gov (United States)

    Qundos, Ulrika; Hong, Mun-Gwan; Tybring, Gunnel; Divers, Mark; Odeberg, Jacob; Uhlen, Mathias; Nilsson, Peter; Schwenk, Jochen M

    2013-12-16

    Several biobanking initiatives have emerged to create extensive collections of specimen for biomedical studies and various analytical platforms. An affinity proteomic analysis with antibody suspension bead arrays was conducted to investigate the influence of the pre-analytical time and temperature conditions on blood derived samples. Serum and EDTA plasma prepared from 16 individuals was centrifuged and aliquots were kept either at 4°C or in ambient temperature for 1h and up to 36h prior to first storage. Multiplexed protein profiles of post-centrifugation delay were generated in 384 biotinylated samples using 373 antibodies that targeted 343 unique proteins. Very few profiles were observed as significantly altered by the studied temperature and time intervals. Single binder and sandwich assays revealed decreasing levels of caldesmon 1 (CALD1) related to EDTA standard tubes and prolonged post-centrifugation delay of 36h. Indications from changes in CALD1 levels require further confirmation in independent material, but the current data suggests that samples should preferentially be frozen during the day of collection when to be profiled with antibody arrays selected for this study. Affinity-based profiling of serum and plasma by microarray assays can provide unique opportunities for the discovery of biomarkers. It is though often not known how differences in sample handling after collection influence the downstream analysis. By profiling three types of blood preparations for alterations in protein profiles with respect to time and temperature post centrifugation, we addressed an important component in the analysis and of such specimen. We believe that this analysis adds valuable information to be considered when biobanking blood derived samples. This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

  15. Dynamic wedge, electron energy and beam profile Q.A. using an ionization chamber linear array

    International Nuclear Information System (INIS)

    Kenny, M.B.; Todd, S.P.

    1996-01-01

    Since the introduction of multi-modal linacs the quality assurance workload of a Physical Sciences department has increased dramatically. The advent of dynamic wedges has further complicated matters because of the need to invent accurate methods to perform Q.A. in a reasonable time. We have been using an ionization chamber linear array, the Thebes 7000 TM by Victoreen, Inc., for some years to measure X-ray and electron beam profiles. Two years ago we developed software to perform Q.A. on our dynamic wedges using the array and more recently included a routine to check electron beam energies using the method described by Rosenow, U.F. et al., Med. Phys. 18(1) 19-25. The integrated beam and profile management system has enabled us to maintain a comprehensive quality assurance programme on all our linaccs. Both our efficiency and accuracy have increased to the point where we are able to keep up with the greater number of tests required without an increase in staff or hours spent in quality assurance. In changing the processor from the Z80 of the Thebes console to the 486 of the PC we have also noticed a marked increase in the calibration stability of the array. (author)

  16. Simulated gamma-ray pulse profile of the Crab pulsar with the Cherenkov Telescope Array

    Science.gov (United States)

    Burtovoi, A.; Zampieri, L.

    2016-07-01

    We present simulations of the very high energy (VHE) gamma-ray light curve of the Crab pulsar as observed by the Cherenkov Telescope Array (CTA). The CTA pulse profile of the Crab pulsar is simulated with the specific goal of determining the accuracy of the position of the interpulse. We fit the pulse shape obtained by the Major Atmospheric Gamma-Ray Imaging Cherenkov (MAGIC) telescope with a three-Gaussian template and rescale it to account for the different CTA instrumental and observational configurations. Simulations are performed for different configurations of CTA and for the ASTRI (Astrofisica con Specchi a Tecnologia Replicante Italiana) mini-array. The northern CTA configuration will provide an improvement of a factor of ˜3 in accuracy with an observing time comparable to that of MAGIC (73 h). Unless the VHE spectrum above 1 TeV behaves differently from what we presently know, unreasonably long observing times are required for a significant detection of the pulsations of the Crab pulsar with the high-energy-range sub-arrays. We also found that an independent VHE timing analysis is feasible with Large Size Telescopes. CTA will provide a significant improvement in determining the VHE pulse shape parameters necessary to constrain theoretical models of the gamma-ray emission of the Crab pulsar. One of such parameters is the shift in phase between peaks in the pulse profile at VHE and in other energy bands that, if detected, may point to different locations of the emission regions.

  17. Symmetry of trapped-field profiles in square columnar Josephson-junction arrays

    International Nuclear Information System (INIS)

    Moreno, J.J.; Chen, D.; Hernando, A.

    1995-01-01

    The remanence of NxN square-columnar Josephson-junction arrays with normalized maximum junction current i max is calculated from the dc and ac Josephson equations, the Ampere theorem, and the gauge invariance. A transition line on the i max- N plane is obtained, on the high-i max side of which the remanence is nonzero. It is found that in the nonzero remanence state the symmetry degree of field profile can be lower than expected by intuition. The meaning and importance of this finding are discussed

  18. Molecular serotyping, virulence gene profiling and pathogenicity of Streptococcus agalactiae isolated from tilapia farms in Thailand by multiplex PCR.

    Science.gov (United States)

    Kannika, K; Pisuttharachai, D; Srisapoome, P; Wongtavatchai, J; Kondo, H; Hirono, I; Unajak, S; Areechon, N

    2017-06-01

    This study aimed to biotype Streptococcus agalactiae isolated from tilapia farms in Thailand based on molecular biotyping methods and to determine the correlation between the serotype and virulence of bacteria. In addition to a biotyping (serotyping) technique based on multiplex PCR of cps genes, in this study, we developed multiplex PCR typing of Group B streptococcus (GBS) virulence genes to examine three clusters of virulence genes and their correlation with the pathogenicity of S. agalactiae. The epidemiology of S. agalactiae in Thailand was analysed to provide bacterial genetic information towards a future rational vaccine strategy for tilapia culture systems. Streptococcus agalactiae were isolated from diseased tilapia from different areas of Thailand. A total of 124 S. agalactiae isolates were identified by phenotypic analysis and confirmed by 16S rRNA PCR. Bacterial genotyping was conducted based on (i) molecular serotyping of the capsular polysaccharide (cps) gene cluster and (ii) virulence gene profiling using multiplex PCR analysis of 14 virulence genes (lmb, scpB, pavA, cspA, spb1, cyl, bca, rib, fbsA, fbsB, cfb, hylB, bac and pbp1A/ponA). Only serotypes Ia and III were found in this study; serotype Ia lacks the lmb, scpB and spb1 genes, whereas serotype III lacks only the bac gene. Virulence tests in juvenile Nile tilapia demonstrated a correlation between the pathogenicity of the bacteria and their virulence gene profile, with serotype III showing higher virulence than serotype Ia. Epidemiological analysis showed an almost equal distribution in all regions of Thailand, except serotype III was found predominantly in the southern areas. Only two serotypes of S. agalactiae were isolated from diseased tilapia in Thailand. Serotype Ia showed fewer virulence genes and lower virulence than serotype III. Both serotypes showed a similar distribution throughout Thailand. We identified two major serotypes of S. agalactiae isolates associated with the outbreak in

  19. Radiation profile measurements for edge transport barrier discharges in Compact Helical System using AXUV photodiode arrays

    International Nuclear Information System (INIS)

    Suzuki, C.; Okamura, S.; Minami, T.; Akiyama, T.; Fujisawa, A.; Ida, K.; Isobe, M.; Matsuoka, K.; Nagaoka, K.; Nishimura, S.; Peterson, B. J.; Shimizu, A.; Takahashi, C.; Toi, K.; Yoshimura, Y.

    2005-01-01

    The formation of edge transport barrier (ETB) has recently been found in Compact Helical System (CHS) plasmas heated by co-injected neutral beam injection (NBI) with strong gas puffing. This regime is characterized by the appearance of the steep gradient of the electron density near the edge following the abrupt drop of hydrogen Balmer alpha (H α ) line intensity. In addition to single channel pyroelectric detector as a conventional bolometer, we have employed unfiltered absolute extreme ultraviolet (AXUV) photodiode arrays as a simple and low-cost diagnostic to investigate spatial and temporal variations of radiation emissivity in the ETB discharges. A compact mounting module for a 20 channel AXUV photodiode array including an in-vacuum preamplifier for immediate current-voltage conversion has successfully been designed and fabricated. Two identical modules installed in the upper and lower viewports provide 40 lines of sight covering the inboard and outboard sides within the horizontally elongated cross section of the CHS plasma with wide viewing angle. Although spectral uniformity of the detector sensitivity of the AXUV photodiode is unsatisfied for photon energies lower than 200 eV, it has been confirmed that the signals of AXUV photodiode and pyroelectric detector in the ETB discharges show roughly the same behavior except for the very beginning and end of the discharges. The results of the measurements in typical ETB discharges show that the signals of all the channels of the AXUV photodiode arrays begin to increase more rapidly at the moment of the transition than before. The rate of the increase is larger for the edge viewing chords than for the center viewing ones, which indicates the flattening of the radiation profile following the change in the electron density profile after the formation of the ETB. However, the signals for the edge chords tend to saturate after several tens of milliseconds, while they still continue to increase for the central chords

  20. Variance decomposition of protein profiles from antibody arrays using a longitudinal twin model

    Directory of Open Access Journals (Sweden)

    Kato Bernet S

    2011-11-01

    Full Text Available Abstract Background The advent of affinity-based proteomics technologies for global protein profiling provides the prospect of finding new molecular biomarkers for common, multifactorial disorders. The molecular phenotypes obtained from studies on such platforms are driven by multiple sources, including genetic, environmental, and experimental components. In characterizing the contribution of different sources of variation to the measured phenotypes, the aim is to facilitate the design and interpretation of future biomedical studies employing exploratory and multiplexed technologies. Thus, biometrical genetic modelling of twin or other family data can be used to decompose the variation underlying a phenotype into biological and experimental components. Results Using antibody suspension bead arrays and antibodies from the Human Protein Atlas, we study unfractionated serum from a longitudinal study on 154 twins. In this study, we provide a detailed description of how the variation in a molecular phenotype in terms of protein profile can be decomposed into familial i.e. genetic and common environmental; individual environmental, short-term biological and experimental components. The results show that across 69 antibodies analyzed in the study, the median proportion of the total variation explained by familial sources is 12% (IQR 1-22%, and the median proportion of the total variation attributable to experimental sources is 63% (IQR 53-72%. Conclusion The variability analysis of antibody arrays highlights the importance to consider variability components and their relative contributions when designing and evaluating studies for biomarker discoveries with exploratory, high-throughput and multiplexed methods.

  1. The Study of a Beam Profile Monitor based on Faraday Cup Array

    Energy Technology Data Exchange (ETDEWEB)

    Park, K. M.; Park, S. H.; Kim, S. G.; Kwon, H. J.; Cho, Y. S. [KAERI, Daejeon (Korea, Republic of)

    2015-05-15

    The metal can then be discharged to measure a small current equivalent to the number of impinging ions. The beam current can be measured and used to determine the number of ions or electrons hitting the cup. Recently, beam profile monitor (BPM) based on Faraday cup array (FCA), which represented beam position through the spatial and temporal distribution of the beam current, has been studied due to advantages of measure of wide-range ion beam current. FCA system is divided into a FC, an electrical circuit and display parts. We have studied FCA to monitor beam profile on an electrostatic accelerator with wide-range ion current. In this paper, we represented basic characteristics and designs for the fabricated FCA. FCA system, which consisted of FC system, electronic readout system, and output display, was suggested to measure ion beam current, efficiently. FC system consisted of a collimator, suppressor, tiny FC, insulator frame, and circuit board divided into elec PCB, cap PCB, and con PCB. FC size was 4 mm diameters and FCA system was considered as 8 x 8 array and whole size of 8 x 8 mm''2. FCA system was set-up in vacuum chamber and an integrator and output display parts were formed out of chamber to minimize number of feed-through.

  2. Comparison of lung cancer cell lines representing four histopathological subtypes with gene expression profiling using quantitative real-time PCR

    Directory of Open Access Journals (Sweden)

    Kawaguchi Makoto

    2010-01-01

    Full Text Available Abstract Background Lung cancers are the most common type of human malignancy and are intractable. Lung cancers are generally classified into four histopathological subtypes: adenocarcinoma (AD, squamous cell carcinoma (SQ, large cell carcinoma (LC, and small cell carcinoma (SC. Molecular biological characterization of these subtypes has been performed mainly using DNA microarrays. In this study, we compared the gene expression profiles of these four subtypes using twelve human lung cancer cell lines and the more reliable quantitative real-time PCR (qPCR. Results We selected 100 genes from public DNA microarray data and examined them by DNA microarray analysis in eight test cell lines (A549, ABC-1, EBC-1, LK-2, LU65, LU99, STC 1, RERF-LC-MA and a normal control lung cell line (MRC-9. From this, we extracted 19 candidate genes. We quantified the expression of the 19 genes and a housekeeping gene, GAPDH, with qPCR, using the same eight cell lines plus four additional validation lung cancer cell lines (RERF-LC-MS, LC-1/sq, 86-2, and MS-1-L. Finally, we characterized the four subtypes of lung cancer cell lines using principal component analysis (PCA of gene expression profiling for 12 of the 19 genes (AMY2A, CDH1, FOXG1, IGSF3, ISL1, MALL, PLAU, RAB25, S100P, SLCO4A1, STMN1, and TGM2. The combined PCA and gene pathway analyses suggested that these genes were related to cell adhesion, growth, and invasion. S100P in AD cells and CDH1 in AD and SQ cells were identified as candidate markers of these lung cancer subtypes based on their upregulation and the results of PCA analysis. Immunohistochemistry for S100P and RAB25 was closely correlated to gene expression. Conclusions These results show that the four subtypes, represented by 12 lung cancer cell lines, were well characterized using qPCR and PCA for the 12 genes examined. Certain genes, in particular S100P and CDH1, may be especially important for distinguishing the different subtypes. Our results

  3. Gene expression profiling of acute myeloid leukemia samples from adult patients with AML-M1 and -M2 through boutique microarrays, real-time PCR and droplet digital PCR.

    Science.gov (United States)

    Handschuh, Luiza; Kaźmierczak, Maciej; Milewski, Marek C; Góralski, Michał; Łuczak, Magdalena; Wojtaszewska, Marzena; Uszczyńska-Ratajczak, Barbara; Lewandowski, Krzysztof; Komarnicki, Mieczysław; Figlerowicz, Marek

    2018-03-01

    Acute myeloid leukemia (AML) is the most common and severe form of acute leukemia diagnosed in adults. Owing to its heterogeneity, AML is divided into classes associated with different treatment outcomes and specific gene expression profiles. Based on previous studies on AML, in this study, we designed and generated an AML-array containing 900 oligonucleotide probes complementary to human genes implicated in hematopoietic cell differentiation and maturation, proliferation, apoptosis and leukemic transformation. The AML-array was used to hybridize 118 samples from 33 patients with AML of the M1 and M2 subtypes of the French-American‑British (FAB) classification and 15 healthy volunteers (HV). Rigorous analysis of the microarray data revealed that 83 genes were differentially expressed between the patients with AML and the HV, including genes not yet discussed in the context of AML pathogenesis. The most overexpressed genes in AML were STMN1, KITLG, CDK6, MCM5, KRAS, CEBPA, MYC, ANGPT1, SRGN, RPLP0, ENO1 and SET, whereas the most underexpressed genes were IFITM1, LTB, FCN1, BIRC3, LYZ, ADD3, S100A9, FCER1G, PTRPE, CD74 and TMSB4X. The overexpression of the CPA3 gene was specific for AML with mutated NPM1 and FLT3. Although the microarray-based method was insufficient to differentiate between any other AML subgroups, quantitative PCR approaches enabled us to identify 3 genes (ANXA3, S100A9 and WT1) whose expression can be used to discriminate between the 2 studied AML FAB subtypes. The expression levels of the ANXA3 and S100A9 genes were increased, whereas those of WT1 were decreased in the AML-M2 compared to the AML-M1 group. We also examined the association between the STMN1, CAT and ABL1 genes, and the FLT3 and NPM1 mutation status. FLT3+/NPM1- AML was associated with the highest expression of STMN1, and ABL1 was upregulated in FLT3+ AML and CAT in FLT3- AML, irrespectively of the NPM1 mutation status. Moreover, our results indicated that CAT and WT1

  4. A performance study on three qPCR quantification kits and their compatibilities with the 6-dye DNA profiling systems.

    Science.gov (United States)

    Lin, Sze-Wah; Li, Christina; Ip, Stephen C Y

    2018-03-01

    DNA quantification plays an integral role in forensic DNA profiling. Not only does it estimate the total amount of amplifiable human autosomal and male DNA to ensure optimal amplification of target DNA for subsequent analysis, but also assesses the extraction efficiency and purity of the DNA extract. Latest DNA quantification systems even offer an estimate for the degree of DNA degradation in a sample. Here, we report the performance of three new generation qPCR kits, namely Investigator ® Quantiplex HYres Kit from QIAGEN, Quantifiler ® Trio DNA Quantification Kit from Applied Biosystems™, and PowerQuant ® System from Promega, and their compatibilities with three 6-dye DNA profiling systems. Our results have demonstrated that all three kits generate standard curves with satisfactory consistency and reproducibility, and are capable of screening out traces of male DNA in the presence of 30-fold excess of female DNA. They also exhibit a higher tolerance to PCR inhibition than Quantifiler ® Human DNA Quantification Kit from Applied Biosystems™ in autosomal DNA quantification. PowerQuant ® , as compared to Quantiplex HYres and Quantifiler ® Trio, shows a better precision for both autosomal and male DNA quantifications. Quantifiler ® Trio and PowerQuant ® in contrast to Quantiplex HYres offer better correlations with lower discrepancies between autosomal and male DNA quantification, and their additional degradation index features provide a detection platform for inhibited and/or degraded DNA template. Regarding the compatibility between these quantification and profiling systems: (1) both Quantifiler ® Trio and PowerQuant ® work well with GlobalFiler and Fusion 6C, allowing a fairly accurate prediction of their DNA typing results based on the quantification values; (2) Quantiplex HYres offers a fairly reliable IPC system for detecting any potential inhibitions on Investigator 24plex, whereas Quantifiler ® Trio and PowerQuant ® suit better for Global

  5. Optimizing the solar array of stand-alone photovoltaic energy systems as a function of time and load profiles

    Science.gov (United States)

    Abou-Hussein, M. S.; El-Maghraby, M. H.; Groumpos, P. P.; El-Geldawy, F. A.; El-Tamaly, H. H.

    This paper presents a proposed novel technique in which an accurate optimum design of the solar array (SCA) can be attained. It depends on an hour-by-hour approach with different daily load profiles. A generalized mathematical formula has been developed for sizing of the solar array given the geographical and one year's insolation data for a particular site in Egypt. This approach can reduce the required size compared to other methods using the same tilt angle.

  6. Genomic profiling of oral squamous cell carcinoma by array-based comparative genomic hybridization.

    Directory of Open Access Journals (Sweden)

    Shunichi Yoshioka

    Full Text Available We designed a study to investigate genetic relationships between primary tumors of oral squamous cell carcinoma (OSCC and their lymph node metastases, and to identify genomic copy number aberrations (CNAs related to lymph node metastasis. For this purpose, we collected a total of 42 tumor samples from 25 patients and analyzed their genomic profiles by array-based comparative genomic hybridization. We then compared the genetic profiles of metastatic primary tumors (MPTs with their paired lymph node metastases (LNMs, and also those of LNMs with non-metastatic primary tumors (NMPTs. Firstly, we found that although there were some distinctive differences in the patterns of genomic profiles between MPTs and their paired LNMs, the paired samples shared similar genomic aberration patterns in each case. Unsupervised hierarchical clustering analysis grouped together 12 of the 15 MPT-LNM pairs. Furthermore, similarity scores between paired samples were significantly higher than those between non-paired samples. These results suggested that MPTs and their paired LNMs are composed predominantly of genetically clonal tumor cells, while minor populations with different CNAs may also exist in metastatic OSCCs. Secondly, to identify CNAs related to lymph node metastasis, we compared CNAs between grouped samples of MPTs and LNMs, but were unable to find any CNAs that were more common in LNMs. Finally, we hypothesized that subpopulations carrying metastasis-related CNAs might be present in both the MPT and LNM. Accordingly, we compared CNAs between NMPTs and LNMs, and found that gains of 7p, 8q and 17q were more common in the latter than in the former, suggesting that these CNAs may be involved in lymph node metastasis of OSCC. In conclusion, our data suggest that in OSCCs showing metastasis, the primary and metastatic tumors share similar genomic profiles, and that cells in the primary tumor may tend to metastasize after acquiring metastasis-associated CNAs.

  7. Genomic GC-content affects the accuracy of 16S rRNA gene sequencing bsed microbial profiling due to PCR bias

    DEFF Research Database (Denmark)

    Laursen, Martin F.; Dalgaard, Marlene Danner; Bahl, Martin Iain

    2017-01-01

    Profiling of microbial community composition is frequently performed by partial 16S rRNA gene sequencing on benchtop platforms following PCR amplification of specific hypervariable regions within this gene. Accuracy and reproducibility of this strategy are two key parameters to consider, which may...... be influenced during all processes from sample collection and storage, through DNA extraction and PCR based library preparation to the final sequencing. In order to evaluate both the reproducibility and accuracy of 16S rRNA gene based microbial profiling using the Ion Torrent PGM platform, we prepared libraries...... be explained partly by premature read truncation, but to larger degree their genomic GC-content, which correlated negatively with the observed relative abundances, suggesting a PCR bias against GC-rich species during library preparation. Increasing the initial denaturation time during the PCR amplification...

  8. Development of Pseudorandom Binary Arrays for Calibration of Surface Profile Metrology Tools

    International Nuclear Information System (INIS)

    Barber, S.K.; Takacs, P.; Soldate, P.; Anderson, E.H.; Cambie, R.; McKinney, W.R.; Voronov, D.L.; Yashchuk, V.V.

    2009-01-01

    measured and simulated PSD distributions gives the MTF of the instrument. The applicability of the MTF concept to phase map measurements with optical interferometric microscopes needs to be experimentally verified as the optical tool and algorithms may introduce nonlinear artifacts into the process. In previous work [V. V. Yashchuk et al., Proc. SPIE 6704, 670408 (2007); Valeriy V. Yashchuk et al., Opt. Eng. (Bellingham) 47, 073602 (2008)] the instrumental MTF of a surface profiler was precisely measured using reference test surfaces based on binary pseudorandom (BPR) gratings. Here, the authors present results of fabricating and using two-dimensional (2D) BPR arrays that allow for a direct 2D calibration of the instrumental MTF. BPR sequences are widely used in engineering and communication applications such as global position systems and wireless communication protocols. The ideal BPR pattern has a flat 'white noise' response over the entire range of spatial frequencies of interest. The BPR array used here is based on the uniformly redundant array (URA) prescription [E. E. Fenimore and T. M. Cannon, Appl. Opt. 17, 337 (1978)] initially used for x-ray and gamma ray astronomy applications. The URA's superior imaging capability originates from the fact that its cyclical autocorrelation function very closely approximates a delta function, which produces a flat PSD. Three different size BPR array patterns were fabricated by electron beam lithography and induction coupled plasma etching of silicon. The basic size units were 200, 400, and 600 nm. Two different etch processes were used, CF 4 /Ar and HBr, which resulted in undercut and vertical sidewall profiles, respectively. The 2D BPR arrays were used as standard test surfaces for MTF calibration of the MicroMap(trademark)-570 interferometric microscope using all available objectives. The MicroMap(trademark)-570 interferometric microscope uses incoherent illumination from a tungsten filament source and common path modulated

  9. Estimates of the Lightning NOx Profile in the Vicinity of the North Alabama Lightning Mapping Array

    Science.gov (United States)

    Koshak, William J.; Peterson, Harold S.; McCaul, Eugene W.; Blazar, Arastoo

    2010-01-01

    The NASA Marshall Space Flight Center Lightning Nitrogen Oxides Model (LNOM) is applied to August 2006 North Alabama Lightning Mapping Array (NALMA) data to estimate the (unmixed and otherwise environmentally unmodified) vertical source profile of lightning nitrogen oxides, NOx = NO + NO2. Data from the National Lightning Detection Network (Trademark) (NLDN) is also employed. This is part of a larger effort aimed at building a more realistic lightning NOx emissions inventory for use by the U.S. Environmental Protection Agency (EPA) Community Multiscale Air Quality (CMAQ) modeling system. Overall, special attention is given to several important lightning variables including: the frequency and geographical distribution of lightning in the vicinity of the NALMA network, lightning type (ground or cloud flash), lightning channel length, channel altitude, channel peak current, and the number of strokes per flash. Laboratory spark chamber results from the literature are used to convert 1-meter channel segments (that are located at a particular known altitude; i.e., air density) to NOx concentration. The resulting lightning NOx source profiles are discussed.

  10. Genetic profiles of gastroesophageal cancer: combined analysis using expression array and tiling array--comparative genomic hybridization

    DEFF Research Database (Denmark)

    Isinger-Ekstrand, Anna; Johansson, Jan; Ohlsson, Mattias

    2010-01-01

    We aimed to characterize the genomic profiles of adenocarcinomas in the gastroesophageal junction in relation to cancers in the esophagus and the stomach. Profiles of gains/losses as well as gene expression profiles were obtained from 27 gastroesophageal adenocarcinomas by means of 32k high......15, 13q34, and 12q13, whereas different profiles with gains at 5p15, 7p22, 2q35, and 13q34 characterized gastric cancers. CDK6 and EGFR were identified as putative target genes in cancers of the esophagus and the gastroesophageal junction, with upregulation in one quarter of the tumors. Gains....../losses and gene expression profiles show strong similarity between cancers in the distal esophagus and the gastroesophageal junction with frequent upregulation of CDK6 and EGFR, whereas gastric cancer displays distinct genetic changes. These data suggest that molecular diagnostics and targeted therapies can...

  11. An automatic evaluation method for the surface profile of a microlens array using an optical interferometric microscope

    International Nuclear Information System (INIS)

    Lin, Chern-Sheng; Loh, Guo-Hao; Fu, Shu-Hsien; Chang, Hsun-Kai; Yang, Shih-Wei; Yeh, Mau-Shiun

    2010-01-01

    In this paper, an automatic evaluation method for the surface profile of a microlens array using an optical interferometric microscope is presented. For inspecting the microlens array, an XY-table is used to position it. With a He–Ne laser beam and optical fiber as a probing light, the measured image is sent to the computer to analyze the surface profile. By binary image slicing and area recognition, this study located the center of each ring and determined the substrate of the microlens array image through the background of the entire microlens array interference image. The maximum and minimum values of every segment brightness curve were determined corresponding to the change in the segment phase angle from 0° to 180°. According to the ratio of the actual ring area and the ideal ring area, the area ratio method was adopted to find the phase-angle variation of the interference ring. Based on the ratio of actual ring brightness and the ideal ring brightness, the brightness ratio method was used to determine the phase-angle variation of the interference ring fringe. The area ratio method and brightness ratio method are interchangeable in precisely determining the phase angles of the innermost and outermost rings of the interference fringe and obtaining different microlens surface altitudes of respective pixels in the segment, to greatly increase the microlens array surface profile inspection accuracy and quality

  12. Prognostic Impact of Array-based Genomic Profiles in Esophageal Squamous Cell Cancer

    International Nuclear Information System (INIS)

    Carneiro, Ana; Isinger, Anna; Karlsson, Anna; Johansson, Jan; Jönsson, Göran; Bendahl, Pär-Ola; Falkenback, Dan; Halvarsson, Britta; Nilbert, Mef

    2008-01-01

    Esophageal squamous cell carcinoma (ESCC) is a genetically complex tumor type and a major cause of cancer related mortality. Although distinct genetic alterations have been linked to ESCC development and prognosis, the genetic alterations have not gained clinical applicability. We applied array-based comparative genomic hybridization (aCGH) to obtain a whole genome copy number profile relevant for identifying deranged pathways and clinically applicable markers. A 32 k aCGH platform was used for high resolution mapping of copy number changes in 30 stage I-IV ESCC. Potential interdependent alterations and deranged pathways were identified and copy number changes were correlated to stage, differentiation and survival. Copy number alterations affected median 19% of the genome and included recurrent gains of chromosome regions 5p, 7p, 7q, 8q, 10q, 11q, 12p, 14q, 16p, 17p, 19p, 19q, and 20q and losses of 3p, 5q, 8p, 9p and 11q. High-level amplifications were observed in 30 regions and recurrently involved 7p11 (EGFR), 11q13 (MYEOV, CCND1, FGF4, FGF3, PPFIA, FAD, TMEM16A, CTTS and SHANK2) and 11q22 (PDFG). Gain of 7p22.3 predicted nodal metastases and gains of 1p36.32 and 19p13.3 independently predicted poor survival in multivariate analysis. aCGH profiling verified genetic complexity in ESCC and herein identified imbalances of multiple central tumorigenic pathways. Distinct gains correlate with clinicopathological variables and independently predict survival, suggesting clinical applicability of genomic profiling in ESCC

  13. Reconstructing 3D profiles of flux distribution in array of unshunted Josephson junctions from 2D scanning SQUID microscope images

    International Nuclear Information System (INIS)

    Nascimento, F.M.; Sergeenkov, S.; Araujo-Moreira, F.M.

    2012-01-01

    By using a specially designed algorithm (based on utilizing the so-called Hierarchical Data Format), we report on successful reconstruction of 3D profiles of local flux distribution within artificially prepared arrays of unshunted Nb-AlO x -Nb Josephson junctions from 2D surface images obtained via the scanning SQUID microscope. The analysis of the obtained results suggest that for large sweep areas, the local flux distribution significantly deviates from the conventional picture and exhibits a more complicated avalanche-type behavior with a prominent dendritic structure. -- Highlights: ► The penetration of external magnetic field into an array of Nb-AlO x -Nb Josephson junctions is studied. ► Using Scanning SQUID Microscope, 2D images of local flux distribution within array are obtained. ► Using specially designed pattern recognition algorithm, 3D flux profiles are reconstructed from 2D images.

  14. Gene array analysis of PD-1H overexpressing monocytes reveals a pro-inflammatory profile

    Directory of Open Access Journals (Sweden)

    Preeti Bharaj

    2018-02-01

    Full Text Available We have previously reported that overexpression of Programmed Death -1 Homolog (PD-1H in human monocytes leads to activation and spontaneous secretion of multiple pro inflammatory cytokines. Here we evaluate changes in monocytes gene expression after enforced PD-1H expression by gene array. The results show that there are significant alterations in 51 potential candidate genes that relate to immune response, cell adhesion and metabolism. Genes corresponding to pro-inflammatory cytokines showed the highest upregulation, 7, 3.2, 3.0, 5.8, 4.4 and 3.1 fold upregulation of TNF-α, IL-1 β, IFN-α, γ, λ and IL-27 relative to vector control. The data are in agreement with cytometric bead array analysis showing induction of proinflammatory cytokines, IL-6, IL-1β and TNF-α by PD-1H. Other genes related to inflammation, include transglutaminase 2 (TG2, NF-κB (p65 and p50 and toll like receptors (TLR 3 and 4 were upregulated 5, 4.5 and 2.5 fold, respectively. Gene set enrichment analysis (GSEA also revealed that signaling pathways related to inflammatory response, such as NFκB, AT1R, PYK2, MAPK, RELA, TNFR1, MTOR and proteasomal degradation, were significantly upregulated in response to PD-1H overexpression. We validated the results utilizing a standard inflammatory sepsis model in humanized BLT mice, finding that PD-1H expression was highly correlated with proinflammatory cytokine production. We therefore conclude that PD-1H functions to enhance monocyte activation and the induction of a pro-inflammatory gene expression profile.

  15. Protein expression profiling by antibody array analysis with use of dried blood spot samples on filter paper.

    Science.gov (United States)

    Jiang, Weidong; Mao, Ying Qing; Huang, Ruochun; Duan, Chaohui; Xi, Yun; Yang, Kai; Huang, Ruo-Pan

    2014-01-31

    Dried blood spot samples (DBSS) on filter paper offer several advantages compared to conventional serum/plasma samples: they do not require any phlebotomy or separation of blood by centrifugation; they are less invasive; they allow sample stability and shipment at room temperature; and they pose a negligible risk of infection with blood-borne viruses, such as HIV, HBV and HCV, to those who handle them. Therefore dried blood spot samples (DBSS) on filter paper can be a quick, convenient and inexpensive means of obtaining blood samples for biomarker discovery, disease screening, diagnosis and treatment monitoring in non-hospitalized, public health settings. In this study, we investigated for the first time the potential application of dried blood spot samples (DBSS) in protein expression profiling using antibody array technology. First, optimal conditions for array assay performance using dried blood spot samples (DBSS) was established, including sample elution buffer, elution time, elution temperature and assay blocking buffer. Second, we analyzed dried blood spot samples (DBSS) using three distinct antibody array platforms, including sandwich-based antibody arrays, quantitative antibody arrays and biotin-label-based antibody arrays. In comparison with paired serum samples, detection of circulating proteins in dried blood spot samples (DBSS) correlated well for both low- and high-abundance proteins on all three antibody array platforms. In conclusion, our study strongly indicates the novel application of multiplex antibody array platforms to analyze dried blood spot samples (DBSS) on filter paper represents a viable, cost-effective method for protein profiling, biomarker discovery and disease screening in a large, population-based survey. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Altered Gene Expression by Low-Dose Arsenic Exposure in Humans and Cultured Cardiomyocytes: Assessment by Real-Time PCR Arrays

    Directory of Open Access Journals (Sweden)

    Judy Mumford

    2011-06-01

    Full Text Available Chronic arsenic exposure results in higher risk of skin, lung, and bladder cancer, as well as cardiovascular disease and diabetes. The purpose of this study was to investigate the effects on expression of selected genes in the blood lymphocytes from 159 people exposed chronically to arsenic in their drinking water using a novel RT-PCR TaqMan low-density array (TLDA. We found that expression of tumor necrosis factor-α (TNF-α, which activates both inflammation and NF-κB-dependent survival pathways, was strongly associated with water and urinary arsenic levels. Expression of KCNA5, which encodes a potassium ion channel protein, was positively associated with water and toe nail arsenic levels. Expression of 2 and 11 genes were positively associated with nail and urinary arsenic, respectively. Because arsenic exposure has been reported to be associated with long QT intervals and vascular disease in humans, we also used this TLDA for analysis of gene expression in human cardiomyocytes exposed to arsenic in vitro. Expression of the ion-channel genes CACNA1, KCNH2, KCNQ1 and KCNE1 were down-regulated by 1-mM arsenic. Alteration of some common pathways, including those involved in oxidative stress, inflammatory signaling, and ion-channel function, may underlay the seemingly disparate array of arsenic-associated diseases, such as cancer, cardiovascular disease, and diabetes.

  17. Multiway real-time PCR gene expression profiling in yeast. Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli

    Czech Academy of Sciences Publication Activity Database

    Stahlberg, A.; Elbing, K.; Andrade-Garda, J.M.; Sjögreen, B.; Forootan, A.; Kubista, Mikael

    2008-01-01

    Roč. 9, č. 170 (2008), s. 1-41 ISSN 1471-2164 Institutional research plan: CEZ:AV0Z50520701 Keywords : Expression Profiling * Real-time PCR * Yeast Subject RIV: EI - Biotechnology ; Bionics Impact factor: 3.926, year: 2008

  18. Self-Assembled TiO2 Nanotube Arrays with U-Shaped Profile by Controlling Anodization Temperature

    Directory of Open Access Journals (Sweden)

    Jingfei Chen

    2010-01-01

    Full Text Available TiO2 nanotube arrays with uniform diameter from top to bottom were fabricated. The synthesizing approach is based on the investigation of the influence of electrolyte temperature on the tube diameter. We found that the inner diameter of the tubes increased with the electrolyte temperature. Accordingly, we improved the tube profile from the general V shape to U shape by raising the electrolyte temperature gradually. This is a simple and fast approach to fabricate uniform TiO2 nanotubes in diameter. The improved TiO2 nanotube arrays may show better properties and have broad potential applications.

  19. Global mass spectrometry and transcriptomics array based drug profiling provides novel insight into glucosamine induced endoplasmic reticulum stress

    DEFF Research Database (Denmark)

    Carvalho, Ana Sofia; Ribeiro, Helena; Voabil, Paula

    2014-01-01

    We investigated the molecular effects of glucosamine supplements, a popular and safe alternative to nonsteroidal anti-inflammatory drugs, for decreasing pain, inflammation, and maintaining healthy joints. Numerous studies have reported an array of molecular effects after glucosamine treatment. We...... questioned whether the differences in the effects observed in previous studies were associated with the focus on a specific subproteome or with the use of specific cell lines or tissues. To address this question, global mass spectrometry- and transcription array-based glucosamine drug profiling was performed....... Further, we hypothesize that O-HexNAcylation induced by glucosamine treatment enhances protein trafficking....

  20. A comparative study of the work involved in measuring profiles using ion chambers, a linear diode array and film

    International Nuclear Information System (INIS)

    Rykers, K.L.; RMIT University, Melbourne, VIC; Royal North Shore Hospital, St Leonards, NSW; Geso, M.; Brown, G.M.; Olilver, L.D.

    1996-01-01

    Full text: The usefulness of film to perform dosimetric measurement is a topic often discussed and not clearly agreed upon. While single point measurement detectors give consistent and reliable results for physically wedged fields they cannot be easily used to measure intensity modulated fields. In this work a method of using film to measure profiles for dynamically wedged (DW) fields is presented. The method of positioning film for the subsequent generation of a conversion function to allow for the variation in films' response with energy is outlined. Furthermore, the profiles determined by film measurement are compared with those measured with single point measurement detector and an array of silicon diodes. Both Leavitt et. al. 8 and Weber et. al. 7 have reported on the successful use of the linear diode array (LDA) in measuring dynamic wedge data. This claim will be investigated. The film used in this work was Kodak X-Omat V. The solid water was RW3 with high water equivalency in the range from 137 CS to 50 MV for photons and electrons. All films were processed in an automatic processor. Both the Wellhoefer and the Scanditronix RFA 300 densitometers were used to take film readings. Wedged field and open field profiles measurements were taken in water using both the Wellhoefer IC-10 chamber, the Scanditronix RFA 300 RK chamber and the Scanditronix LDA . The energy investigated was 6 MV at 1.5, 5.0, 10.0, 15.0 and 20.0 cm for a Varian 2100C machine. More consistent density readings were obtained when films were processed with the edge of the film that was parallel to the beam axis was fed into the processor first; rather than when the beam incident edge was fed into the processor first. Comparing the position of the central axis (CAX) of open films from the geometric method developed in this work to the software determined CAX (as available with the Wellhoefer software), it was found that the difference in CAX positions varied between -0.03 to +0.04 cm at 2.5 cm

  1. A pilot trial assessing urinary gene expression profiling with an mRNA array for diabetic nephropathy.

    Directory of Open Access Journals (Sweden)

    Min Zheng

    Full Text Available BACKGROUND: The initiation and progression of diabetic nephropathy (DN is complex. Quantification of mRNA expression in urinary sediment has emerged as a novel strategy for studying renal diseases. Considering the numerous molecules involved in DN development, a high-throughput platform with parallel detection of multiple mRNAs is needed. In this study, we constructed a self-assembling mRNA array to analyze urinary mRNAs in DN patients with aims to reveal its potential in searching novel biomarkers. METHODS: mRNA array containing 88 genes were fabricated and its performance was evaluated. A pilot study with 9 subjects including 6 DN patients and 3 normal controls were studied with the array. DN patients were assigned into two groups according to their estimate glomerular rate (eGFR: DNI group (eGFR>60 ml/min/1.73 m(2, n = 3 and DNII group (eGFR<60 ml/min/1.73 m(2, n = 3. Urinary cell pellet was collected from each study participant. Relative abundance of these target mRNAs from urinary pellet was quantified with the array. RESULTS: The array we fabricated displayed high sensitivity and specificity. Moreover, the Cts of Positive PCR Controls in our experiments were 24±0.5 which indicated high repeatability of the array. A total of 29 mRNAs were significantly increased in DN patients compared with controls (p<0.05. Among these genes, α-actinin4, CDH2, ACE, FAT1, synaptopodin, COL4α, twist, NOTCH3 mRNA expression were 15-fold higher than those in normal controls. In contrast, urinary TIMP-1 mRNA was significantly decreased in DN patients (p<0.05. It was shown that CTGF, MCP-1, PAI-1, ACE, CDH1, CDH2 mRNA varied significantly among the 3 study groups, and their mRNA levels increased with DN progression (p<0.05. CONCLUSION: Our pilot study demonstrated that mRNA array might serve as a high-throughput and sensitive tool for detecting mRNA expression in urinary sediment. Thus, this primary study indicated that mRNA array probably could be a

  2. Comparative analytical evaluation of the respiratory TaqMan Array Card with real-time PCR and commercial multi-pathogen assays.

    Science.gov (United States)

    Harvey, John J; Chester, Stephanie; Burke, Stephen A; Ansbro, Marisela; Aden, Tricia; Gose, Remedios; Sciulli, Rebecca; Bai, Jing; DesJardin, Lucy; Benfer, Jeffrey L; Hall, Joshua; Smole, Sandra; Doan, Kimberly; Popowich, Michael D; St George, Kirsten; Quinlan, Tammy; Halse, Tanya A; Li, Zhen; Pérez-Osorio, Ailyn C; Glover, William A; Russell, Denny; Reisdorf, Erik; Whyte, Thomas; Whitaker, Brett; Hatcher, Cynthia; Srinivasan, Velusamy; Tatti, Kathleen; Tondella, Maria Lucia; Wang, Xin; Winchell, Jonas M; Mayer, Leonard W; Jernigan, Daniel; Mawle, Alison C

    2016-02-01

    In this study, a multicenter evaluation of the Life Technologies TaqMan(®) Array Card (TAC) with 21 custom viral and bacterial respiratory assays was performed on the Applied Biosystems ViiA™ 7 Real-Time PCR System. The goal of the study was to demonstrate the analytical performance of this platform when compared to identical individual pathogen specific laboratory developed tests (LDTs) designed at the Centers for Disease Control and Prevention (CDC), equivalent LDTs provided by state public health laboratories, or to three different commercial multi-respiratory panels. CDC and Association of Public Health Laboratories (APHL) LDTs had similar analytical sensitivities for viral pathogens, while several of the bacterial pathogen APHL LDTs demonstrated sensitivities one log higher than the corresponding CDC LDT. When compared to CDC LDTs, TAC assays were generally one to two logs less sensitive depending on the site performing the analysis. Finally, TAC assays were generally more sensitive than their counterparts in three different commercial multi-respiratory panels. TAC technology allows users to spot customized assays and design TAC layout, simplify assay setup, conserve specimen, dramatically reduce contamination potential, and as demonstrated in this study, analyze multiple samples in parallel with good reproducibility between instruments and operators. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Simultaneous Profiling of DNA Mutation and Methylation by Melting Analysis Using Magnetoresistive Biosensor Array

    DEFF Research Database (Denmark)

    Rizzi, Giovanni; Lee, Jung-Rok; Dahl, Christina

    2017-01-01

    specificity. Genomic (mutation) or bisulphite-treated (methylation) DNA is amplified using nondiscriminatory primers, and the amplicons are then hybridized to a giant magnetoresistive (GMR) biosensor array followed by melting curve measurements. The GMR biosensor platform offers scalable multiplexed detection...

  4. IDENTIFIKASI PROFIL DASAR LAUT MENGGUNAKAN INSTRUMEN SIDE SCAN SONAR DENGAN METODE BEAM PATTERN DISCRETE-EQUI-SPACED UNSHADED LINE ARRAY

    Directory of Open Access Journals (Sweden)

    Muhammad Zainuddin Lubis

    2017-05-01

    Full Text Available Laut Punggur merupakan laut yang terletak di Batam, Kepulauan Riau yang mempunyai beragam habitat objek,dan bentuk struktur bawah laut yang memiliki dinamika laut yang sangat tinggi. Side scan sonar (SSS merupakan instrumen pengembangan sistem sonar yang mampu menunjukkan dalam gambar dua dimensional permukaan dasar laut dengan kondisi kontur, topografi, dan target secara bersamaan. Metode Beam Pattern Discrete-Equi-Spaced Unshaded Line Array digunakan untuk menghitung beam pattern dua dimensi yang tergantung pada sudut dari gelombang suara yang masuk dari sumbu array yang diterima tergantung pada sudut di mana sinar suara pada array. Penelitian ini dilakukan pada Desember 2016 di laut Punggur,Batam, Kepulauan Riau-Indonesia, dengan koordinat 104 ° 08,7102 E dan 1° 03,2448 N sampai 1 ° 03.3977 N dan 104 ° 08,8133 E, menggunakan instrumen Side Scan Sonar C-Max CM2 Tow fish dengan frekuensi 325 kHz. Hasil yang diperoleh dari perekaman terdapat 7 target, dan Beam pattern dari metode Beam Discrete-Equi-Spaced Unshaded Line Array target 4 memiliki nilai tertinggi pada directivity Pattern yaitu 21.08 dB. Hasil model beam pattern ini memiliki nilai pusat pada incidence angle (o terhadap Directivity pattern (dB tidak berada di nilai 0 ataupun pada pusat beam pattern yang dihasilkan pada target 6 dengan nilai incident angle -1.5 o dan 1.5o mengalami penurunan hingga -40 dB. Karakteristik sedimen dasar perairan di laut punggur ditemukan lebih banyak pasir. Hasil metode Beam Discrete-Equi-Spaced Unshaded Line Array ditemukan bangkai kapal tenggelam.Kata Kunci: Side Scan Sonar, Beam Pattern Discrete-Equi-Spaced Unshaded Line Array, Incidence angle, Directivity pattern IDENTIFICATION OF SEABED PROFILE USING SIDE SCAN SONAR INSTRUMENT WITH PATTERN DISCRETE-EQUI-SPACED UNSHADED LINE ARRAY METHODRiau Islands is an island that has a variety of habitat objects, and forms of submarine structures that have a very high ocean dynamics, Punggur Sea is the sea

  5. Transcript profiling of common bean (Phaseolus vulgaris L. using the GeneChip® Soybean Genome Array: optimizing analysis by masking biased probes

    Directory of Open Access Journals (Sweden)

    Gronwald John W

    2010-05-01

    Full Text Available Abstract Background Common bean (Phaseolus vulgaris L. and soybean (Glycine max both belong to the Phaseoleae tribe and share significant coding sequence homology. This suggests that the GeneChip® Soybean Genome Array (soybean GeneChip may be used for gene expression studies using common bean. Results To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and accuracy of measuring differential gene expression in common bean cross-species hybridization (CSH GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and accuracy of measuring differential gene expression. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR (qRT-PCR analysis of 20 randomly selected genes and purine-ureide pathway genes demonstrated an increased accuracy of measuring differential gene expression after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The sequence divergence pattern analysis suggested that the genes for basic cellular functions and metabolism were highly conserved between soybean and common bean. Additionally, our results show that some classes of genes, particularly those associated with environmental adaptation, are highly divergent. Conclusions The soybean GeneChip is a suitable cross-species platform for transcript profiling in common bean when used in combination with the masking protocol described. In

  6. Understanding the radiosensitivity of hematopoietic stem cells through CDNA micro-arrays profiling

    Energy Technology Data Exchange (ETDEWEB)

    Pawlik, A.; Cebo, Ch.; Vaigot, P.; Tronik-Le Roux, D. [Evry Univ., Lab. de Genomique et Radiobiologie de l' Hematopoiese, Service de Genomique Fonctionnelle, CEA, 91 (France)

    2006-07-01

    transcriptional modulations identified as early as 1 hour after IR exposure. Many of the modulated genes were never described before as playing a role in the IR response. Clustering the modulated genes using a Q.T. clustering method led to select two specific clusters of up-regulated genes in the spleen. Cluster 1 includes transcripts that are rapidly but transiently up-regulated. Cluster 2 contains genes for which the high level of transcripts persists at least for 3 hours. This cluster includes many known p-53 target genes such as p21, Ba x and Mdm2. Promoter sequence analysis revealed that the majority of gene s included in this cluster possess p-53 cis-responsive elements. This suggests that these genes might be potentially co-regulated and might constitute novel targets of the tumor suppressor gene. This hypothesis was assessed by chromatin immunoprecipitation. We next compared the behavior of stem/early progenitor cells to that of the more sensitive mature B-lymphoid cell population after whole body irradiation. The comparison of transcription profiles of both populations revealed that the elicited response was highly dependent on the stage of differentiation of the cell. In particular, the early population mobilized many more genes than the more mature population in response to IR. To give a biological significance to the micro array results, genes identified a modulated after radiation exposure were assigned to functional categories using the G.O. annotations. This tool assigns gene products to common biological processes, molecular functions and cellular components. Moreover, a rea l statistical significance to the gene list is attributed, since the % is calculated wit h respect to the total number of genes assayed. Some of the mobilized categories were as one could expect, cell death, cellular growth and proliferation, however many of the identified genes were not studied before in the context of a radiation exposure response .Modulated genes were also analyzed

  7. Adaptation of the Biolog Phenotype MicroArrayTM Technology to Profile the Obligate Anaerobe Geobacter metallireducens

    Energy Technology Data Exchange (ETDEWEB)

    Joyner, Dominique; Fortney, Julian; Chakraborty, Romy; Hazen, Terry

    2010-05-17

    The Biolog OmniLog? Phenotype MicroArray (PM) plate technology was successfully adapted to generate a select phenotypic profile of the strict anaerobe Geobacter metallireducens (G.m.). The profile generated for G.m. provides insight into the chemical sensitivity of the organism as well as some of its metabolic capabilities when grown with a basal medium containing acetate and Fe(III). The PM technology was developed for aerobic organisms. The reduction of a tetrazolium dye by the test organism represents metabolic activity on the array which is detected and measured by the OmniLog(R) system. We have previously adapted the technology for the anaerobic sulfate reducing bacterium Desulfovibrio vulgaris. In this work, we have taken the technology a step further by adapting it for the iron reducing obligate anaerobe Geobacter metallireducens. In an osmotic stress microarray it was determined that the organism has higher sensitivity to impermeable solutes 3-6percent KCl and 2-5percent NaNO3 that result in osmotic stress by osmosis to the cell than to permeable non-ionic solutes represented by 5-20percent ethylene glycol and 2-3percent urea. The osmotic stress microarray also includes an array of osmoprotectants and precursor molecules that were screened to identify substrates that would provide osmotic protection to NaCl stress. None of the substrates tested conferred resistance to elevated concentrations of salt. Verification studies in which G.m. was grown in defined medium amended with 100mM NaCl (MIC) and the common osmoprotectants betaine, glycine and proline supported the PM findings. Further verification was done by analysis of transcriptomic profiles of G.m. grown under 100mM NaCl stress that revealed up-regulation of genes related to degradation rather than accumulation of the above-mentioned osmoprotectants. The phenotypic profile, supported by additional analysis indicates that the accumulation of these osmoprotectants as a response to salt stress does not

  8. A novel genotoxin-specific qPCR array based on the metabolically competent human HepaRG™ cell line as a rapid and reliable tool for improved in vitro hazard assessment.

    Science.gov (United States)

    Ates, Gamze; Mertens, Birgit; Heymans, Anja; Verschaeve, Luc; Milushev, Dimiter; Vanparys, Philippe; Roosens, Nancy H C; De Keersmaecker, Sigrid C J; Rogiers, Vera; Doktorova, Tatyana Y

    2018-04-01

    Although the value of the regulatory accepted batteries for in vitro genotoxicity testing is recognized, they result in a high number of false positives. This has a major impact on society and industries developing novel compounds for pharmaceutical, chemical, and consumer products, as afflicted compounds have to be (prematurely) abandoned or further tested on animals. Using the metabolically competent human HepaRG ™ cell line and toxicogenomics approaches, we have developed an upgraded, innovative, and proprietary gene classifier. This gene classifier is based on transcriptomic changes induced by 12 genotoxic and 12 non-genotoxic reference compounds tested at sub-cytotoxic concentrations, i.e., IC10 concentrations as determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The resulting gene classifier was translated into an easy-to-handle qPCR array that, as shown by pathway analysis, covers several different cellular processes related to genotoxicity. To further assess the predictivity of the tool, a set of 5 known positive and 5 known negative test compounds for genotoxicity was evaluated. In addition, 2 compounds with debatable genotoxicity data were tested to explore how the qPCR array would classify these. With an accuracy of 100%, when equivocal results were considered positive, the results showed that combining HepaRG ™ cells with a genotoxin-specific qPCR array can improve (geno)toxicological hazard assessment. In addition, the developed qPCR array was able to provide additional information on compounds for which so far debatable genotoxicity data are available. The results indicate that the new in vitro tool can improve human safety assessment of chemicals in general by basing predictions on mechanistic toxicogenomics information.

  9. Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression.

    Science.gov (United States)

    Kadam, Anagha; Janto, Benjamin; Eutsey, Rory; Earl, Joshua P; Powell, Evan; Dahlgren, Margaret E; Hu, Fen Z; Ehrlich, Garth D; Hiller, N Luisa

    2015-02-02

    There is extensive genomic diversity among Streptococcus pneumoniae isolates. Approximately half of the comprehensive set of genes in the species (the supragenome or pangenome) is present in all the isolates (core set), and the remaining is unevenly distributed among strains (distributed set). The Streptococcus pneumoniae Supragenome Hybridization (SpSGH) array provides coverage for an extensive set of genes and polymorphisms encountered within this species, capturing this genomic diversity. Further, the capture is quantitative. In this manner, the SpSGH array allows for both genomic and transcriptomic analyses of diverse S. pneumoniae isolates on a single platform. In this unit, we present the SpSGH array, and describe in detail its design and implementation for both genomic and transcriptomic analyses. The methodology can be applied to construction and modification of SpSGH array platforms, as well to other bacterial species as long as multiple whole-genome sequences are available that collectively capture the vast majority of the species supragenome. Copyright © 2015 John Wiley & Sons, Inc.

  10. DNA-Sequence Based Typing of the Cronobacter Genus Using MLST, CRISPR-cas Array and Capsular Profiling

    Directory of Open Access Journals (Sweden)

    Pauline Ogrodzki

    2017-09-01

    Full Text Available The Cronobacter genus is composed of seven species, within which a number of pathovars have been described. The most notable infections by Cronobacter spp. are of infants through the consumption of contaminated infant formula. The description of the genus has greatly improved in recent years through DNA sequencing techniques, and this has led to a robust means of identification. However some species are highly clonal and this limits the ability to discriminate between unrelated strains by some methods of genotyping. This article updates the application of three genotyping methods across the Cronobacter genus. The three genotyping methods were multilocus sequence typing (MLST, capsular profiling of the K-antigen and colanic acid (CA biosynthesis regions, and CRISPR-cas array profiling. A total of 1654 MLST profiled and 286 whole genome sequenced strains, available by open access at the PubMLST Cronobacter database, were used this analysis. The predominance of C. sakazakii and C. malonaticus in clinical infections was confirmed. The majority of clinical strains being in the C. sakazakii clonal complexes (CC 1 and 4, sequence types (ST 8 and 12 and C. malonaticus ST7. The capsular profile K2:CA2, previously proposed as being strongly associated with C. sakazakii and C. malonaticus isolates from severe neonatal infections, was also found in C. turicensis, C. dublinensis and C. universalis. The majority of CRISPR-cas types across the genus was the I-E (Ecoli type. Some strains of C. dublinensis and C. muytjensii encoded the I-F (Ypseudo type, and others lacked the cas gene loci. The significance of the expanding profiling will be of benefit to researchers as well as governmental and industrial risk assessors.

  11. DNA-Sequence Based Typing of the Cronobacter Genus Using MLST, CRISPR-cas Array and Capsular Profiling.

    Science.gov (United States)

    Ogrodzki, Pauline; Forsythe, Stephen J

    2017-01-01

    The Cronobacter genus is composed of seven species, within which a number of pathovars have been described. The most notable infections by Cronobacter spp. are of infants through the consumption of contaminated infant formula. The description of the genus has greatly improved in recent years through DNA sequencing techniques, and this has led to a robust means of identification. However some species are highly clonal and this limits the ability to discriminate between unrelated strains by some methods of genotyping. This article updates the application of three genotyping methods across the Cronobacter genus. The three genotyping methods were multilocus sequence typing (MLST), capsular profiling of the K -antigen and colanic acid (CA) biosynthesis regions, and CRISPR- cas array profiling. A total of 1654 MLST profiled and 286 whole genome sequenced strains, available by open access at the PubMLST Cronobacter database, were used this analysis. The predominance of C. sakazakii and C. malonaticus in clinical infections was confirmed. The majority of clinical strains being in the C. sakazakii clonal complexes (CC) 1 and 4, sequence types (ST) 8 and 12 and C. malonaticus ST7. The capsular profile K2:CA2, previously proposed as being strongly associated with C. sakazakii and C. malonaticus isolates from severe neonatal infections, was also found in C. turicensis , C. dublinensis and C. universalis . The majority of CRISPR- cas types across the genus was the I-E (Ecoli) type. Some strains of C. dublinensis and C. muytjensii encoded the I-F (Ypseudo) type, and others lacked the cas gene loci. The significance of the expanding profiling will be of benefit to researchers as well as governmental and industrial risk assessors.

  12. Monitoring Metabolite Profiles of Cannabis sativa L. Trichomes during Flowering Period Using 1H NMR-Based Metabolomics and Real-Time PCR.

    Science.gov (United States)

    Happyana, Nizar; Kayser, Oliver

    2016-08-01

    Cannabis sativa trichomes are glandular structures predominantly responsible for the biosynthesis of cannabinoids, the biologically active compounds unique to this plant. To the best of our knowledge, most metabolomic works on C. sativa that have been reported previously focused their investigations on the flowers and leaves of this plant. In this study, (1)H NMR-based metabolomics and real-time PCR analysis were applied for monitoring the metabolite profiles of C. sativa trichomes, variety Bediol, during the last 4 weeks of the flowering period. Partial least squares discriminant analysis models successfully classified metabolites of the trichomes based on the harvest time. Δ (9)-Tetrahydrocannabinolic acid (1) and cannabidiolic acid (2) constituted the vital differential components of the organic preparations, while asparagine, glutamine, fructose, and glucose proved to be their water-extracted counterparts. According to RT-PCR analysis, gene expression levels of olivetol synthase and olivetolic acid cyclase influenced the accumulation of cannabinoids in the Cannabis trichomes during the monitoring time. Moreover, quantitative (1)H NMR and RT-PCR analysis of the Cannabis trichomes suggested that the gene regulation of cannabinoid biosynthesis in the C. sativa variety Bediol is unique when compared with other C. sativa varieties. Georg Thieme Verlag KG Stuttgart · New York.

  13. Improved intra-array and interarray normalization of peptide microarray phosphorylation for phosphorylome and kinome profiling by rational selection of relevant spots

    Science.gov (United States)

    Scholma, Jetse; Fuhler, Gwenny M.; Joore, Jos; Hulsman, Marc; Schivo, Stefano; List, Alan F.; Reinders, Marcel J. T.; Peppelenbosch, Maikel P.; Post, Janine N.

    2016-01-01

    Massive parallel analysis using array technology has become the mainstay for analysis of genomes and transcriptomes. Analogously, the predominance of phosphorylation as a regulator of cellular metabolism has fostered the development of peptide arrays of kinase consensus substrates that allow the charting of cellular phosphorylation events (often called kinome profiling). However, whereas the bioinformatical framework for expression array analysis is well-developed, no advanced analysis tools are yet available for kinome profiling. Especially intra-array and interarray normalization of peptide array phosphorylation remain problematic, due to the absence of “housekeeping” kinases and the obvious fallacy of the assumption that different experimental conditions should exhibit equal amounts of kinase activity. Here we describe the development of analysis tools that reliably quantify phosphorylation of peptide arrays and that allow normalization of the signals obtained. We provide a method for intraslide gradient correction and spot quality control. We describe a novel interarray normalization procedure, named repetitive signal enhancement, RSE, which provides a mathematical approach to limit the false negative results occuring with the use of other normalization procedures. Using in silico and biological experiments we show that employing such protocols yields superior insight into cellular physiology as compared to classical analysis tools for kinome profiling. PMID:27225531

  14. Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli.

    Science.gov (United States)

    Ståhlberg, Anders; Elbing, Karin; Andrade-Garda, José Manuel; Sjögreen, Björn; Forootan, Amin; Kubista, Mikael

    2008-04-16

    The large sensitivity, high reproducibility and essentially unlimited dynamic range of real-time PCR to measure gene expression in complex samples provides the opportunity for powerful multivariate and multiway studies of biological phenomena. In multiway studies samples are characterized by their expression profiles to monitor changes over time, effect of treatment, drug dosage etc. Here we perform a multiway study of the temporal response of four yeast Saccharomyces cerevisiae strains with different glucose uptake rates upon altered metabolic conditions. We measured the expression of 18 genes as function of time after addition of glucose to four strains of yeast grown in ethanol. The data are analyzed by matrix-augmented PCA, which is a generalization of PCA for 3-way data, and the results are confirmed by hierarchical clustering and clustering by Kohonen self-organizing map. Our approach identifies gene groups that respond similarly to the change of nutrient, and genes that behave differently in mutant strains. Of particular interest is our finding that ADH4 and ADH6 show a behavior typical of glucose-induced genes, while ADH3 and ADH5 are repressed after glucose addition. Multiway real-time PCR gene expression profiling is a powerful technique which can be utilized to characterize functions of new genes by, for example, comparing their temporal response after perturbation in different genetic variants of the studied subject. The technique also identifies genes that show perturbed expression in specific strains.

  15. Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli

    Directory of Open Access Journals (Sweden)

    Andrade-Garda José

    2008-04-01

    Full Text Available Abstract Background The large sensitivity, high reproducibility and essentially unlimited dynamic range of real-time PCR to measure gene expression in complex samples provides the opportunity for powerful multivariate and multiway studies of biological phenomena. In multiway studies samples are characterized by their expression profiles to monitor changes over time, effect of treatment, drug dosage etc. Here we perform a multiway study of the temporal response of four yeast Saccharomyces cerevisiae strains with different glucose uptake rates upon altered metabolic conditions. Results We measured the expression of 18 genes as function of time after addition of glucose to four strains of yeast grown in ethanol. The data are analyzed by matrix-augmented PCA, which is a generalization of PCA for 3-way data, and the results are confirmed by hierarchical clustering and clustering by Kohonen self-organizing map. Our approach identifies gene groups that respond similarly to the change of nutrient, and genes that behave differently in mutant strains. Of particular interest is our finding that ADH4 and ADH6 show a behavior typical of glucose-induced genes, while ADH3 and ADH5 are repressed after glucose addition. Conclusion Multiway real-time PCR gene expression profiling is a powerful technique which can be utilized to characterize functions of new genes by, for example, comparing their temporal response after perturbation in different genetic variants of the studied subject. The technique also identifies genes that show perturbed expression in specific strains.

  16. Measurement of impurity emission profiles in CHS Plasma using AXUV photodiode arrays and VUV bandpass filters

    International Nuclear Information System (INIS)

    Suzuki, C.; Peterson, B.J.; Ida, K.

    2004-01-01

    We have designed a compact and low-cost diagnostic system for spatiotemporal distributions of specific vacuum ultraviolet (VUV) emission lines from impurities in Compact Helical System (CHS) plasmas. The system consists of 20 channel absolute extreme ultraviolet photodiode arrays combined with interchangeable thin foil filters which have passbands in the VUV region. A compact mounting module which contains all the components including an in-vacuum preamplifier for immediate current-voltage conversion has been designed and successfully fabricated. A preliminary measurement with a single module using an aluminum foil filter has been carried out for monitoring the behavior of oxygen impurity in CHS, and initial results have been obtained. Two identical modules equipped with Versa Module European bus-based analog-digital converters will be available for future tomographic measurements

  17. Multiplex flow cytometry barcoding and antibody arrays identify surface antigen profiles of primary and metastatic colon cancer cell lines.

    Directory of Open Access Journals (Sweden)

    Kumar Sukhdeo

    Full Text Available Colon cancer is a deadly disease affecting millions of people worldwide. Current treatment challenges include management of disease burden as well as improvements in detection and targeting of tumor cells. To identify disease state-specific surface antigen signatures, we combined fluorescent cell barcoding with high-throughput flow cytometric profiling of primary and metastatic colon cancer lines (SW480, SW620, and HCT116. Our multiplexed technique offers improvements over conventional methods by permitting the simultaneous and rapid screening of cancer cells with reduced effort and cost. The method uses a protein-level analysis with commercially available antibodies on live cells with intact epitopes to detect potential tumor-specific targets that can be further investigated for their clinical utility. Multiplexed antibody arrays can easily be applied to other tumor types or pathologies for discovery-based approaches to target identification.

  18. Different Array CGH profiles within hereditary breast cancer tumors associated to BRCA1 expression and overall survival

    International Nuclear Information System (INIS)

    Alvarez, Carolina; Aravena, Andrés; Tapia, Teresa; Rozenblum, Ester; Solís, Luisa; Corvalán, Alejandro; Camus, Mauricio; Alvarez, Manuel; Munroe, David; Maass, Alejandro; Carvallo, Pilar

    2016-01-01

    Array CGH analysis of breast tumors has contributed to the identification of different genomic profiles in these tumors. Loss of DNA repair by BRCA1 functional deficiency in breast cancer has been proposed as a relevant contribution to breast cancer progression for tumors with no germline mutation. Identifying the genomic alterations taking place in BRCA1 not expressing tumors will lead us to a better understanding of the cellular functions affected in this heterogeneous disease. Moreover, specific genomic alterations may contribute to the identification of potential therapeutic targets and offer a more personalized treatment to breast cancer patients. Forty seven tumors from hereditary breast cancer cases, previously analyzed for BRCA1 expression, and screened for germline BRCA1 and 2 mutations, were analyzed by Array based Comparative Genomic Hybridization (aCGH) using Agilent 4x44K arrays. Overall survival was established for tumors in different clusters using Log-rank (Mantel-Cox) Test. Gene lists obtained from aCGH analysis were analyzed for Gene Ontology enrichment using GOrilla and DAVID tools. Genomic profiling of the tumors showed specific alterations associated to BRCA1 or 2 mutation status, and BRCA1 expression in the tumors, affecting relevant cellular processes. Similar cellular functions were found affected in BRCA1 not expressing and BRCA1 or 2 mutated tumors. Hierarchical clustering classified hereditary breast tumors in four major, groups according to the type and amount of genomic alterations, showing one group with a significantly poor overall survival (p = 0.0221). Within this cluster, deletion of PLEKHO1, GDF11, DARC, DAG1 and CD63 may be associated to the worse outcome of the patients. These results support the fact that BRCA1 lack of expression in tumors should be used as a marker for BRCAness and to select these patients for synthetic lethality approaches such as treatment with PARP inhibitors. In addition, the identification of specific

  19. Accurate 3-D Profile Extraction of Skull Bone Using an Ultrasound Matrix Array.

    Science.gov (United States)

    Hajian, Mehdi; Gaspar, Robert; Maev, Roman Gr

    2017-12-01

    The present study investigates the feasibility, accuracy, and precision of 3-D profile extraction of the human skull bone using a custom-designed ultrasound matrix transducer in Pulse-Echo. Due to the attenuative scattering properties of the skull, the backscattered echoes from the inner surface of the skull are severely degraded, attenuated, and at some points overlapped. Furthermore, the speed of sound (SOS) in the skull varies significantly in different zones and also from case to case; if considered constant, it introduces significant error to the profile measurement. A new method for simultaneous estimation of the skull profiles and the sound speed value is presented. The proposed method is a two-folded procedure: first, the arrival times of the backscattered echoes from the skull bone are estimated using multi-lag phase delay (MLPD) and modified space alternating generalized expectation maximization (SAGE) algorithms. Next, these arrival times are fed into an adaptive sound speed estimation algorithm to compute the optimal SOS value and subsequently, the skull bone thickness. For quantitative evaluation, the estimated bone phantom thicknesses were compared with the mechanical measurements. The accuracies of the bone thickness measurements using MLPD and modified SAGE algorithms combined with the adaptive SOS estimation were 7.93% and 4.21%, respectively. These values were 14.44% and 10.75% for the autocorrelation and cross-correlation methods. Additionally, the Bland-Altman plots showed the modified SAGE outperformed the other methods with -0.35 and 0.44 mm limits of agreement. No systematic error that could be related to the skull bone thickness was observed for this method.

  20. Changes in Growth, Genomic DNA, Protein Profiles in Wheat Plant Using Physiological and RAPD-PCR Techniques

    International Nuclear Information System (INIS)

    El-Tarras, A.

    2002-01-01

    Wheat is the major winter cereal crop in the world. The total cultivated area of this crop in Egypt is about two million feddans. Soil salinity represent a serious problem to agriculture in arid and semi-arid in the world. Mexico wheat (Triticum vulgar var. Ycora rojo) was imported in 1999 for cultivation. Mexico wheat was exposed to gamma rays (cobalt 60) from 10 to 80 Krad The unirradiated and irradiated wheat were cultivated in the presence of 0, 5000,10000 and 20000 mg/L of salt solution and 16 hour light /25 degree C. The previous treatment was repeated in combination with 5, 10 mg/l ABA and 10, 20 mg/l GA3 separately. Different accessed parameters were used for evaluation, these parameters were: germination percentage, length of shoots and roots, pigment contents (chl. a,b and a/b carotenoids and total pigments), total protein patterns and RAPD, PCR techniques. The results showed that both of radiation and salinity reduced the percentage of germination. Soaking grains in GA3 considerably increased the shoot and root lengths. Highest value of carotenoids obtained act as a defense mechanism against harmful salinity action. Also, the seedling exposed to 80 Krad and treated with ABA (5 or 10 mg/l) can survive during the experimental period, while plants treated with 10 and 20 mg/l GA3 and exposed to 80 Krad can not survive. At low radiation doses (10 and 20 Krad) there was no difference in the number and density of bands of the total protein patterns, while in the RAPD, PCR technique in presence and/or absence of DNA band in unirradiated and irradiated wheat seeds were observed

  1. Diagnóstico de virus respiratorios utilizando un sistema automatizado de PCR múltiples (FilmArray y su comparación con métodos convencionales

    Directory of Open Access Journals (Sweden)

    Débora N Marcone

    2015-03-01

    Full Text Available Las infecciones respiratorias agudas producen una importante morbimortalidad y comúnmente son causadas por virus. En Argentina, los programas de vigilancia epidemiológica se basan en la detección de antígenos virales por inmunofluorescencia (IF, aunque es bien conocido que los métodos moleculares son más sensibles. El panel respiratorio (PR FilmArray (PR-FilmArray es un equipo comercial automatizado de PCR múltiples que detecta 17 virus respiratorios y 3 bacterias, en un sistema cerrado que requiere 5 min de procesamiento y una 1 h de instrumentación. Se evaluó un total de 315 muestras respiratorias de niños menores de 6 años con infecciones respiratorias agudas por IF para 8 virus respiratorios y por RT-PCR para rinovirus. Posteriormente, estas muestras se estudiaron con el PR-FilmArray. La frecuencia de positividad al considerar los 9 virus estudiados por IF y RT-PCR fue del 75 %; por PR-FilmArray fue del 92 %. El porcentaje de acuerdo positivo entre ambas metodologías fue del 70,5 % y el de acuerdo negativo fue del 99,6 % (intervalo de confianza 95 %: 65,5-75,1 y 99,2-99,8, respectivamente. El PR-FilmArray permitió obtener un mayor diagnóstico positivo (97 % y detectó otros virus, como los coronavirus NL63, 229E, OC43 y HKU1 (10 % y los bocavirus (18 %. Además, permitió identificar coinfecciones múltiples (39 % con 2, 3, 4 y hasta 5 virus. Actualmente, la IF continúa siendo el método más utilizado en los países latinoamericanos para el diagnóstico de virus respiratorios por su bajo costo, por su capacidad para procesar un alto número de muestras simultáneamente y porque los resultados de los virus más frecuentes están disponibles en 5 h. Sin embargo, la futura incorporación de métodos moleculares aumentaría notablemente la capacidad diagnóstica.

  2. Prognostic impact of array-based genomic profiles in esophageal squamous cell cancer

    DEFF Research Database (Denmark)

    Carneiro, Ana; Isinger, Anna; Karlsson, Anna

    2008-01-01

    BACKGROUND: Esophageal squamous cell carcinoma (ESCC) is a genetically complex tumor type and a major cause of cancer related mortality. Although distinct genetic alterations have been linked to ESCC development and prognosis, the genetic alterations have not gained clinical applicability. We...... interdependent alterations and deranged pathways were identified and copy number changes were correlated to stage, differentiation and survival. RESULTS: Copy number alterations affected median 19% of the genome and included recurrent gains of chromosome regions 5p, 7p, 7q, 8q, 10q, 11q, 12p, 14q, 16p, 17p, 19p......p13.3 independently predicted poor survival in multivariate analysis. CONCLUSION: aCGH profiling verified genetic complexity in ESCC and herein identified imbalances of multiple central tumorigenic pathways. Distinct gains correlate with clinicopathological variables and independently predict...

  3. Accurate quantification of microorganisms in PCR-inhibiting environmental DNA extracts by a novel Internal Amplification Control approach using Biotrove OpenArrays

    NARCIS (Netherlands)

    Van Doorn, R.; Klerks, M.; van Gent-Pelzer, M.; Speksnijder, A.G.C.L.; Kowalchuk, G.A.; Schoen, C.D.

    2009-01-01

    PCR-based detection assays are prone to inhibition by substances present in environmental samples, thereby potentially leading to inaccurate target quantification or false-negative results. Internal amplification controls (IACs) have been developed to help alleviate this problem but are generally

  4. Optimizing laser beam profiles using micro-lens arrays for efficient material processing: applications to solar cells

    Science.gov (United States)

    Hauschild, Dirk; Homburg, Oliver; Mitra, Thomas; Ivanenko, Mikhail; Jarczynski, Manfred; Meinschien, Jens; Bayer, Andreas; Lissotschenko, Vitalij

    2009-02-01

    High power laser sources are used in various production tools for microelectronic products and solar cells, including the applications annealing, lithography, edge isolation as well as dicing and patterning. Besides the right choice of the laser source suitable high performance optics for generating the appropriate beam profile and intensity distribution are of high importance for the right processing speed, quality and yield. For industrial applications equally important is an adequate understanding of the physics of the light-matter interaction behind the process. In advance simulations of the tool performance can minimize technical and financial risk as well as lead times for prototyping and introduction into series production. LIMO has developed its own software founded on the Maxwell equations taking into account all important physical aspects of the laser based process: the light source, the beam shaping optical system and the light-matter interaction. Based on this knowledge together with a unique free-form micro-lens array production technology and patented micro-optics beam shaping designs a number of novel solar cell production tool sub-systems have been built. The basic functionalities, design principles and performance results are presented with a special emphasis on resilience, cost reduction and process reliability.

  5. Micropatch-arrayed pads for non-invasive spatial and temporal profiling of topical drugs on skin surface.

    Science.gov (United States)

    Dutkiewicz, Ewelina P; Chiu, Hsien-Yi; Urban, Pawel L

    2015-11-01

    Micropatch-arrayed pads (MAPAs) are presented as a facile and sensitive sampling method for spatial profiling of topical agents adsorbed on the surface of skin. MAPAs are 28 × 28 mm sized pieces of polytetrafluoroethylene containing plurality of cavities filled with agarose hydrogel. They are affixed onto skin for 10 min with the purpose to collect drugs applied topically. Polar compounds are absorbed by the hydrogel micropatches. The probes are subsequently scanned by an automated nanospray desorption electrospray ionization mass spectrometry system operated in the tapping dual-polarity mode. When the liquid junction gets into contact with every micropatch, polar compounds absorbed in the hydrogel matrix are desorbed and transferred to the ion source. A 3D-printed interface prevents evaporation of hydrogel micropatches assuring good reproducibility and sensitivity. MAPAs have been applied to follow dispersion of topical drugs applied to human skin in vivo and to porcine skin ex vivo, in the form of self-adhesive patches. Spatiotemporal characteristics of the drug dispersion process have been revealed using this non-invasive test. Differences between drug dispersion in vivo and ex vivo could be observed. We envision that MAPAs can be used to investigate spatiotemporal kinetics of various topical agents utilized in medical treatment. Copyright © 2015 John Wiley & Sons, Ltd.

  6. CGI: Java software for mapping and visualizing data from array-based comparative genomic hybridization and expression profiling.

    Science.gov (United States)

    Gu, Joyce Xiuweu-Xu; Wei, Michael Yang; Rao, Pulivarthi H; Lau, Ching C; Behl, Sanjiv; Man, Tsz-Kwong

    2007-10-06

    With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.

  7. CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling

    Directory of Open Access Journals (Sweden)

    Joyce Xiuweu-Xu Gu

    2007-01-01

    Full Text Available With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator that matches the BAC clones from array-based comparative genomic hybridization (aCGH to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specifi c BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.

  8. Design, Construction, and Initial Test of High Spatial Resolution Thermometry Arrays for Detection of Surface Temperature Profiles on SRF Cavities in Super Fluid Helium

    Energy Technology Data Exchange (ETDEWEB)

    Ari Palczewski, Rongli Geng, Grigory Eremeev

    2011-07-01

    We designed and built two high resolution (0.6-0.55mm special resolution [1.1-1.2mm separation]) thermometry arrays prototypes out of the Allen Bradley 90-120 ohm 1/8 watt resistor to measure surface temperature profiles on SRF cavities. One array was designed to be physically flexible and conform to any location on a SRF cavity; the other was modeled after the common G-10/stycast 2850 thermometer and designed to fit on the equator of an ILC (Tesla 1.3GHz) SRF cavity. We will discuss the advantages and disadvantages of each array and their construction. In addition we will present a case study of the arrays performance on a real SRF cavity TB9NR001. TB9NR001 presented a unique opportunity to test the performance of each array as it contained a dual (4mm separation) cat eye defect which conventional methods such as OST (Oscillating Superleak second-sound Transducers) and full coverage thermometry mapping were unable to distinguish between. We will discuss the new arrays ability to distinguish between the two defects and their preheating performance.

  9. Eight-plex PCR and liquid-array detection of bacterial and viral pathogens in cerebrospinal fluid from patients with suspected meningitis

    DEFF Research Database (Denmark)

    Bøving, Mette Kusk; Pedersen, Lisbeth Nørum; Møller, Jens Kjølseth

    2009-01-01

    pneumoniae, Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, Streptococcus agalactiae, herpes simplex virus types 1 and 2, and varicella-zoster virus. The study was based on 1,187 samples, of which 55 were found to be positive by PCR. The assay was found to have an excellent sensitivity...... and an excellent specificity compared to the results of a "gold standard," defined by routine laboratory tests, for the two most important pathogens, S. pneumoniae (95 and 99.1%, respectively) and N. meningitidis (100 and 99.7%, respectively). The method provides a valuable supplement to the traditional microscopy...

  10. Detection of siRNA Mediated Target mRNA Cleavage Activities in Human Cells by a Novel Stem-Loop Array RT-PCR Analysis

    Science.gov (United States)

    2016-09-07

    sequences of the target mRNA, and a double stranded stem at the 5′ end that forms a stem -loop to function as a forceps to stabilize the secondary...E-mjournal homepage: www.elsevier.com/locate/bbrepDetection of siRNA-mediated target mRNA cleavage activities in human cells by a novel stem -loop...challenges for the accurate and efficient detection and verification of cleavage sites on target mRNAs. Here we used a sensitive stem -loop array reverse

  11. Quantitative Real Time PCR approach to study gene expression profile during prenatal growth of skeletal muscle in pig of Duroc and Pietrain breeds

    Directory of Open Access Journals (Sweden)

    M. Cagnazzo

    2010-01-01

    Full Text Available The quantitative real time-PCR (QRT-PCR is a very sensitive method used to quantify mRNA level in gene expression analysis. Combining amplification, detection and quantification in a single step, allows a more accurate measurement compared to the traditional PCR end point analysis (Pfaffl, 2001; Bustin, 2002.

  12. Performance of the digene LQ, RH and PS HPVs genotyping systems on clinical samples and comparison with HC2 and PCR-based Linear Array.

    Science.gov (United States)

    Godínez, Jose M; Tous, Sara; Baixeras, Nuria; Moreno-Crespi, Judith; Alejo, María; Lejeune, Marylène; Bravo, Ignacio G; Bosch, F Xavier; de Sanjosé, Silvia

    2011-11-18

    Certain Human Papillomaviruses (HPVs) are the infectious agents involved in cervical cancer development. Detection of HPVs DNA is part of the cervical cancer screening protocols and HPVs genotyping has been proposed for its inclusion in these preventive programs. The aim of this study was to evaluate three novel genotyping tests, namely Qiagen LQ, RH and PS, in clinical samples with and without abnormalities. For this, 305 cervical samples were processed and the results of the evaluated techniques were compared with those obtained in the HPVs diagnostic process in our lab, by using HC2 and Linear Array (LA) technologies. The concordances and kappa statistics (k) for each technique compared with HC2 were 98.69% (k = 0.94) for LQ, 98.03% (k = 0.91) for RH and 91.80% (k = 0.82) for PS. There was a very good agreement in HPVs type-specific concordance for the most prevalent types HPV16 (kappa range = 0.83-0.90), HPV18 (k.r.= 0.74-0.80) and HPV45 (k.r.= 0.82-0.90). The three tests showed an overall good concordance for HPVs detection when compared with HR-HC2 system. LQ and RH rendered lower detection rate for multiple infections than LA genotyping. However, our understanding of the clinical significance of multiple HPVs infections is still incomplete and therefore the relevance of the lower ability to detect multiple infections needs to be evaluated.

  13. Analysis of ultrasonic beam profile due to change of elements' number for phased array transducer (part 2)

    International Nuclear Information System (INIS)

    Choi, Sang Woo; Lee, Joon Hyun

    1998-01-01

    The phased array offers many advantages and improvements over conventional single-element transducers such as the straight-beam and angle-beam. The advantages of array sensors for large structures are two folds; firstly, array transducers provide a method of rapid beam steering and sequential addressing of a large area of interest without requiring mechanical or manual scanning which is particularly important in real-time application. Secondly, array transducer provide a method of dynamic focusing, in which the focal length of the ultrasonic beam varies as the pulse propagates through the material. There are some parameters such as number, size, center to center space of elements to design phased array transducer. In previous study. the characteristics of beam steering and dynamic focusing had been simulated for ultrasonic SH-wave with varying the number of phased array transducer's element. In this study, the characteristic of beam steering for phased array transducer has been simulated for ultrasonic SH-wave on the basis of Huygen's principle with varying center to center space of elements. Ultrasonic beam directivity and focusing due to change of time delay of each element were discussed with varying center to center space of elements.

  14. Performance of the digene LQ, RH and PS HPVs genotyping systems on clinical samples and comparison with HC2 and PCR-based Linear Array

    Directory of Open Access Journals (Sweden)

    Godínez Jose M

    2011-11-01

    Full Text Available Abstract Background Certain Human Papillomaviruses (HPVs are the infectious agents involved in cervical cancer development. Detection of HPVs DNA is part of the cervical cancer screening protocols and HPVs genotyping has been proposed for its inclusion in these preventive programs. The aim of this study was to evaluate three novel genotyping tests, namely Qiagen LQ, RH and PS, in clinical samples with and without abnormalities. For this, 305 cervical samples were processed and the results of the evaluated techniques were compared with those obtained in the HPVs diagnostic process in our lab, by using HC2 and Linear Array (LA technologies. Results The concordances and kappa statistics (k for each technique compared with HC2 were 98.69% (k = 0.94 for LQ, 98.03% (k = 0.91 for RH and 91.80% (k = 0.82 for PS. There was a very good agreement in HPVs type-specific concordance for the most prevalent types HPV16 (kappa range = 0.83-0.90, HPV18 (k.r.= 0.74-0.80 and HPV45 (k.r.= 0.82-0.90. Conclusions The three tests showed an overall good concordance for HPVs detection when compared with HR-HC2 system. LQ and RH rendered lower detection rate for multiple infections than LA genotyping. However, our understanding of the clinical significance of multiple HPVs infections is still incomplete and therefore the relevance of the lower ability to detect multiple infections needs to be evaluated.

  15. DNA microarray-based PCR ribotyping of Clostridium difficile.

    Science.gov (United States)

    Schneeberg, Alexander; Ehricht, Ralf; Slickers, Peter; Baier, Vico; Neubauer, Heinrich; Zimmermann, Stefan; Rabold, Denise; Lübke-Becker, Antina; Seyboldt, Christian

    2015-02-01

    This study presents a DNA microarray-based assay for fast and simple PCR ribotyping of Clostridium difficile strains. Hybridization probes were designed to query the modularly structured intergenic spacer region (ISR), which is also the template for conventional and PCR ribotyping with subsequent capillary gel electrophoresis (seq-PCR) ribotyping. The probes were derived from sequences available in GenBank as well as from theoretical ISR module combinations. A database of reference hybridization patterns was set up from a collection of 142 well-characterized C. difficile isolates representing 48 seq-PCR ribotypes. The reference hybridization patterns calculated by the arithmetic mean were compared using a similarity matrix analysis. The 48 investigated seq-PCR ribotypes revealed 27 array profiles that were clearly distinguishable. The most frequent human-pathogenic ribotypes 001, 014/020, 027, and 078/126 were discriminated by the microarray. C. difficile strains related to 078/126 (033, 045/FLI01, 078, 126, 126/FLI01, 413, 413/FLI01, 598, 620, 652, and 660) and 014/020 (014, 020, and 449) showed similar hybridization patterns, confirming their genetic relatedness, which was previously reported. A panel of 50 C. difficile field isolates was tested by seq-PCR ribotyping and the DNA microarray-based assay in parallel. Taking into account that the current version of the microarray does not discriminate some closely related seq-PCR ribotypes, all isolates were typed correctly. Moreover, seq-PCR ribotypes without reference profiles available in the database (ribotype 009 and 5 new types) were correctly recognized as new ribotypes, confirming the performance and expansion potential of the microarray. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  16. Comparison of global brain gene expression profiles between inbred long-sleep and inbred short-sleep mice by high-density gene array hybridization.

    Science.gov (United States)

    Xu, Y; Ehringer, M; Yang, F; Sikela, J M

    2001-06-01

    Inbred long-sleep (ILS) and short-sleep (ISS) mice show significant central nervous system-mediated differences in sleep time for sedative dose of ethanol and are frequently used as a rodent model for ethanol sensitivity. In this study, we have used complementary DNA (cDNA) array hybridization methodology to identify genes that are differentially expressed between the brains of ILS and ISS mice. To carry out this analysis, we used both the gene discovery array (GDA) and the Mouse GEM 1 Microarray. GDA consists of 18,378 nonredundant mouse cDNA clones on a single nylon filter. Complex probes were prepared from total brain mRNA of ILS or ISS mice by using reverse transcription and 33P labeling. The labeled probes were hybridized in parallel to the gene array filters. Data from GDA experiments were analyzed with SQL-Plus and Oracle 8. The GEM microarray includes 8,730 sequence-verified clones on a glass chip. Two fluorescently labeled probes were used to hybridize a microarray simultaneously. Data from GEM experiments were analyzed by using the GEMTools software package (Incyte). Differentially expressed genes identified from each method were confirmed by relative quantitative reverse transcription-polymerase chain reaction (RT-PCR). A total of 41 genes or expressed sequence tags (ESTs) display significant expression level differences between brains of ILS and ISS mice after GDA, GEM1 hybridization, and quantitative RT-PCR confirmation. Among them, 18 clones were expressed higher in ILS mice, and 23 clones were expressed higher in ISS mice. The individual gene or EST's function and mapping information have been analyzed. This study identified 41 genes that are differentially expressed between brains of ILS and ISS mice. Some of them may have biological relevance in mediation of phenotypic variation between ILS and ISS mice for ethanol sensitivity. This study also demonstrates that parallel gene expression comparison with high-density cDNA arrays is a rapid and

  17. Real-Time PCR (qPCR) Primer Design Using Free Online Software

    Science.gov (United States)

    Thornton, Brenda; Basu, Chhandak

    2011-01-01

    Real-time PCR (quantitative PCR or qPCR) has become the preferred method for validating results obtained from assays which measure gene expression profiles. The process uses reverse transcription polymerase chain reaction (RT-PCR), coupled with fluorescent chemistry, to measure variations in transcriptome levels between samples. The four most…

  18. Numerical Analysis of Ultrasonic Beam Profile Due to the Change of the Number of Piezoelectric Elements for Phased Array Transducer

    International Nuclear Information System (INIS)

    Choi, Sang Woo; Lee, Joon Hyun

    1999-01-01

    A phased array is a multi-element piezoelectric device whose elements are individually excited by electric pulses at programmed delay time. One of the advantages of using phased array in nondestructive evaluation (NDE) application over conventional ultrasonic transducers is their great maneuverability of ultrasonic beam. There are some parameters such as the number and the size of the piezoelectric elements and the inter-element spacing of the elements to design phased array transducer. In this study, the characteristic of ultrasonic beam for phased array transducer due to the variation of the number of elements has been simulated for ultrasonic SH-wave on the basis of Huygen's principle. Ultrasonic beam directivity and focusing due to the change of time delay of each element were discussed due to the change of the number of piezoelectric elements. It was found that ultrasonic beam was much more spreaded and hence its sound pressure was decreased as steering angle of ultrasonic beam was increased. In addition, the ability of ultrasonic bean focusing decreased gradually with the increase of focal length at the same piezoelectric elements. However, the ability of beam focusing was improved as the number of consisting elements was increased

  19. Distributed Acoustic Sensing (DAS) Array near a Highway for Traffic Monitoring and Near-Surface Shear-Wave Velocity Profiles

    Science.gov (United States)

    Wang, H. F.; Fratta, D.; Lancelle, C.; Ak, E. Ms; Lord, N. E.

    2017-12-01

    Monitoring traffic is important for many technical reasons. It allows for better design of future roads and assessment of the state of current roads. The number, size, weight, and speed of vehicles control deterioration rate. Also, real-time information supplies data to intelligent information systems to help control traffic. Recently there have been studies looking at monitoring traffic seismically as vibrations from traffic are not sensitive to weather and poor visibility. Furthermore, traffic noise can be used to image S-wave velocity distribution in the near surface by capturing and interpreting Rayleigh and Love waves (Nakata, 2016; Zeng et al. 2016). The capability of DAS for high spatial sampling (1 m), temporal sampling (up to 10 kHz), and distributed nature (tens of kilometers) allows for a closer look at the traffic as it passes and how the speed of the vehicle may change over the length of the array. The potential and difficulties of using DAS for these objectives were studied using two DAS arrays. One at Garner Valley in Southern California (a 700-meter array adjacent to CA Highway 74) and another in Brady Hot Springs, Nevada (an 8700-meter array adjacent to Interstate 80). These studies experimentally evaluated the use of DAS data for monitoring traffic and assessing the use of traffic vibration as non-localized sources for seismic imaging. DAS arrays should also be resilient to issues with lighting conditions that are problematic for video monitoring and it may be sensitive to the weight of a vehicle. This study along a major interstate provides a basis for examining DAS' potential and limitations as a key component of intelligent highway systems.

  20. Evaluation of expression of the Wnt signaling components in canine mammary tumors via RT2 Profiler PCR Array and immunochemistry assays.

    Science.gov (United States)

    Yu, Fang; Rasotto, Roberta; Zhang, Hong; Pei, Shimin; Zhou, Bin; Yang, Xu; Jin, Yipeng; Zhang, Di; Lin, Degui

    2017-09-30

    The Wnt signaling pathway and its key component β-catenin have critical roles in the development of diseases such as tumors in mammals. However, little has been reported about involvement of the Wnt/β-catenin signaling pathway in canine mammary tumors (CMTs). The present study detected expression of 30 Wnt signaling pathway-related genes in CMTs; the results are potentially useful for molecular-based diagnosis of CMTs and the development of new targeted therapies. Significant upregulations of dickkopf-1 protein, secreted frizzled-related sequence protein 1 (SFRP1), frizzled 3, β-catenin, and lymphoid enhancer-binding factor 1 (LEF1) were detected in highly malignant CMTs compared to levels in normal mammary gland tissues; moreover, highly significant upregulation of WNT5A was observed in low malignancy CMTs. Downregulation was only detected for SFRP4 in malignant CMT samples. The subcellular location of β-catenin and cyclin D1 in 100 CMT samples was investigated via immunohistochemical analysis, and significantly increased expressions of β-catenin in cytoplasm and cyclin D1 in nuclei were revealed. Western blotting analysis revealed that the expression of β-catenin and LEF1 increased in in the majority of CMT samples. Taken together, the results provide important evidence of the activation status of the Wnt pathway in CMTs and valuable clues to identifying biomarkers for molecular-based diagnosis of CMT.

  1. Spatial profile measurements of ion-confining potentials using novel position-sensitive ion-energy spectrometer arrays

    International Nuclear Information System (INIS)

    Yoshida, M.; Cho, T.; Hirata, M.; Ito, H.; Kohagura, J.; Yatsu, K.; Miyoshi, S.

    2003-01-01

    The first experimental demonstration of simultaneous measurements of temporally and spatially resolved ion-confining potentials phi c and end-loss-ion fluxes I ELA has been carried out during a single plasma discharge alone by the use of newly designed ion-energy-spectrometer arrays installed in both end regions of the GAMMA 10 tandem mirror. This position-sensitive ion-detector structure is proposed to obtain precise ion-energy spectra without any perturbations from simultaneously incident energetic electrons into the arrays. The relation between phi c and I ELA is physically interpreted in terms of Pastukhov's potential confinement theory. In particular, the importance of axisymmetric phi c formation is found for the plasma confinement

  2. Profiles

    International Nuclear Information System (INIS)

    2004-01-01

    Profiles is a synthetic overview of more than 100 national energy markets in the world, providing insightful facts and key energy statistics. A Profile is structured around 6 main items and completed by key statistics: Ministries, public agencies, energy policy are concerned; main companies in the oil, gas, electricity and coal sectors, status, shareholders; reserve, production, imports and exports, electricity and refining capacities; deregulation of prices, subsidies, taxes; consumption trends by sector, energy market shares; main energy projects, production and consumption prospects. Statistical Profiles are present in about 3 pages the main data and indicators on oil, gas, coal and electricity. (A.L.B.)

  3. Development of a Post-Processing Algorithm for Accurate Human Skull Profile Extraction via Ultrasonic Phased Arrays

    Science.gov (United States)

    Al-Ansary, Mariam Luay Y.

    Ultrasound Imaging has been favored by clinicians for its safety, affordability, accessibility, and speed compared to other imaging modalities. However, the trade-offs to these benefits are a relatively lower image quality and interpretability, which can be addressed by, for example, post-processing methods. One particularly difficult imaging case is associated with the presence of a barrier, such as a human skull, with significantly different acoustical properties than the brain tissue as the target medium. Some methods were proposed in the literature to account for this structure if the skull's geometry is known. Measuring the skull's geometry is therefore an important task that requires attention. In this work, a new edge detection method for accurate human skull profile extraction via post-processing of ultrasonic A-Scans is introduced. This method, referred to as the Selective Echo Extraction algorithm, SEE, processes each A-Scan separately and determines the outermost and innermost boundaries of the skull by means of adaptive filtering. The method can also be used to determine the average attenuation coefficient of the skull. When applied to simulated B-Mode images of the skull profile, promising results were obtained. The profiles obtained from the proposed process in simulations were found to be within 0.15lambda +/- 0.11lambda or 0.09 +/- 0.07mm from the actual profiles. Experiments were also performed to test SEE on skull mimicking phantoms with major acoustical properties similar to those of the actual human skull. With experimental data, the profiles obtained with the proposed process were within 0.32lambda +/- 0.25lambda or 0.19 +/- 0.15mm from the actual profile.

  4. Large-scale image-based profiling of single-cell phenotypes in arrayed CRISPR-Cas9 gene perturbation screens.

    Science.gov (United States)

    de Groot, Reinoud; Lüthi, Joel; Lindsay, Helen; Holtackers, René; Pelkmans, Lucas

    2018-01-23

    High-content imaging using automated microscopy and computer vision allows multivariate profiling of single-cell phenotypes. Here, we present methods for the application of the CISPR-Cas9 system in large-scale, image-based, gene perturbation experiments. We show that CRISPR-Cas9-mediated gene perturbation can be achieved in human tissue culture cells in a timeframe that is compatible with image-based phenotyping. We developed a pipeline to construct a large-scale arrayed library of 2,281 sequence-verified CRISPR-Cas9 targeting plasmids and profiled this library for genes affecting cellular morphology and the subcellular localization of components of the nuclear pore complex (NPC). We conceived a machine-learning method that harnesses genetic heterogeneity to score gene perturbations and identify phenotypically perturbed cells for in-depth characterization of gene perturbation effects. This approach enables genome-scale image-based multivariate gene perturbation profiling using CRISPR-Cas9. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

  5. Online extraction-high performance liquid chromatography-diode array detector-quadrupole time-of-flight tandem mass spectrometry for rapid flavonoid profiling of Fructus aurantii immaturus.

    Science.gov (United States)

    Tong, Runna; Peng, Mijun; Tong, Chaoying; Guo, Keke; Shi, Shuyun

    2018-03-01

    Chemical profiling of natural products by high performance liquid chromatography (HPLC) was critical for understanding of their clinical bioactivities, and sample pretreatment steps have been considered as a bottleneck for analysis. Currently, concerted efforts have been made to develop sample pretreatment methods with high efficiency, low solvent and time consumptions. Here, a simple and efficient online extraction (OLE) strategy coupled with HPLC-diode array detector-quadrupole time-of-flight tandem mass spectrometry (HPLC-DAD-QTOF-MS/MS) was developed for rapid chemical profiling. For OLE strategy, guard column inserted with ground sample (2 mg) instead of sample loop was connected with manual injection valve, in which components were directly extracted and transferred to HPLC-DAD-QTOF-MS/MS system only by mobile phase without any extra time, solvent, instrument and operation. By comparison with offline heat-reflux extraction for Fructus aurantii immaturus (Zhishi), OLE strategy presented higher extraction efficiency perhaps because of the high pressure and gradient elution mode. A total of eighteen flavonoids were detected according to their retention times, UV spectra, exact mass, and fragmentation ions in MS/MS spectra, and compound 9, natsudaidain-3-O-glucoside, was discovered in Zhishi for the first time. It is concluded that the developed OLE-HPLC-DAD-QTOF-MS/MS system offers new perspectives for rapid chemical profiling of natural products. Copyright © 2018. Published by Elsevier B.V.

  6. TH-CD-207B-05: Measurement of CT Bow-Tie Profiles Using a Linear Array Detector

    Energy Technology Data Exchange (ETDEWEB)

    Yang, K; Li, X; Liu, B [Massachusetts General Hospital, Boston, MA (United States)

    2016-06-15

    Purpose: To accurately measure CT bow-tie profiles from various manufacturers and to provide non-proprietary information for CT system modeling. Methods: A GOS-based linear detector (0.8 mm per pixel and 51.2 cm in length) with a fast data sampling speed (0.24 ms/sample) was used to measure the relative profiles of bow-tie filters from a collection of eight CT scanners by three different vendors, GE (LS Xtra, LS VCT, Discovery HD750), Siemens (Sensation 64, Edge, Flash, Force), and Philips (iBrilliance 256). The linear detector was first calibrated for its energy response within typical CT beam quality ranges and compared with an ion chamber and analytical modeling (SPECTRA and TASMIP). A geometrical calibration process was developed to determine key parameters including the distance from the focal spot to the linear detector, the angular increment of the gantry at each data sampling, the location of the central x-ray on the linear detector, and the angular response of the detector pixel. Measurements were performed under axial-scan modes for most representative bow-tie filters and kV selections from each scanner. Bow-tie profiles were determined by re-binning the measured rotational data with an angular accuracy of 0.1 degree using the calibrated geometrical parameters. Results: The linear detector demonstrated an energy response as a solid state detector, which is close to the CT imaging detector. The geometrical calibration was proven to be sufficiently accurate (< 1mm in error for distances >550 mm) and the bow-tie profiles measured from rotational mode matched closely to those from the gantry-stationary mode. Accurate profiles were determined for a total of 21 bow-tie filters and 83 filter/kV combinations from the abovementioned scanner models. Conclusion: A new improved approach of CT bow-tie measurement was proposed and accurate bow-tie profiles were provided for a broad list of CT scanner models.

  7. Modifying the strength and strain concentration profile within collagen scaffolds using customizable arrays of poly-lactic acid fibers.

    Science.gov (United States)

    Mozdzen, Laura C; Vucetic, Alan; Harley, Brendan A C

    2017-02-01

    The tendon-to-bone junction is a highly specialized tissue which dissipates stress concentrations between mechanically dissimilar tendon and bone. Upon injury, the local heterogeneities across this insertion are not regenerated, leading to poor functional outcomes such as formation of scar tissue at the insertion and re-failure rates exceeding 90%. Although current tissue engineering methods are moving towards the development of spatially-graded biomaterials to begin to address these injuries, significant opportunities remain to engineer the often complex local mechanical behavior of such biomaterials to enhance their bioactivity. Here, we describe the use of three-dimensional printing techniques to create customizable arrays of poly-lactic acid (PLA) fibers that can be incorporated into a collagen scaffold under development for tendon bone junction repair. Notably, we use additive manufacturing concepts to generate arrays of spatially-graded fibers from biodegradable PLA that are incorporated into collagen scaffolds to create a collagen-PLA composite. We demonstrate the ability to tune the mechanical performance of the fiber-scaffold composite at the bulk scale. We also demonstrate the incorporation of spatially-heterogeneous fiber designs to establish non-uniform local mechanical performance of the composite biomaterial under tensile load, a critical element in the design of multi-compartment biomaterials for tendon-to-bone regeneration applications. Together, this work highlights the capacity to use multi-scale composite biomaterials to control local and bulk mechanical properties, and provides key insights into design elements under consideration for mechanically competent, multi-tissue regeneration platforms. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Whole genome expression array profiling highlights differences in mucosal defense genes in Barrett's esophagus and esophageal adenocarcinoma.

    Directory of Open Access Journals (Sweden)

    Derek J Nancarrow

    Full Text Available Esophageal adenocarcinoma (EAC has become a major concern in Western countries due to rapid rises in incidence coupled with very poor survival rates. One of the key risk factors for the development of this cancer is the presence of Barrett's esophagus (BE, which is believed to form in response to repeated gastro-esophageal reflux. In this study we performed comparative, genome-wide expression profiling (using Illumina whole-genome Beadarrays on total RNA extracted from esophageal biopsy tissues from individuals with EAC, BE (in the absence of EAC and those with normal squamous epithelium. We combined these data with publically accessible raw data from three similar studies to investigate key gene and ontology differences between these three tissue states. The results support the deduction that BE is a tissue with enhanced glycoprotein synthesis machinery (DPP4, ATP2A3, AGR2 designed to provide strong mucosal defenses aimed at resisting gastro-esophageal reflux. EAC exhibits the enhanced extracellular matrix remodeling (collagens, IGFBP7, PLAU effects expected in an aggressive form of cancer, as well as evidence of reduced expression of genes associated with mucosal (MUC6, CA2, TFF1 and xenobiotic (AKR1C2, AKR1B10 defenses. When our results are compared to previous whole-genome expression profiling studies keratin, mucin, annexin and trefoil factor gene groups are the most frequently represented differentially expressed gene families. Eleven genes identified here are also represented in at least 3 other profiling studies. We used these genes to discriminate between squamous epithelium, BE and EAC within the two largest cohorts using a support vector machine leave one out cross validation (LOOCV analysis. While this method was satisfactory for discriminating squamous epithelium and BE, it demonstrates the need for more detailed investigations into profiling changes between BE and EAC.

  9. Antibody profiling using a recombinant protein-based multiplex ELISA array accelerates recombinant vaccine development: Case study on red sea bream iridovirus as a reverse vaccinology model.

    Science.gov (United States)

    Matsuyama, Tomomasa; Sano, Natsumi; Takano, Tomokazu; Sakai, Takamitsu; Yasuike, Motoshige; Fujiwara, Atushi; Kawato, Yasuhiko; Kurita, Jun; Yoshida, Kazunori; Shimada, Yukinori; Nakayasu, Chihaya

    2018-05-03

    Predicting antigens that would be protective is crucial for the development of recombinant vaccine using genome based vaccine development, also known as reverse vaccinology. High-throughput antigen screening is effective for identifying vaccine target genes, particularly for pathogens for which minimal antigenicity data exist. Using red sea bream iridovirus (RSIV) as a research model, we developed enzyme-linked immune sorbent assay (ELISA) based RSIV-derived 72 recombinant antigen array to profile antiviral antibody responses in convalescent Japanese amberjack (Seriola quinqueradiata). Two and three genes for which the products were unrecognized and recognized, respectively, by antibodies in convalescent serum were selected for recombinant vaccine preparation, and the protective effect was examined in infection tests using Japanese amberjack and greater amberjack (S. dumerili). No protection was provided by vaccines prepared from gene products unrecognized by convalescent serum antibodies. By contrast, two vaccines prepared from gene products recognized by serum antibodies induced protective immunity in both fish species. These results indicate that ELISA array screening is effective for identifying antigens that induce protective immune responses. As this method does not require culturing of pathogens, it is also suitable for identifying protective antigens to un-culturable etiologic agents. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. Power deposition profiles and Poynting vector distribution of phased antenna arrays in the ion-cyclotron resonance heating of a NET/INTOR-type tokamak

    International Nuclear Information System (INIS)

    Bhatnagar, V.P.; Koch, R.

    1986-01-01

    The heating produced by magnetosonic waves launched from phased antenna arrays in the ion-cyclotron range of frequencies is studied for a large tokamak with NET/INTOR-like parameters. The model used combines a 3-D planar, cold-plasma, antenna-plasma coupling code and a 3-D non-circular, toroidal, hot-plasma/ray-tracing code. First, the fractional power absorption of a ray during a single transit through the absorption layer is studied in a D-T plasma indicating total absorption in all INTOR cases except during the initial state characterized by low plasma temperature and density. However, in this case the single-pass wave absorption can be increased considerably by adding a few per cent of hydrogen. Further, complete power deposition profiles and Poynting vector distributions are presented for 'symmetric' and 'antisymmetric' 2x2 antenna array configurations with ksub(parallel)-shaping. Excitation of coaxial modes has, for the first time, been demonstrated explicitly by analysis of the Poynting vector distribution in real space. An antenna configuration with a π-phasing in the z-direction (such that the radiated power spectrum peaks at ksub(parallel) approx.= 5 m -1 ) and the choice of 3lambda/4 long antenna elements with 'symmetric' excitation in the y-direction, are found to produce central RF power deposition profiles in the second-harmonic and minority heating of INTOR. Finally, from a comparison of results for circular and non-circular NET/INTOR plasmas with elongation kappa=1.6, it is found that in the latter wave focusing is greatly reduced and that the power density figures are lower by approximately a factor of 1.9 for the case treated. (author)

  11. High similarity of Trypanosoma cruzi kDNA genetic profiles detected by LSSP-PCR within family groups in an endemic area of Chagas disease in Brazil

    Directory of Open Access Journals (Sweden)

    Sandra Maria Alkmim-Oliveira

    2014-10-01

    Full Text Available Introduction Determining the genetic similarities among Trypanosoma cruzi populations isolated from different hosts and vectors is very important to clarify the epidemiology of Chagas disease. Methods An epidemiological study was conducted in a Brazilian endemic area for Chagas disease, including 76 chronic chagasic individuals (96.1% with an indeterminate form; 46.1% with positive hemoculture. Results T. cruzi I (TcI was isolated from one child and TcII was found in the remaining (97.1% subjects. Low-stringency single-specific-primer-polymerase chain reaction (LSSP-PCR showed high heterogeneity among TcII populations (46% of shared bands; however, high similarities (80-100% among pairs of mothers/children, siblings, or cousins were detected. Conclusions LSSP-PCR showed potential for identifying similar parasite populations among individuals with close kinship in epidemiological studies of Chagas disease.

  12. Comparison of Multiplex Suspension Array Large-Panel Kits for Profiling Cytokines and Chemokines in Rheumatoid Arthritis Patients

    Science.gov (United States)

    Khan, Imran H.; Krishnan, V.V.; Ziman, Melanie; Janatpour, Kim; Wun, Ted; Luciw, Paul A.; Tuscano, Joseph

    2015-01-01

    Background Multiplex analysis allows measurements of a large number of analytes simultaneously in each sample. Based on the Luminex multiplex technology (xMAP), kits for measuring multiple cytokines and chemokines (immunomodulators) are commercially available and are useful in investigations on inflammatory diseases. This study evaluated four multiplex kits (Bio-Plex, LINCOplex, Fluorokine, and Beadlyte) that contained 27, 29, 20 and 22 analytes each, respectively, for the analysis of immunomodulators in plasma of rheumatoid arthritis (RA) patients who underwent treatment with antibody against CD20 (rituximab), a B-cell reductive therapy. Methods Multiplex kits were tested on serial plasma samples obtained from six RA patients at baseline and multiple time points (3, 6, and 9 months) post-treatment with rituximab. The RA patients included in this study had previously failed therapy with disease modifying anti-arthritis drugs (DMARD) and treatment with anti-TNFα antibody (infliximab). Results Computer modeling and hierarchical cluster analysis of the multiplex data allowed a comparison of the performance of multiplex assay kits and revealed profiles of immunomodulators in the RA patients. Conclusions In plasma of RA patients who appeared to have benefited from rituximab treatment the profile of significantly elevated immunomodulators by at least two of the three kits (BioPlex, LINCOplex, Beadlyte), is as follows: IL-12p70, Eotaxin, IL-4, TNFα, Il-9, IL-1β, IFNγ, IL-10, IL-6, and IL-13. Immunomodulator profiling by multiplex analysis may provide useful plasma biomarkers for monitoring response to B-cell reductive therapy in RA patients. PMID:18823005

  13. Assessment of the real-time PCR and different digital PCR platforms for DNA quantification.

    Science.gov (United States)

    Pavšič, Jernej; Žel, Jana; Milavec, Mojca

    2016-01-01

    Digital PCR (dPCR) is beginning to supersede real-time PCR (qPCR) for quantification of nucleic acids in many different applications. Several analytical properties of the two most commonly used dPCR platforms, namely the QX100 system (Bio-Rad) and the 12.765 array of the Biomark system (Fluidigm), have already been evaluated and compared with those of qPCR. However, to the best of our knowledge, direct comparison between the three of these platforms using the same DNA material has not been done, and the 37 K array on the Biomark system has also not been evaluated in terms of linearity, analytical sensitivity and limit of quantification. Here, a first assessment of qPCR, the QX100 system and both arrays of the Biomark system was performed with plasmid and genomic DNA from human cytomegalovirus. With use of PCR components that alter the efficiency of qPCR, each dPCR platform demonstrated consistent copy-number estimations, which indicates the high resilience of dPCR. Two approaches, one considering the total reaction volume and the other considering the effective reaction size, were used to assess linearity, analytical sensitivity and variability. When the total reaction volume was considered, the best performance was observed with qPCR, followed by the QX100 system and the Biomark system. In contrast, when the effective reaction size was considered, all three platforms showed almost equal limits of detection and variability. Although dPCR might not always be more appropriate than qPCR for quantification of low copy numbers, dPCR is a suitable method for robust and reproducible quantification of viral DNA, and a promising technology for the higher-order reference measurement method.

  14. High-throughput cardiac safety evaluation and multi-parameter arrhythmia profiling of cardiomyocytes using microelectrode arrays

    Energy Technology Data Exchange (ETDEWEB)

    Gilchrist, Kristin H., E-mail: kgilchrist@rti.org; Lewis, Gregory F.; Gay, Elaine A.; Sellgren, Katelyn L.; Grego, Sonia

    2015-10-15

    Microelectrode arrays (MEAs) recording extracellular field potentials of human-induced pluripotent stem cell-derived cardiomyocytes (hiPS-CM) provide a rich data set for functional assessment of drug response. The aim of this work is the development of a method for a systematic analysis of arrhythmia using MEAs, with emphasis on the development of six parameters accounting for different types of cardiomyocyte signal irregularities. We describe a software approach to carry out such analysis automatically including generation of a heat map that enables quick visualization of arrhythmic liability of compounds. We also implemented signal processing techniques for reliable extraction of the repolarization peak for field potential duration (FPD) measurement even from recordings with low signal to noise ratios. We measured hiPS-CM's on a 48 well MEA system with 5 minute recordings at multiple time points (0.5, 1, 2 and 4 h) after drug exposure. We evaluated concentration responses for seven compounds with a combination of hERG, QT and clinical proarrhythmia properties: Verapamil, Ranolazine, Flecainide, Amiodarone, Ouabain, Cisapride, and Terfenadine. The predictive utility of MEA parameters as surrogates of these clinical effects were examined. The beat rate and FPD results exhibited good correlations with previous MEA studies in stem cell derived cardiomyocytes and clinical data. The six-parameter arrhythmia assessment exhibited excellent predictive agreement with the known arrhythmogenic potential of the tested compounds, and holds promise as a new method to predict arrhythmic liability. - Highlights: • Six parameters describing arrhythmia were defined and measured for known compounds. • Software for efficient parameter extraction from large MEA data sets was developed. • The proposed cellular parameter set is predictive of clinical drug proarrhythmia.

  15. Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis

    Directory of Open Access Journals (Sweden)

    Chavez Adela

    2008-07-01

    Full Text Available Abstract Background Anaplasma phagocytophilum (Ap is an obligate intracellular bacterium and the agent of human granulocytic anaplasmosis, an emerging tick-borne disease. Ap alternately infects ticks and mammals and a variety of cell types within each. Understanding the biology behind such versatile cellular parasitism may be derived through the use of tiling microarrays to establish high resolution, genome-wide transcription profiles of the organism as it infects cell lines representative of its life cycle (tick; ISE6 and pathogenesis (human; HL-60 and HMEC-1. Results Detailed, host cell specific transcriptional behavior was revealed. There was extensive differential Ap gene transcription between the tick (ISE6 and the human (HL-60 and HMEC-1 cell lines, with far fewer differentially transcribed genes between the human cell lines, and all disproportionately represented by membrane or surface proteins. There were Ap genes exclusively transcribed in each cell line, apparent human- and tick-specific operons and paralogs, and anti-sense transcripts that suggest novel expression regulation processes. Seven virB2 paralogs (of the bacterial type IV secretion system showed human or tick cell dependent transcription. Previously unrecognized genes and coding sequences were identified, as were the expressed p44/msp2 (major surface proteins paralogs (of 114 total, through elevated signal produced to the unique hypervariable region of each – 2/114 in HL-60, 3/114 in HMEC-1, and none in ISE6. Conclusion Using these methods, whole genome transcription profiles can likely be generated for Ap, as well as other obligate intracellular organisms, in any host cells and for all stages of the cell infection process. Visual representation of comprehensive transcription data alongside an annotated map of the genome renders complex transcription into discernable patterns.

  16. Serum protein profiling using an aptamer array predicts clinical outcomes of stage IIA colon cancer: A leave-one-out crossvalidation

    Science.gov (United States)

    Huh, Jung Wook; Kim, Sung Chun; Sohn, Insuk; Jung, Sin-Ho; Kim, Hee Cheol

    2016-01-01

    Background In this study, we established and validated a model for predicting prognosis of stage IIA colon cancer patients based on expression profiles of aptamers in serum. Methods Bloods samples were collected from 227 consecutive patients with pathologic T3N0M0 (stage IIA) colon cancer. We incubated 1,149 serum molecule-binding aptamer pools of clinical significance with serum from patients to obtain aptamers bound to serum molecules, which were then amplified and marked. Oligonucleotide arrays were constructed with the base sequences of the 1,149 aptamers, and the marked products identified above were reacted with one another to produce profiles of the aptamers bound to serum molecules. These profiles were organized into low- and high-risk groups of colon cancer patients based on clinical information for the serum samples. Cox proportional hazards model and leave-one-out cross-validation (LOOCV) were used to evaluate predictive performance. Results During a median follow-up period of 5 years, 29 of the 227 patients (11.9%) experienced recurrence. There were 212 patients (93.4%) in the low-risk group and 15 patients (6.6%) in the high-risk group in our aptamer prognosis model. Postoperative recurrence significantly correlated with age and aptamer risk stratification (p = 0.046 and p = 0.001, respectively). In multivariate analysis, aptamer risk stratification (p recurrence. Disease-free survival curves calculated according to aptamer risk level predicted through a LOOCV procedure and age showed significant differences (p < 0.001 from permutations). Conclusion Aptamer risk stratification can be a valuable prognostic factor in stage II colon cancer patients. PMID:26908450

  17. Epidemiological, clinical and laboratory profile of scrub typhus cases detected by serology and RT-PCR in Kumaon, Uttarakhand: a hospital-based study.

    Science.gov (United States)

    Rawat, Vinita; Singh, Rajesh Kumar; Kumar, Ashok; Saxena, Sandip R; Varshney, Umesh; Kumar, Mukesh

    2018-04-01

    We analysed the epidemiology, clinical and laboratory data of the 168 scrub typhus cases confirmed by a combination of any one of the following: real time polymerase chain reaction (RT-PCR) and/or immunofluorescence assay (IFA) (IgM and/or IgG). The peak season for scrub typhus was from July to October. By multivariate binary logistic regression analysis, the risk of scrub typhus was about four times in those working in occupation related to forest work. Major clinical manifestations were fever (100%), myalgia (65%), cough (51%) and vomiting (46%); major complications were meningitis/meningoencephatilitis (12.5%) and multi-organ failure (MOF) and pneumonia (5.3% each). Laboratory investigations revealed raised aminotranferase levels and thrombocytopenia in most confirmed cases. We conclude that scrub typhus is an important cause of febrile illness in the Kumaon hills of Uttarakhand where this disease had not previously been considered to exist.

  18. A probe-based qRT-PCR method to profile immunological gene expression in blood of captive beluga whales (Delphinapterus leucas

    Directory of Open Access Journals (Sweden)

    Ming-An Tsai

    2017-09-01

    Full Text Available Cytokines are fundamental for a functioning immune system, and thus potentially serve as important indicators of animal health. Quantitation of mRNA using quantitative reverse transcription polymerase chain reaction (qRT-PCR is an established immunological technique. It is particularly suitable for detecting the expression of proteins against which monoclonal antibodies are not available. In this study, we developed a probe-based quantitative gene expression assay for immunological assessment of captive beluga whales (Delphinapterus leucas that is one of the most common cetacean species on display in aquariums worldwide. Six immunologically relevant genes (IL-2Rα, -4, -10, -12, TNFα, and IFNγ were selected for analysis, and two validated housekeeping genes (PGK1 and RPL4 with stable expression were used as reference genes. Sixteen blood samples were obtained from four animals with different health conditions and stored in RNAlater™ solution. These samples were used for RNA extraction followed by qRT-PCR analysis. Analysis of gene transcripts was performed by relative quantitation using the comparative Cq method with the integration of amplification efficiency and two reference genes. The expression levels of each gene in the samples from clinically healthy animals were normally distributed. Transcript outliers for IL-2Rα, IL-4, IL-12, TNFα, and IFNγ were noticed in four samples collected from two clinically unhealthy animals. This assay has the potential to identify immune system deviation from normal state, which is caused by health problems. Furthermore, knowing the immune status of captive cetaceans could help both trainers and veterinarians in implementing preventive approaches prior to disease onset.

  19. Protein array profiling of tic patient sera reveals a broad range and enhanced immune response against Group A Streptococcus antigens.

    Directory of Open Access Journals (Sweden)

    Mauro Bombaci

    Full Text Available The human pathogen Group A Streptococcus (Streptococcus pyogenes, GAS is widely recognized as a major cause of common pharyngitis as well as of severe invasive diseases and non-suppurative sequelae associated with the existence of GAS antigens eliciting host autoantibodies. It has been proposed that a subset of paediatric disorders characterized by tics and obsessive-compulsive symptoms would exacerbate in association with relapses of GAS-associated pharyngitis. This hypothesis is however still controversial. In the attempt to shed light on the contribution of GAS infections to the onset of neuropsychiatric or behavioral disorders affecting as many as 3% of children and adolescents, we tested the antibody response of tic patient sera to a representative panel of GAS antigens. In particular, 102 recombinant proteins were spotted on nitrocellulose-coated glass slides and probed against 61 sera collected from young patients with typical tic neuropsychiatric symptoms but with no overt GAS infection. Sera from 35 children with neither tic disorder nor overt GAS infection were also analyzed. The protein recognition patterns of these two sera groups were compared with those obtained using 239 sera from children with GAS-associated pharyngitis. This comparative analysis identified 25 antigens recognized by sera of the three patient groups and 21 antigens recognized by tic and pharyngitis sera, but poorly or not recognized by sera from children without tic. Interestingly, these antigens appeared to be, in quantitative terms, more immunogenic in tic than in pharyngitis patients. Additionally, a third group of antigens appeared to be preferentially and specifically recognized by tic sera. These findings provide the first evidence that tic patient sera exhibit immunological profiles typical of individuals who elicited a broad, specific and strong immune response against GAS. This may be relevant in the context of one of the hypothesis proposing that GAS

  20. Systematic chemical profiling of Citrus grandis 'Tomentosa' by ultra-fast liquid chromatography/diode-array detector/quadrupole time-of-flight tandem mass spectrometry.

    Science.gov (United States)

    Li, Pan-lin; Liu, Meng-hua; Hu, Jie-hui; Su, Wei-wei

    2014-03-01

    Citrus grandis 'Tomentosa', as the original plant of the traditional Chinese medicine "Huajuhong", has been used as antitussive and expectorant in clinic for thousands of years. The fruit epicarp and whole fruit of this plant were both literarily recorded and commonly used. In the present study, an ultra-fast liquid chromatography coupled with diode-array detection and quadrupole/time-of-flight mass spectrometry (UFLC-DAD-Q-TOF-MS/MS) based chemical profiling method was developed for rapid holistic quality evaluation of C. grandis 'Tomentosa', which laid basis for chemical comparison of two medicinal parts. As a result, forty-eight constituents, mainly belonging to flavonoids and coumarins, were unambiguously identified by comparison with reference standards and/or tentatively characterized by elucidating UV spectra, quasi-molecular ions and fragment ions referring to information available in literature. Both of the epicarp and whole fruit samples were rich in flavonoids and coumarins, but major flavonoids contents in whole fruit were significantly higher than in epicarp (P<0.5). The proposed method could be useful in quality control and standardization of C. grandis 'Tomentosa' raw materials and its products. Results obtained in this study will provide a basis for quality assessment and further study in vivo. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Determination of haemolytic and non haemolytic genes profiles of Bacillus cereus strains isolated from food samples by polymerase chain reaction (pcr) technique

    Science.gov (United States)

    Jawad, Nisreen; Ahemd, Asmat; Abdullah, Aminah

    2018-04-01

    The aim of this study was to investigate the presence of Bacillus cereus and detection of enterotoxigenic genes in food samples by utilizing a Polymerase Chain Reaction technique (PCR). In this study the providence of B. cereus was carried out to food samples. The B. cereus isolates were investigated for enterotoxigenic gene. The cooked seafood, and raw milk samples were purchased from several restaurants and market in the area of (Bangi, Kajang, Serdang and UKM) Selangor, Malaysia. A total of 60 samples have been analyzed. B. cereus contamination has been formed between 1.4×105 - 3×105 cfu/mL of cooked seafood and raw milk samples. Five colonies have been detected as B. cereus using biochemical test. All B. cereus isolates named BC1 to BC27, were characterized for haemolytic enterotoxin (HBL) complex encoding genes (hblA), non-haemolytic enterotoxin encoding gene (NheA). 10 isolates have been reported to be positive towards hblA and 12 isolates were positive towards NheA. The presence of B. cereus and their enterotoxigenic genes in cooked seafood and raw milk from to food samples obtained may pose a potential risk for public health.

  2. Expression Profile of IL-35 mRNA in Gingiva of Chronic Periodontitis and Aggressive Periodontitis Patients: A Semiquantitative RT-PCR Study

    Directory of Open Access Journals (Sweden)

    Nagaraj B. Kalburgi

    2013-01-01

    Full Text Available Background. Proinflammatory and anti-inflammatory cytokines play a key role in the pathogenesis of periodontal diseases. Secretion of bioactive IL-35 has been described by T regulatory cells ( and is required for their maximal suppressive activity. are involved in the modulation of local immune response in chronic periodontitis patients. Objective. Hence, the present study was aimed to investigate the expression of IL-35 mRNA in chronic periodontitis and aggressive periodontitis patients. Materials and Methods. The present study was carried out in 60 subjects, which included 20 chronic periodontitis patients, 20 aggressive periodontitis patients, and 20 periodontally healthy controls. IL-35 mRNA expression in gingival tissue samples of all subjects was semiquantitatively analyzed using Reverse Transcriptase Polymerase Chain Reaction (RT-PCR. Results. The present study demonstrated the expression of IL-35 mRNA in gingival tissues of all the three groups. IL-35 mRNA expression was highest in chronic periodontitis subjects ( as compared to the aggressive periodontitis group ( and least seen in healthy patients (. Conclusion. The increased expression of IL-35 in chronic and aggressive periodontitis suggests its possible role in pathogenesis of periodontitis. Future studies done on large samples with intervention will strengthen our result.

  3. Gene expression profile and immunological evaluation of unique hypothetical unknown proteins of Mycobacterium leprae by using quantitative real-time PCR.

    Science.gov (United States)

    Kim, Hee Jin; Prithiviraj, Kalyani; Groathouse, Nathan; Brennan, Patrick J; Spencer, John S

    2013-02-01

    The cell-mediated immunity (CMI)-based in vitro gamma interferon release assay (IGRA) of Mycobacterium leprae-specific antigens has potential as a promising diagnostic means to detect those individuals in the early stages of M. leprae infection. Diagnosis of leprosy is a major obstacle toward ultimate disease control and has been compromised in the past by the lack of specific markers. Comparative bioinformatic analysis among mycobacterial genomes identified potential M. leprae-specific proteins called "hypothetical unknowns." Due to massive gene decay and the prevalence of pseudogenes, it is unclear whether any of these proteins are expressed or are immunologically relevant. In this study, we performed cDNA-based quantitative real-time PCR to investigate the expression status of 131 putative open reading frames (ORFs) encoding hypothetical unknowns. Twenty-six of the M. leprae-specific antigen candidates showed significant levels of gene expression compared to that of ESAT-6 (ML0049), which is an important T cell antigen of low abundance in M. leprae. Fifteen of 26 selected antigen candidates were expressed and purified in Escherichia coli. The seroreactivity to these proteins of pooled sera from lepromatous leprosy patients and cavitary tuberculosis patients revealed that 9 of 15 recombinant hypothetical unknowns elicited M. leprae-specific immune responses. These nine proteins may be good diagnostic reagents to improve both the sensitivity and specificity of detection of individuals with asymptomatic leprosy.

  4. Clinical profile of uveitis in Hansen’s disease after completion of treatment – A study of 50 cases using Polymerase Chain Reaction (PCR on aqueous humour

    Directory of Open Access Journals (Sweden)

    Radha Annamalai

    2016-05-01

    Full Text Available Chronic low grade anterior uveitis is the commonest cause of blindness in leprosy. It is usually asymptomatic until the late stages and patients seek help only after irreversible visual loss. We analysed patients who had a recurrence of uveitis after completion of treatment with anti-leprosy drugs and had been proven as histopathologically negative. The presence of chronic uveitis, complications and the extent of ocular damage it may cause, can continue even after treatment, emphasising the importance of follow-up, early detection and treatment. This is a prospective cohort study. Ophthalmic evaluation was performed using slit lamp examination, biomicroscopy, indirect ophthalmoscopy, applanation tonometry, corneal sensation and Schirmer’s test. Split skin microscopy was done to confirm the activity of leprosy. In patients with recalcitrant iridocyclitis, anterior chamber paracentesis was performed. The sample was analysed both by smear and polymerase chain reaction. The sequences that were targeted using PCR included genes encoding the DNA of 36-kDa antigen, 18-kDa antigen, 65-kDa antigen and the repetitive sequences among other M. leprae genes. Aqueous aspirate showed copies of mycobacterium leprae DNA in five out of twelve patients with recalcitrant anterior uveitis. Direct smear and staining with Ziehl- Neelson staining for mycobacteria was positive showing both live and dead bacilli. Live bacilli can persist in the aqueous humour even after completion of treatment. In our study this was more frequently observed in tuberculoid leprosy. This is possibly due to an immune mediated response combined with inadequate treatment dose in these patients.

  5. Real-time PCR expression profiling of genes encoding potential virulence factors in Candida albicans biofilms: identification of model-dependent and -independent gene expression

    Directory of Open Access Journals (Sweden)

    Řičicová Markéta

    2010-04-01

    Full Text Available Abstract Background Candida albicans infections are often associated with biofilm formation. Previous work demonstrated that the expression of HWP1 (hyphal wall protein and of genes belonging to the ALS (agglutinin-like sequence, SAP (secreted aspartyl protease, PLB (phospholipase B and LIP (lipase gene families is associated with biofilm growth on mucosal surfaces. We investigated using real-time PCR whether genes encoding potential virulence factors are also highly expressed in biofilms associated with abiotic surfaces. For this, C. albicans biofilms were grown on silicone in microtiter plates (MTP or in the Centres for Disease Control (CDC reactor, on polyurethane in an in vivo subcutaneous catheter rat (SCR model, and on mucosal surfaces in the reconstituted human epithelium (RHE model. Results HWP1 and genes belonging to the ALS, SAP, PLB and LIP gene families were constitutively expressed in C. albicans biofilms. ALS1-5 were upregulated in all model systems, while ALS9 was mostly downregulated. ALS6 and HWP1 were overexpressed in all models except in the RHE and MTP, respectively. The expression levels of SAP1 were more pronounced in both in vitro models, while those of SAP2, SAP4 and SAP6 were higher in the in vivo model. Furthermore, SAP5 was highly upregulated in the in vivo and RHE models. For SAP9 and SAP10 similar gene expression levels were observed in all model systems. PLB genes were not considerably upregulated in biofilms, while LIP1-3, LIP5-7 and LIP9-10 were highly overexpressed in both in vitro models. Furthermore, an elevated lipase activity was detected in supernatans of biofilms grown in the MTP and RHE model. Conclusions Our findings show that HWP1 and most of the genes belonging to the ALS, SAP and LIP gene families are upregulated in C. albicans biofilms. Comparison of the fold expression between the various model systems revealed similar expression levels for some genes, while for others model-dependent expression

  6. Transcriptional profiling of root-knot nematode induced feeding sites in cowpea (Vigna unguiculata L. Walp. using a soybean genome array

    Directory of Open Access Journals (Sweden)

    Das Sayan

    2010-08-01

    Full Text Available Abstract Background The locus Rk confers resistance against several species of root-knot nematodes (Meloidogyne spp., RKN in cowpea (Vigna unguiculata. Based on histological and reactive oxygen species (ROS profiles, Rk confers a delayed but strong resistance mechanism without a hypersensitive reaction-mediated cell death process, which allows nematode development but blocks reproduction. Results Responses to M. incognita infection in roots of resistant genotype CB46 and a susceptible near-isogenic line (null-Rk were investigated using a soybean Affymetrix GeneChip expression array at 3 and 9 days post-inoculation (dpi. At 9 dpi 552 genes were differentially expressed in incompatible interactions (infected resistant tissue compared with non-infected resistant tissue and 1,060 genes were differentially expressed in compatible interactions (infected susceptible tissue compared with non-infected susceptible tissue. At 3 dpi the differentially expressed genes were 746 for the incompatible and 623 for the compatible interactions. When expression between infected resistant and susceptible genotypes was compared, 638 and 197 genes were differentially expressed at 9 and 3 dpi, respectively. Conclusions In comparing the differentially expressed genes in response to nematode infection, a greater number and proportion of genes were down-regulated in the resistant than in the susceptible genotype, whereas more genes were up-regulated in the susceptible than in the resistant genotype. Gene ontology based functional categorization revealed that the typical defense response was partially suppressed in resistant roots, even at 9 dpi, allowing nematode juvenile development. Differences in ROS concentrations, induction of toxins and other defense related genes seem to play a role in this unique resistance mechanism.

  7. Influence of the plasma profile and the antenna geometry on the matching and current distribution control of the ITER ICRF antenna array. Optimization of the decoupling-matching system

    Energy Technology Data Exchange (ETDEWEB)

    Messiaen, A., E-mail: a.messiaen@fz-juelich.de [LPP-ERM/KMS, EURATOM-Belgian State Association, TEC Partner, CYCLE, B-1000 Brussels (Belgium); Swain, D. [US ITER Team, ORNL (United States); Vervier, M.; Dumortier, P.; Durodié, F.; Grine, D. [LPP-ERM/KMS, EURATOM-Belgian State Association, TEC Partner, CYCLE, B-1000 Brussels (Belgium)

    2013-10-15

    Highlights: ► Analysis of the matching-decoupling system of the ICRF antenna array of ITER. ► Control of the array phasing by the decouplers for the same power of power sources. ► Computation for the 2012 design status of the antenna plug. ► 7 decouplers needed but 10 can be used to decrease the ratings of components. ► Effects of plasma profile and antenna geometry. -- Abstract: The eight triplets of straps of the ITER ICRF antenna array are fed through 8 matching circuits and 4 hybrids to ensure load resilience. Decouplers are used to mitigate the effects of triplet mutual coupling. They also control the array phasing. The electrical constraints on the decouplers for different layouts with heating (H) or current drive (CD) phasing are compared starting from the TOPICA matrix computed for the last antenna plug design and the reference (most pessimistic) plasma profile “2010low” provided by IO. It is shown that this last profile provides a significant decrease of plasma coupling and increase of mutual coupling with respect to the previous reference profile “Sc2short17”. This results in a larger range of decoupler reactance X{sub dec} and voltage V{sub Xdec} needed. This range can be reduced when using 10 decouplers instead of the 7 needed for the same forward power P{sub Gk+} of the 4 power sources. For H phasing only 4 decouplers could be used but with different P{sub Gk+} (P{sub Gk+} ratio up to 1.5–2.5). For CD phasing and same plasma profile the power capability P{sub tot} is increased by 25% with a decoupler layout allowing much smaller poloidal phasing than the 90° provided by the hybrids. A decrease of the distance antenna-plasma profile reduces the normalized decoupler voltage V{sub Xdec}/√P{sub tot} with no significant change of the X{sub dec} range. The recess of the vertical septa between the strap boxes increases the plasma coupling but has the drawback of also increasing the mutual coupling between triplets: the needed range of X

  8. Genomic profiling using array comparative genomic hybridization define distinct subtypes of diffuse large b-cell lymphoma: a review of the literature

    Directory of Open Access Journals (Sweden)

    Tirado Carlos A

    2012-09-01

    Full Text Available Abstract Diffuse large B-cell lymphoma (DLBCL is the most common type of non-Hodgkin Lymphoma comprising of greater than 30% of adult non-Hodgkin Lymphomas. DLBCL represents a diverse set of lymphomas, defined as diffuse proliferation of large B lymphoid cells. Numerous cytogenetic studies including karyotypes and fluorescent in situ hybridization (FISH, as well as morphological, biological, clinical, microarray and sequencing technologies have attempted to categorize DLBCL into morphological variants, molecular and immunophenotypic subgroups, as well as distinct disease entities. Despite such efforts, most lymphoma remains undistinguishable and falls into DLBCL, not otherwise specified (DLBCL-NOS. The advent of microarray-based studies (chromosome, RNA, gene expression, etc has provided a plethora of high-resolution data that could potentially facilitate the finer classification of DLBCL. This review covers the microarray data currently published for DLBCL. We will focus on these types of data; 1 array based CGH; 2 classical CGH; and 3 gene expression profiling studies. The aims of this review were three-fold: (1 to catalog chromosome loci that are present in at least 20% or more of distinct DLBCL subtypes; a detailed list of gains and losses for different subtypes was generated in a table form to illustrate specific chromosome loci affected in selected subtypes; (2 to determine common and distinct copy number alterations among the different subtypes and based on this information, characteristic and similar chromosome loci for the different subtypes were depicted in two separate chromosome ideograms; and, (3 to list re-classified subtypes and those that remained indistinguishable after review of the microarray data. To the best of our knowledge, this is the first effort to compile and review available literatures on microarray analysis data and their practical utility in classifying DLBCL subtypes. Although conventional cytogenetic methods such

  9. Physically based method for measuring suspended-sediment concentration and grain size using multi-frequency arrays of acoustic-doppler profilers

    Science.gov (United States)

    Topping, David J.; Wright, Scott A.; Griffiths, Ronald; Dean, David

    2014-01-01

    As the result of a 12-year program of sediment-transport research and field testing on the Colorado River (6 stations in UT and AZ), Yampa River (2 stations in CO), Little Snake River (1 station in CO), Green River (1 station in CO and 2 stations in UT), and Rio Grande (2 stations in TX), we have developed a physically based method for measuring suspended-sediment concentration and grain size at 15-minute intervals using multifrequency arrays of acoustic-Doppler profilers. This multi-frequency method is able to achieve much higher accuracies than single-frequency acoustic methods because it allows removal of the influence of changes in grain size on acoustic backscatter. The method proceeds as follows. (1) Acoustic attenuation at each frequency is related to the concentration of silt and clay with a known grain-size distribution in a river cross section using physical samples and theory. (2) The combination of acoustic backscatter and attenuation at each frequency is uniquely related to the concentration of sand (with a known reference grain-size distribution) and the concentration of silt and clay (with a known reference grain-size distribution) in a river cross section using physical samples and theory. (3) Comparison of the suspended-sand concentrations measured at each frequency using this approach then allows theory-based calculation of the median grain size of the suspended sand and final correction of the suspended-sand concentration to compensate for the influence of changing grain size on backscatter. Although this method of measuring suspended-sediment concentration is somewhat less accurate than using conventional samplers in either the EDI or EWI methods, it is much more accurate than estimating suspended-sediment concentrations using calibrated pump measurements or single-frequency acoustics. Though the EDI and EWI methods provide the most accurate measurements of suspended-sediment concentration, these measurements are labor-intensive, expensive, and

  10. Effect of the plasma production rate on the implosion dynamics of cylindrical wire/fiber arrays with a profiled linear mass

    International Nuclear Information System (INIS)

    Aleksandrov, V. V.; Mitrofanov, K. N.; Gritsuk, A. N.; Frolov, I. N.; Grabovski, E. V.; Laukhin, Ya. N.

    2013-01-01

    Results are presented from experimental studies on the implosion of arrays made of wires and metalized fibers under the action of current pulses with an amplitude of up to 3.5 MA at the Angara-5-1 facility. The effect of the parameters of an additional linear mass of bismuth and gold deposited on the wires/fibers is investigated. It is examined how the material of the wires/fibers and the metal coating deposited on them affect the penetration of the plasma with the frozen-in magnetic field into a cylindrical array. Information on the plasma production rate for different metals is obtained by analyzing optical streak images of imploding arrays. The plasma production rate m-dot m for cylindrical arrays made of the kapron fibers coated with bismuth is determined. For the initial array radius of R 0 = 1 cm and discharge current of I = 1 MA, the plasma production rate is found to be m-dot m approx. 0.095 ± 0.015 μg/(cm 2 ns)

  11. Eliminating PCR contamination

    International Nuclear Information System (INIS)

    Fox, J.C.; Ait-Khaled, Mounir; Webster, Alison; Emery, V.C.

    1991-01-01

    The sensitivity of polymerase chain reaction (PCR) can mean that even very low levels of contamination with the target DNA will result in a positive signal. At present this aspect is a major limitation in the use of PCR as a routine diagnostic method. By exposing PCR reagents to UV light, contaminating DNA can be inactivated, thus providing an opportunity to eradicate false positive reactions. UV irradiation was applied to PCR systems used for detection of human cytomegalovirus CMV and human immunodeficiency virus (HIV) and shown to be effective in eradicating both laboratory encountered contamination and plasmid DNA (below 100 pg) added to PCR systems prior to UV exposure. Sensitivity of a PCR system to amplify the long terminal repeat (LTR) sequence of HIV-1 was not affected by the irradiation procedure; however, ultimate sensitivity of a PCR system for the amplification of an early gene pro-motor sequence of the CMV genome was reduced 1000-fold. UV irradiation did not affect the size of the PCR product as determined by strand separating polyacrylamide gel electrophoresis of a 32 P-labelled amplimer. Thus, a simple pre-exposure to UV light would seem a worth-wile step to incorporate into PCR protocols provided that the effects on sensitivity have been determined empirically for each PCR system. (author). 11 refs.; 3 figs

  12. Implementation of a Novel Low-Cost Low-Profile Ku-Band Antenna Array for Single Beam Steering from Space

    Science.gov (United States)

    Host, Nicholas K.; Chen, Chi-Chih; Volakis, John L.; Miranda, Felix A.

    2013-01-01

    Phased array antennas afford many advantages over traditional reflector antennas due to their conformality, high aperture efficiency, and unfettered beam steering capability at the price of increased cost and complexity. This paper eliminates the complex and costly array backend via the implementation of a series fed array employing a propagation constant reconfigurable transmission line connecting each element in series. Scanning can then be accomplished through one small (less than or equal to 100mil) linear motion that controls propagation constant. Specifically, each element is fed via a reconfigurable coplanar stripline transmission line with a tapered dielectric insert positioned between the transmission line traces. The dielectric insert is allowed to move up and down to control propagation constant and therefore induce scanning. We present a 20 element patch array design, scanning from -25 deg. less than or equal to theta less than or equal to 21 deg. at 13GHz. Measurements achieve only10.5 deg. less than or equal to theta less than or equal to 22 deg. scanning due to a faulty, yet correctable, manufacturing process. Beam squint is measured to be plus or minus 3 deg. for a 600MHz bandwidth. This prototype was improved to give scanning of 3.5 deg. less than or equal to theta less than or equal to 22 deg. Cross-pol patterns were shown to be -15dB below the main beam. Simulations accounting for fabrication errors match measured patterns, thus validating the designs.

  13. External PCR, ASN's decision

    International Nuclear Information System (INIS)

    Anon.

    2012-01-01

    The French law imposes in some situations the presence of a person skilled in radiation protection (PCR). This article describes the cases when this person must belong to the staff of the enterprise or when this person may be sub-contracted. For instance in most nuclear facilities the PCR must be on the payroll, for enterprises dedicated to nuclear transport the PCR's job can be sub-contracted. A decision given by the ASN (French Nuclear Safety Authority) sets the minimal requests (in terms of training, job contract, activities) of the sub-contracted PCR. (A.C.)

  14. Array capabilities and future arrays

    International Nuclear Information System (INIS)

    Radford, D.

    1993-01-01

    Early results from the new third-generation instruments GAMMASPHERE and EUROGAM are confirming the expectation that such arrays will have a revolutionary effect on the field of high-spin nuclear structure. When completed, GAMMASHPERE will have a resolving power am order of magnitude greater that of the best second-generation arrays. When combined with other instruments such as particle-detector arrays and fragment mass analysers, the capabilites of the arrays for the study of more exotic nuclei will be further enhanced. In order to better understand the limitations of these instruments, and to design improved future detector systems, it is important to have some intelligible and reliable calculation for the relative resolving power of different instrument designs. The derivation of such a figure of merit will be briefly presented, and the relative sensitivities of arrays currently proposed or under construction presented. The design of TRIGAM, a new third-generation array proposed for Chalk River, will also be discussed. It is instructive to consider how far arrays of Compton-suppressed Ge detectors could be taken. For example, it will be shown that an idealised open-quote perfectclose quotes third-generation array of 1000 detectors has a sensitivity an order of magnitude higher again than that of GAMMASPHERE. Less conventional options for new arrays will also be explored

  15. Inverse fusion PCR cloning.

    Directory of Open Access Journals (Sweden)

    Markus Spiliotis

    Full Text Available Inverse fusion PCR cloning (IFPC is an easy, PCR based three-step cloning method that allows the seamless and directional insertion of PCR products into virtually all plasmids, this with a free choice of the insertion site. The PCR-derived inserts contain a vector-complementary 5'-end that allows a fusion with the vector by an overlap extension PCR, and the resulting amplified insert-vector fusions are then circularized by ligation prior transformation. A minimal amount of starting material is needed and experimental steps are reduced. Untreated circular plasmid, or alternatively bacteria containing the plasmid, can be used as templates for the insertion, and clean-up of the insert fragment is not urgently required. The whole cloning procedure can be performed within a minimal hands-on time and results in the generation of hundreds to ten-thousands of positive colonies, with a minimal background.

  16. SNP Arrays

    Directory of Open Access Journals (Sweden)

    Jari Louhelainen

    2016-10-01

    Full Text Available The papers published in this Special Issue “SNP arrays” (Single Nucleotide Polymorphism Arrays focus on several perspectives associated with arrays of this type. The range of papers vary from a case report to reviews, thereby targeting wider audiences working in this field. The research focus of SNP arrays is often human cancers but this Issue expands that focus to include areas such as rare conditions, animal breeding and bioinformatics tools. Given the limited scope, the spectrum of papers is nothing short of remarkable and even from a technical point of view these papers will contribute to the field at a general level. Three of the papers published in this Special Issue focus on the use of various SNP array approaches in the analysis of three different cancer types. Two of the papers concentrate on two very different rare conditions, applying the SNP arrays slightly differently. Finally, two other papers evaluate the use of the SNP arrays in the context of genetic analysis of livestock. The findings reported in these papers help to close gaps in the current literature and also to give guidelines for future applications of SNP arrays.

  17. electrode array

    African Journals Online (AJOL)

    PROF EKWUEME

    A geoelectric investigation employing vertical electrical soundings (VES) using the Ajayi - Makinde Two-Electrode array and the ... arrangements used in electrical D.C. resistivity survey. These include ..... Refraction Tomography to Study the.

  18. Comprehensive high-resolution genomic profiling and cytogenetics of human chondrocyte cultures by GTG-banding, locus-specific FISH, SKY and SNP array.

    Science.gov (United States)

    Wallenborn, M; Petters, O; Rudolf, D; Hantmann, H; Richter, M; Ahnert, P; Rohani, L; Smink, J J; Bulwin, G C; Krupp, W; Schulz, R M; Holland, H

    2018-04-23

    In the development of cell-based medicinal products, it is crucial to guarantee that the application of such an advanced therapy medicinal product (ATMP) is safe for the patients. The consensus of the European regulatory authorities is: "In conclusion, on the basis of the state of art, conventional karyotyping can be considered a valuable and useful technique to analyse chromosomal stability during preclinical studies". 408 chondrocyte samples (84 monolayers and 324 spheroids) from six patients were analysed using trypsin-Giemsa staining, spectral karyotyping and fluorescence in situ hybridisation, to evaluate the genetic stability of an ATMP named Spherox®. Single nucleotide polymorphism (SNP) array analysis was performed on chondrocyte spheroids from five of the six donors. Applying this combination of techniques, the genetic analyses performed revealed no significant genetic instability until passage 3 in monolayer cells and interphase cells from spheroid cultures at different time points. Clonal occurrence of polyploid metaphases and endoreduplications were identified associated with prolonged cultivation time. Also, gonosomal losses were observed in chondrocyte spheroids, with increasing passage and duration of the differentiation phase. Interestingly, in one of the donors, chromosomal aberrations that are also described in extraskeletal myxoid chondrosarcoma were identified. The SNP array analysis exhibited chromosomal aberrations in two donors and copy neutral losses of heterozygosity regions in four donors. This study showed the necessity of combined genetic analyses at defined cultivation time points in quality studies within the field of cell therapy.

  19. Molecular diagnostic PCR handbook

    International Nuclear Information System (INIS)

    Viljoen, G.J.; Crowther, J.R.; Nel, L.H.

    2005-01-01

    The uses of nucleic acid-directed methods have increased significantly in the past five years and have made important contributions to disease control country programmes for improving national and international trade. These developments include the more routine use of PCR as a diagnostic tool in veterinary diagnostic laboratories. However, there are many problems associated with the transfer and particularly, the application of this technology. These include lack of consideration of: the establishment of quality-assured procedures, the required set-up of the laboratory and the proper training of staff. This can lead to a situation where results are not assured. This book gives a comprehensive account of the practical aspects of PCR and strong consideration is given to ensure its optimal use in a laboratory environment. This includes the setting-up of a PCR laboratory; Good Laboratory Practice and standardised PCR protocols to detect animal disease pathogens. Examples of Standard Operating Procedures as used in individual specialist laboratories and an outline of training materials necessary for PCR technology transfer are presented. The difficulties, advantages and disadvantages in PCR applications are explained and placed in context with other test systems. Emphasis is placed on the use of PCR for detection of pathogens, with a particular focus on diagnosticians and scientists from the developing world. It is hoped that this book will enable readers from various disciplines and levels of expertise to better judge the merits of PCR and to increase their skills and knowledge in order to assist in a more logical, efficient and assured use of this technology

  20. Filter arrays

    Science.gov (United States)

    Page, Ralph H.; Doty, Patrick F.

    2017-08-01

    The various technologies presented herein relate to a tiled filter array that can be used in connection with performance of spatial sampling of optical signals. The filter array comprises filter tiles, wherein a first plurality of filter tiles are formed from a first material, the first material being configured such that only photons having wavelengths in a first wavelength band pass therethrough. A second plurality of filter tiles is formed from a second material, the second material being configured such that only photons having wavelengths in a second wavelength band pass therethrough. The first plurality of filter tiles and the second plurality of filter tiles can be interspersed to form the filter array comprising an alternating arrangement of first filter tiles and second filter tiles.

  1. Lectin-Array Blotting.

    Science.gov (United States)

    Pazos, Raquel; Echevarria, Juan; Hernandez, Alvaro; Reichardt, Niels-Christian

    2017-09-01

    Aberrant protein glycosylation is a hallmark of cancer, infectious diseases, and autoimmune or neurodegenerative disorders. Unlocking the potential of glycans as disease markers will require rapid and unbiased glycoproteomics methods for glycan biomarker discovery. The present method is a facile and rapid protocol for qualitative analysis of protein glycosylation in complex biological mixtures. While traditional lectin arrays only provide an average signal for the glycans in the mixture, which is usually dominated by the most abundant proteins, our method provides individual lectin binding profiles for all proteins separated in the gel electrophoresis step. Proteins do not have to be excised from the gel for subsequent analysis via the lectin array but are transferred by contact diffusion from the gel to a glass slide presenting multiple copies of printed lectin arrays. Fluorescently marked glycoproteins are trapped by the printed lectins via specific carbohydrate-lectin interactions and after a washing step their binding profile with up to 20 lectin probes is analyzed with a fluorescent scanner. The method produces the equivalent of 20 lectin blots in a single experiment, giving detailed insight into the binding epitopes present in the fractionated proteins. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  2. Transgene detection by digital droplet PCR.

    Directory of Open Access Journals (Sweden)

    Dirk A Moser

    Full Text Available Somatic gene therapy is a promising tool for the treatment of severe diseases. Because of its abuse potential for performance enhancement in sports, the World Anti-Doping Agency (WADA included the term 'gene doping' in the official list of banned substances and methods in 2004. Several nested PCR or qPCR-based strategies have been proposed that aim at detecting long-term presence of transgene in blood, but these strategies are hampered by technical limitations. We developed a digital droplet PCR (ddPCR protocol for Insulin-Like Growth Factor 1 (IGF1 detection and demonstrated its applicability monitoring 6 mice injected into skeletal muscle with AAV9-IGF1 elements and 2 controls over a 33-day period. A duplex ddPCR protocol for simultaneous detection of Insulin-Like Growth Factor 1 (IGF1 and Erythropoietin (EPO transgenic elements was created. A new DNA extraction procedure with target-orientated usage of restriction enzymes including on-column DNA-digestion was established. In vivo data revealed that IGF1 transgenic elements could be reliably detected for a 33-day period in DNA extracted from whole blood. In vitro data indicated feasibility of IGF1 and EPO detection by duplex ddPCR with high reliability and sensitivity. On-column DNA-digestion allowed for significantly improved target detection in downstream PCR-based approaches. As ddPCR provides absolute quantification, it ensures excellent day-to-day reproducibility. Therefore, we expect this technique to be used in diagnosing and monitoring of viral and bacterial infection, in detecting mutated DNA sequences as well as profiling for the presence of foreign genetic material in elite athletes in the future.

  3. High-resolution array CGH profiling identifies Na/K transporting ATPase interacting 2 (NKAIN2) as a predisposing candidate gene in neuroblastoma.

    Science.gov (United States)

    Romania, Paolo; Castellano, Aurora; Surace, Cecilia; Citti, Arianna; De Ioris, Maria Antonietta; Sirleto, Pietro; De Mariano, Marilena; Longo, Luca; Boldrini, Renata; Angioni, Adriano; Locatelli, Franco; Fruci, Doriana

    2013-01-01

    Neuroblastoma (NB), the most common solid cancer in early childhood, usually occurs sporadically but also its familial occurance is known in 1-2% of NB patients. Germline mutations in the ALK and PHOX2B genes have been found in a subset of familial NBs. However, because some individuals harbouring mutations in these genes do not develop this tumor, additional genetic alterations appear to be required for NB pathogenesis. Herein, we studied an Italian family with three NB patients, two siblings and a first cousin, carrying an ALK germline-activating mutation R1192P, that was inherited from their unaffected mothers and with no mutations in the PHOX2B gene. A comparison between somatic and germline DNA copy number changes in the two affected siblings by a high resolution array-based Comparative Genomic Hybridization (CGH) analysis revealed a germline gain at NKAIN2 (Na/K transporting ATPase interacting 2) locus in one of the sibling, that was inherited from the parent who does not carry the ALK mutation. Surprisingly, NKAIN2 was expressed at high levels also in the affected sibling that lacks the genomic gain at this locus, clearly suggesting the existance of other regulatory mechanisms. High levels of NKAIN2 were detected in the MYCN-amplified NB cell lines and in the most aggressive NB lesions as well as in the peripheral blood of a large cohort of NB patients. Consistent with a role of NKAIN2 in NB development, NKAIN2 was down-regulated during all-trans retinoic acid differentiation in two NB cell lines. Taken together, these data indicate a potential role of NKAIN2 gene in NB growth and differentiation.

  4. High-resolution array CGH profiling identifies Na/K transporting ATPase interacting 2 (NKAIN2 as a predisposing candidate gene in neuroblastoma.

    Directory of Open Access Journals (Sweden)

    Paolo Romania

    Full Text Available Neuroblastoma (NB, the most common solid cancer in early childhood, usually occurs sporadically but also its familial occurance is known in 1-2% of NB patients. Germline mutations in the ALK and PHOX2B genes have been found in a subset of familial NBs. However, because some individuals harbouring mutations in these genes do not develop this tumor, additional genetic alterations appear to be required for NB pathogenesis. Herein, we studied an Italian family with three NB patients, two siblings and a first cousin, carrying an ALK germline-activating mutation R1192P, that was inherited from their unaffected mothers and with no mutations in the PHOX2B gene. A comparison between somatic and germline DNA copy number changes in the two affected siblings by a high resolution array-based Comparative Genomic Hybridization (CGH analysis revealed a germline gain at NKAIN2 (Na/K transporting ATPase interacting 2 locus in one of the sibling, that was inherited from the parent who does not carry the ALK mutation. Surprisingly, NKAIN2 was expressed at high levels also in the affected sibling that lacks the genomic gain at this locus, clearly suggesting the existance of other regulatory mechanisms. High levels of NKAIN2 were detected in the MYCN-amplified NB cell lines and in the most aggressive NB lesions as well as in the peripheral blood of a large cohort of NB patients. Consistent with a role of NKAIN2 in NB development, NKAIN2 was down-regulated during all-trans retinoic acid differentiation in two NB cell lines. Taken together, these data indicate a potential role of NKAIN2 gene in NB growth and differentiation.

  5. Genomic profiling of plasmablastic lymphoma using array comparative genomic hybridization (aCGH: revealing significant overlapping genomic lesions with diffuse large B-cell lymphoma

    Directory of Open Access Journals (Sweden)

    Lu Xin-Yan

    2009-11-01

    Full Text Available Abstract Background Plasmablastic lymphoma (PL is a subtype of diffuse large B-cell lymphoma (DLBCL. Studies have suggested that tumors with PL morphology represent a group of neoplasms with clinopathologic characteristics corresponding to different entities including extramedullary plasmablastic tumors associated with plasma cell myeloma (PCM. The goal of the current study was to evaluate the genetic similarities and differences among PL, DLBCL (AIDS-related and non AIDS-related and PCM using array-based comparative genomic hybridization. Results Examination of genomic data in PL revealed that the most frequent segmental gain (> 40% include: 1p36.11-1p36.33, 1p34.1-1p36.13, 1q21.1-1q23.1, 7q11.2-7q11.23, 11q12-11q13.2 and 22q12.2-22q13.3. This correlated with segmental gains occurring in high frequency in DLBCL (AIDS-related and non AIDS-related cases. There were some segmental gains and some segmental loss that occurred in PL but not in the other types of lymphoma suggesting that these foci may contain genes responsible for the differentiation of this lymphoma. Additionally, some segmental gains and some segmental loss occurred only in PL and AIDS associated DLBCL suggesting that these foci may be associated with HIV infection. Furthermore, some segmental gains and some segmental loss occurred only in PL and PCM suggesting that these lesions may be related to plasmacytic differentiation. Conclusion To the best of our knowledge, the current study represents the first genomic exploration of PL. The genomic aberration pattern of PL appears to be more similar to that of DLBCL (AIDS-related or non AIDS-related than to PCM. Our findings suggest that PL may remain best classified as a subtype of DLBCL at least at the genome level.

  6. Real-time PCR (qPCR) primer design using free online software.

    Science.gov (United States)

    Thornton, Brenda; Basu, Chhandak

    2011-01-01

    Real-time PCR (quantitative PCR or qPCR) has become the preferred method for validating results obtained from assays which measure gene expression profiles. The process uses reverse transcription polymerase chain reaction (RT-PCR), coupled with fluorescent chemistry, to measure variations in transcriptome levels between samples. The four most commonly used fluorescent chemistries are SYBR® Green dyes and TaqMan®, Molecular Beacon or Scorpion probes. SYBR® Green is very simple to use and cost efficient. As SYBR® Green dye binds to any double-stranded DNA product, its success depends greatly on proper primer design. Many types of online primer design software are available, which can be used free of charge to design desirable SYBR® Green-based qPCR primers. This laboratory exercise is intended for those who have a fundamental background in PCR. It addresses the basic fluorescent chemistries of real-time PCR, the basic rules and pitfalls of primer design, and provides a step-by-step protocol for designing SYBR® Green-based primers with free, online software. Copyright © 2010 Wiley Periodicals, Inc.

  7. Custom CGH array profiling of copy number variations (CNVs) on chromosome 6p21.32 (HLA locus) in patients with venous malformations associated with multiple sclerosis

    Science.gov (United States)

    2010-01-01

    Background Multiple sclerosis (MS) is a complex disorder thought to result from an interaction between environmental and genetic predisposing factors which have not yet been characterised, although it is known to be associated with the HLA region on 6p21.32. Recently, a picture of chronic cerebrospinal venous insufficiency (CCSVI), consequent to stenosing venous malformation of the main extra-cranial outflow routes (VM), has been described in patients affected with MS, introducing an additional phenotype with possible pathogenic significance. Methods In order to explore the presence of copy number variations (CNVs) within the HLA locus, a custom CGH array was designed to cover 7 Mb of the HLA locus region (6,899,999 bp; chr6:29,900,001-36,800,000). Genomic DNA of the 15 patients with CCSVI/VM and MS was hybridised in duplicate. Results In total, 322 CNVs, of which 225 were extragenic and 97 intragenic, were identified in 15 patients. 234 known polymorphic CNVs were detected, the majority of these being situated in non-coding or extragenic regions. The overall number of CNVs (both extra- and intragenic) showed a robust and significant correlation with the number of stenosing VMs (Spearman: r = 0.6590, p = 0.0104; linear regression analysis r = 0.6577, p = 0.0106). The region we analysed contains 211 known genes. By using pathway analysis focused on angiogenesis and venous development, MS, and immunity, we tentatively highlight several genes as possible susceptibility factor candidates involved in this peculiar phenotype. Conclusions The CNVs contained in the HLA locus region in patients with the novel phenotype of CCSVI/VM and MS were mapped in detail, demonstrating a significant correlation between the number of known CNVs found in the HLA region and the number of CCSVI-VMs identified in patients. Pathway analysis revealed common routes of interaction of several of the genes involved in angiogenesis and immunity contained within this region. Despite the small

  8. Tomographic array

    International Nuclear Information System (INIS)

    1976-01-01

    The configuration of a tomographic array in which the object can rotate about its axis is described. The X-ray detector is a cylindrical screen perpendicular to the axis of rotation. The X-ray source has a line-shaped focus coinciding with the axis of rotation. The beam is fan-shaped with one side of this fan lying along the axis of rotation. The detector screen is placed inside an X-ray image multiplier tube

  9. Tomographic array

    International Nuclear Information System (INIS)

    1976-01-01

    A tomographic array with the following characteristics is described. An X-ray screen serving as detector is placed before a photomultiplier tube which itself is placed in front of a television camera connected to a set of image processors. The detector is concave towards the source and is replacable. Different images of the object are obtained simultaneously. Optical fibers and lenses are used for transmission within the system

  10. PCR in forensic genetics

    DEFF Research Database (Denmark)

    Morling, Niels

    2009-01-01

    Since the introduction in the mid-1980s of analyses of minisatellites for DNA analyses, a revolution has taken place in forensic genetics. The subsequent invention of the PCR made it possible to develop forensic genetics tools that allow both very informative routine investigations and still more...... and more advanced, special investigations in cases concerning crime, paternity, relationship, disaster victim identification etc. The present review gives an update on the use of DNA investigations in forensic genetics.......Since the introduction in the mid-1980s of analyses of minisatellites for DNA analyses, a revolution has taken place in forensic genetics. The subsequent invention of the PCR made it possible to develop forensic genetics tools that allow both very informative routine investigations and still more...

  11. Evaluation of PCR and multiplex PCR in relation to nested PCR for diagnosing Theileria equi

    Directory of Open Access Journals (Sweden)

    Danielle C. Leal

    2011-07-01

    Full Text Available Conventional PCR (PCRTeq for diagnosing Theileria equi and multiplex PCR (M/PCRTeq-Bc for diagnosing T. equi and Babesia caballi were comparatively evaluated with nested PCR (N/PCR-Teq for diagnosing equine piroplasmosis. In DNA sensitivity determinations, in multiple dilutions of equine blood that had tested positive for T. equi, PCR-Teq and N/PCR-Teq detected hemoparasite DNA in the larger dilutions (1:128, but did not differ significantly from the M/PCRTeq-Bc (1:64. In analyses on equine serum tested by ELISA, there was high agreement between this serological test and PCR-Teq (k = 0.780 and moderate agreement with N/PCR-Teq (k = 0.562 and M/PCRTeq-Bc (k = 0.488. PCR-Teq found a higher frequency of T. equi both in extensively and intensively reared horses, but this was not significant in relation to N/PCR-Teq (P>0.05, and both PCRs indicated that there was an endemic situation regarding T. equi in the population of horses of this sample. PCR-Teq was only significantly different from M/PCR-Teq-Bc (P<0.05. PCR-Teq presented high sensitivity and specificity, comparable to N/PCR-Teq, but with the advantage of higher speed in obtaining results and lower costs and risks of laboratory contamination. This accredits PCR-Teq for epidemiological studies and for determinations on affected horses.

  12. Molecular profiling of ADAM12 in human bladder cancer

    DEFF Research Database (Denmark)

    Albrechtsen, Reidar; Dyrskjøt, Lars; Rudkjaer, Lise

    2006-01-01

    PURPOSE: We have previously found ADAM12, a disintegrin and metalloprotease, to be an interesting biomarker for breast cancer. The purpose of this study was to determine the gene and protein expression profiles of ADAM12 in different grades and stages of bladder cancer. EXPERIMENTAL DESIGN: ADAM12...... gene expression was evaluated in tumors from 96 patients with bladder cancer using a customized Affymetrix GeneChip. Gene expression in bladder cancer was validated using reverse transcription-PCR, quantitative PCR, and in situ hybridization. Protein expression was evaluated by immunohistochemical...... staining on tissue arrays of bladder cancers. The presence and relative amount of ADAM12 in the urine of cancer patients were determined by Western blotting and densitometric measurements, respectively. RESULTS: ADAM12 mRNA expression was significantly up-regulated in bladder cancer, as determined...

  13. Biomarker discovery for colon cancer using a 761 gene RT-PCR assay

    Directory of Open Access Journals (Sweden)

    Hackett James R

    2007-08-01

    Full Text Available Abstract Background Reverse transcription PCR (RT-PCR is widely recognized to be the gold standard method for quantifying gene expression. Studies using RT-PCR technology as a discovery tool have historically been limited to relatively small gene sets compared to other gene expression platforms such as microarrays. We have recently shown that TaqMan® RT-PCR can be scaled up to profile expression for 192 genes in fixed paraffin-embedded (FPE clinical study tumor specimens. This technology has also been used to develop and commercialize a widely used clinical test for breast cancer prognosis and prediction, the Onco typeDX™ assay. A similar need exists in colon cancer for a test that provides information on the likelihood of disease recurrence in colon cancer (prognosis and the likelihood of tumor response to standard chemotherapy regimens (prediction. We have now scaled our RT-PCR assay to efficiently screen 761 biomarkers across hundreds of patient samples and applied this process to biomarker discovery in colon cancer. This screening strategy remains attractive due to the inherent advantages of maintaining platform consistency from discovery through clinical application. Results RNA was extracted from formalin fixed paraffin embedded (FPE tissue, as old as 28 years, from 354 patients enrolled in NSABP C-01 and C-02 colon cancer studies. Multiplexed reverse transcription reactions were performed using a gene specific primer pool containing 761 unique primers. PCR was performed as independent TaqMan® reactions for each candidate gene. Hierarchal clustering demonstrates that genes expected to co-express form obvious, distinct and in certain cases very tightly correlated clusters, validating the reliability of this technical approach to biomarker discovery. Conclusion We have developed a high throughput, quantitatively precise multi-analyte gene expression platform for biomarker discovery that approaches low density DNA arrays in numbers of

  14. Development of Candida-Specific Real-Time PCR Assays for the Detection and Identification of Eight Medically Important Candida Species.

    Science.gov (United States)

    Zhang, Jing; Hung, Guo-Chiuan; Nagamine, Kenjiro; Li, Bingjie; Tsai, Shien; Lo, Shyh-Ching

    2016-01-01

    Culture-based identification methods have been the gold standard for the diagnosis of fungal infection. Currently, molecular technologies such as real-time PCR assays with short turnaround time can provide desirable alternatives for the rapid detection of Candida microbes. However, most of the published PCR primer sets are not Candida specific and likely to amplify DNA from common environmental contaminants, such as Aspergillus microbes. In this study, we designed pan-Candida primer sets based on the ribosomal DNA-coding regions conserved within Candida but distinct from those of Aspergillus and Penicillium. We demonstrate that the final two selected pan-Candida primer sets would not amplify Aspergillus DNA and could be used to differentiate eight medically important Candida pathogens in real-time PCR assays based on their melting profiles, with a sensitivity of detection as low as 10 fg of Candida genomic DNA. Moreover, we further evaluated and selected species-specific primer sets covering Candida albicans, Candida glabrata, Candida tropicalis, and Candida dubliniensis and show that they had high sensitivity and specificity. These real-time PCR primer sets could potentially be assembled into a single PCR array for the rapid detection of Candida species in various clinical settings, such as corneal transplantation.

  15. Arraying proteins by cell-free synthesis.

    Science.gov (United States)

    He, Mingyue; Wang, Ming-Wei

    2007-10-01

    Recent advances in life science have led to great motivation for the development of protein arrays to study functions of genome-encoded proteins. While traditional cell-based methods have been commonly used for generating protein arrays, they are usually a time-consuming process with a number of technical challenges. Cell-free protein synthesis offers an attractive system for making protein arrays, not only does it rapidly converts the genetic information into functional proteins without the need for DNA cloning, but also presents a flexible environment amenable to production of folded proteins or proteins with defined modifications. Recent advancements have made it possible to rapidly generate protein arrays from PCR DNA templates through parallel on-chip protein synthesis. This article reviews current cell-free protein array technologies and their proteomic applications.

  16. Application of affymetrix array and massively parallel signature sequencing for identification of genes involved in prostate cancer progression

    International Nuclear Information System (INIS)

    Oudes, Asa J; Roach, Jared C; Walashek, Laura S; Eichner, Lillian J; True, Lawrence D; Vessella, Robert L; Liu, Alvin Y

    2005-01-01

    Affymetrix GeneChip Array and Massively Parallel Signature Sequencing (MPSS) are two high throughput methodologies used to profile transcriptomes. Each method has certain strengths and weaknesses; however, no comparison has been made between the data derived from Affymetrix arrays and MPSS. In this study, two lineage-related prostate cancer cell lines, LNCaP and C4-2, were used for transcriptome analysis with the aim of identifying genes associated with prostate cancer progression. Affymetrix GeneChip array and MPSS analyses were performed. Data was analyzed with GeneSpring 6.2 and in-house perl scripts. Expression array results were verified with RT-PCR. Comparison of the data revealed that both technologies detected genes the other did not. In LNCaP, 3,180 genes were only detected by Affymetrix and 1,169 genes were only detected by MPSS. Similarly, in C4-2, 4,121 genes were only detected by Affymetrix and 1,014 genes were only detected by MPSS. Analysis of the combined transcriptomes identified 66 genes unique to LNCaP cells and 33 genes unique to C4-2 cells. Expression analysis of these genes in prostate cancer specimens showed CA1 to be highly expressed in bone metastasis but not expressed in primary tumor and EPHA7 to be expressed in normal prostate and primary tumor but not bone metastasis. Our data indicates that transcriptome profiling with a single methodology will not fully assess the expression of all genes in a cell line. A combination of transcription profiling technologies such as DNA array and MPSS provides a more robust means to assess the expression profile of an RNA sample. Finally, genes that were differentially expressed in cell lines were also differentially expressed in primary prostate cancer and its metastases

  17. PCR, exit stage left ...

    CERN Multimedia

    2004-01-01

    The Prevessin Control Room during LEP's start up in 1989. The Prévessin Control Room (PCR) was recently engulfed in a wave of nostalgia. The PCR, scene of some of the greatest moments in CERN's history, is being dismantled to prepare for a complete overhaul. In February 2006, a new combined control centre for all the accelerators will open its doors on the same site, together with a new building currently under construction (see Bulletin issue 27/2004 of 28 June 2004). This marks the end of an important chapter in CERN's history. The Prévessin Control Room saw its first momentous event 28 years ago when the 400 GeV beam for the SPS was commissioned in the presence of Project Leader John Adams. It was also here that the first proton-antiproton collisions were observed, in 1981. Eight years later, in 1989, operators and directors alike jumped for joy at the announcement of the first electron-positron collisions at the start up of LEP, the biggest accelerator in the world. Today the 80 terminals and PCs have b...

  18. Quantitative (real-time) PCR

    International Nuclear Information System (INIS)

    Denman, S.E.; McSweeney, C.S.

    2005-01-01

    Many nucleic acid-based probe and PCR assays have been developed for the detection tracking of specific microbes within the rumen ecosystem. Conventional PCR assays detect PCR products at the end stage of each PCR reaction, where exponential amplification is no longer being achieved. This approach can result in different end product (amplicon) quantities being generated. In contrast, using quantitative, or real-time PCR, quantification of the amplicon is performed not at the end of the reaction, but rather during exponential amplification, where theoretically each cycle will result in a doubling of product being created. For real-time PCR, the cycle at which fluorescence is deemed to be detectable above the background during the exponential phase is termed the cycle threshold (Ct). The Ct values obtained are then used for quantitation, which will be discussed later

  19. Coupling in reflector arrays

    DEFF Research Database (Denmark)

    Appel-Hansen, Jørgen

    1968-01-01

    In order to reduce the space occupied by a reflector array, it is desirable to arrange the array antennas as close to each other as possible; however, in this case coupling between the array antennas will reduce the reflecting properties of the reflector array. The purpose of the present communic......In order to reduce the space occupied by a reflector array, it is desirable to arrange the array antennas as close to each other as possible; however, in this case coupling between the array antennas will reduce the reflecting properties of the reflector array. The purpose of the present...

  20. Expression profiles of the immune genes CD4, CD8β, IFNγ, IL-4, IL-6 and IL-10 in mitogen-stimulated koala lymphocytes (Phascolarctos cinereus by qRT-PCR

    Directory of Open Access Journals (Sweden)

    Iona E. Maher

    2014-03-01

    Full Text Available Investigation of the immune response of the koala (Phascolarctos cinereus is needed urgently, but has been limited by scarcity of species-specific reagents and methods for this unique and divergent marsupial. Infectious disease is an important threat to wild populations of koalas; the most widespread and important of these is Chlamydial disease, caused by Chlamydia pecorum and Chlamydia pneumoniae. In addition, koala retrovirus (KoRV, which is of 100% prevalence in northern Australia, has been proposed as an important agent of immune suppression that could explain the koala’s susceptibility to disease. The correct balance of T regulatory, T helper 1 (Th1 and Th2 lymphocyte responses are important to an individual’s susceptibility or resistance to chlamydial infection. The ability to study chlamydial or KoRV pathogenesis, effects of environmental stressors on immunity, and the response of koalas to vaccines under development, by examining the koala’s adaptive response to natural infection or in-vitro stimulation, has been limited to date by a paucity of species- specific reagents. In this study we have used cytokine sequences from four marsupial genomes to identify mRNA sequences for key T regulatory, Th1 and Th2 cytokines interleukin 4 (IL-4, interleukin 6 (IL-6, interleukin 10 (IL-10 and interferon gamma (IFNγ along with CD4 and CD8β. The koala sequences used for primer design showed >58% homology with grey short-tailed opossum, >71% with tammar wallaby and 78% with Tasmanian devil amino acid sequences. We report the development of real-time RT-PCR assays to measure the expression of these genes in unstimulated cells and after three common mitogen stimulation protocols (phorbol myristate acetate/ionomycin, phorbol myristate acetate/phytohemagglutinin and concanavalin A. Phorbol myristate acetate/ionomycin was found to be the most effective mitogen to up-regulate the production of IL-4, IL-10 and IFNγ. IL-6 production was not

  1. Expression profiles of the immune genes CD4, CD8β, IFNγ, IL-4, IL-6 and IL-10 in mitogen-stimulated koala lymphocytes (Phascolarctos cinereus) by qRT-PCR.

    Science.gov (United States)

    Maher, Iona E; Griffith, Joanna E; Lau, Quintin; Reeves, Thomas; Higgins, Damien P

    2014-01-01

    Investigation of the immune response of the koala (Phascolarctos cinereus) is needed urgently, but has been limited by scarcity of species-specific reagents and methods for this unique and divergent marsupial. Infectious disease is an important threat to wild populations of koalas; the most widespread and important of these is Chlamydial disease, caused by Chlamydia pecorum and Chlamydia pneumoniae. In addition, koala retrovirus (KoRV), which is of 100% prevalence in northern Australia, has been proposed as an important agent of immune suppression that could explain the koala's susceptibility to disease. The correct balance of T regulatory, T helper 1 (Th1) and Th2 lymphocyte responses are important to an individual's susceptibility or resistance to chlamydial infection. The ability to study chlamydial or KoRV pathogenesis, effects of environmental stressors on immunity, and the response of koalas to vaccines under development, by examining the koala's adaptive response to natural infection or in-vitro stimulation, has been limited to date by a paucity of species- specific reagents. In this study we have used cytokine sequences from four marsupial genomes to identify mRNA sequences for key T regulatory, Th1 and Th2 cytokines interleukin 4 (IL-4), interleukin 6 (IL-6), interleukin 10 (IL-10) and interferon gamma (IFNγ) along with CD4 and CD8β. The koala sequences used for primer design showed >58% homology with grey short-tailed opossum, >71% with tammar wallaby and 78% with Tasmanian devil amino acid sequences. We report the development of real-time RT-PCR assays to measure the expression of these genes in unstimulated cells and after three common mitogen stimulation protocols (phorbol myristate acetate/ionomycin, phorbol myristate acetate/phytohemagglutinin and concanavalin A). Phorbol myristate acetate/ionomycin was found to be the most effective mitogen to up-regulate the production of IL-4, IL-10 and IFNγ. IL-6 production was not consistently up-regulated by

  2. One-stop polymerase chain reaction (PCR): An improved PCR ...

    African Journals Online (AJOL)

    Yomi

    2011-12-21

    Dec 21, 2011 ... membrane filtration was carried out with a commercial PCR product purification kit (Generay, Shanghai), according to the manufacture's instruction. In brief, 50 µl PCR product was mixed thoroughly with binding buffer, and the resultant mixture was loaded directly onto a silica membrane Gelclean column.

  3. Design and operation of a portable scanner for high performance microchip capillary array electrophoresis.

    Science.gov (United States)

    Scherer, James R; Liu, Peng; Mathies, Richard A

    2010-11-01

    We have developed a compact, laser-induced fluorescence detection scanner, the multichannel capillary array electrophoresis portable scanner (McCAEPs) as a platform for electrophoretic detection and control of high-throughput, integrated microfluidic devices for genetic and other analyses. The instrument contains a confocal optical system with a rotary objective for detecting four different fluorescence signals, a pneumatic system consisting of two pressure/vacuum pumps and 28 individual addressable solenoid valves for control of on-chip microvalves and micropumps, four Polymerase Chain Reaction (PCR) temperature control systems, and four high voltage power supplies for electrophoresis. The detection limit of the instrument is ~20 pM for on-chip capillary electrophoresis of fluorescein dyes. To demonstrate the system performance for forensic short tandem repeat (STR) analysis, two experiments were conducted: (i) electrophoretic separation and detection of STR samples on a 96-lane microfabricated capillary array electrophoresis microchip. Fully resolved PowerPlex(®) 16 STR profiles amplified from 1 ng of 9947A female standard DNA were successfully obtained; (ii) nine-plex STR amplification, sample injection, separation, and fluorescence detection of 100-copy 9948 male standard DNA in a single integrated PCR- capillary electrophoresis microchip. These results demonstrate that the McCAEPs can be used as a versatile control and detection instrument that operates integrated microfluidic devices for high-performance forensic human identification.

  4. The construction and use of bacterial DNA microarrays based on an optimized two-stage PCR strategy

    Directory of Open Access Journals (Sweden)

    Pesta David

    2003-06-01

    Full Text Available Abstract Background DNA microarrays are a powerful tool with important applications such as global gene expression profiling. Construction of bacterial DNA microarrays from genomic sequence data using a two-stage PCR amplification approach for the production of arrayed DNA is attractive because it allows, in principal, the continued re-amplification of DNA fragments and facilitates further utilization of the DNA fragments for additional uses (e.g. over-expression of protein. We describe the successful construction and use of DNA microarrays by the two-stage amplification approach and discuss the technical challenges that were met and resolved during the project. Results Chimeric primers that contained both gene-specific and shared, universal sequence allowed the two-stage amplification of the 3,168 genes identified on the genome of Synechocystis sp. PCC6803, an important prokaryotic model organism for the study of oxygenic photosynthesis. The gene-specific component of the primer was of variable length to maintain uniform annealing temperatures during the 1st round of PCR synthesis, and situated to preserve full-length ORFs. Genes were truncated at 2 kb for efficient amplification, so that about 92% of the PCR fragments were full-length genes. The two-stage amplification had the additional advantage of normalizing the yield of PCR products and this improved the uniformity of DNA features robotically deposited onto the microarray surface. We also describe the techniques utilized to optimize hybridization conditions and signal-to-noise ratio of the transcription profile. The inter-lab transportability was demonstrated by the virtual error-free amplification of the entire genome complement of 3,168 genes using the universal primers in partner labs. The printed slides have been successfully used to identify differentially expressed genes in response to a number of environmental conditions, including salt stress. Conclusions The technique detailed

  5. Physical profile data collected in the Equatorial Pacific during cruises to service the TAO/TRITON array, a network of deep ocean moored buoys, February 23 - December 16, 2005 (NODC Accession 0002644)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — During 2005, CTD data were collected in the equatorial Pacific Ocean during cruises to service the TAO/TRITON array, a network of deep ocean moored buoys to support...

  6. Vibration energy harvesting using the Halbach array

    International Nuclear Information System (INIS)

    Zhu, Dibin; Beeby, Steve; Tudor, John; Harris, Nick

    2012-01-01

    This paper studies the feasibility of vibration energy harvesting using a Halbach array. A Halbach array is a specific arrangement of permanent magnets that concentrates the magnetic field on one side of the array while cancelling the field to almost zero on the other side. This arrangement can improve electromagnetic coupling in a limited space. The Halbach array offers an advantage over conventional layouts of magnets in terms of its concentrated magnetic field and low-profile structure, which helps improve the output power of electromagnetic energy harvesters while minimizing their size. Another benefit of the Halbach array is that due to the existence of an almost-zero magnetic field zone, electronic components can be placed close to the energy harvester without any chance of interference, which can potentially reduce the overall size of a self-powered device. The first reported example of a low-profile, planar electromagnetic vibration energy harvester utilizing a Halbach array was built and tested. Results were compared to ones for energy harvesters with conventional magnet layouts. By comparison, it is concluded that although energy harvesters with a Halbach array can have higher magnetic field density, a higher output power requires careful design in order to achieve the maximum magnetic flux gradient. (paper)

  7. Shape based kinetic outlier detection in real-time PCR

    Directory of Open Access Journals (Sweden)

    D'Atri Mario

    2010-04-01

    Full Text Available Abstract Background Real-time PCR has recently become the technique of choice for absolute and relative nucleic acid quantification. The gold standard quantification method in real-time PCR assumes that the compared samples have similar PCR efficiency. However, many factors present in biological samples affect PCR kinetic, confounding quantification analysis. In this work we propose a new strategy to detect outlier samples, called SOD. Results Richards function was fitted on fluorescence readings to parameterize the amplification curves. There was not a significant correlation between calculated amplification parameters (plateau, slope and y-coordinate of the inflection point and the Log of input DNA demonstrating that this approach can be used to achieve a "fingerprint" for each amplification curve. To identify the outlier runs, the calculated parameters of each unknown sample were compared to those of the standard samples. When a significant underestimation of starting DNA molecules was found, due to the presence of biological inhibitors such as tannic acid, IgG or quercitin, SOD efficiently marked these amplification profiles as outliers. SOD was subsequently compared with KOD, the current approach based on PCR efficiency estimation. The data obtained showed that SOD was more sensitive than KOD, whereas SOD and KOD were equally specific. Conclusion Our results demonstrated, for the first time, that outlier detection can be based on amplification shape instead of PCR efficiency. SOD represents an improvement in real-time PCR analysis because it decreases the variance of data thus increasing the reliability of quantification.

  8. Digital PCR: A brief history

    OpenAIRE

    Morley, Alexander A.

    2014-01-01

    Digital PCR for quantification of a target of interest has been independently developed several times, being described in 1990 and 1991 using the term “limiting dilution PCR” and in 1999 using the term “digital PCR”. It came into use in the decade following its first development but its use was cut short by the description of real-time PCR in 1996. However digital PCR has now had a renaissance due to the recent development of new instruments and chemistry which have made it a much simpler and...

  9. Wind loads on flat plate photovoltaic array fields

    Science.gov (United States)

    Miller, R. D.; Zimmerman, D. K.

    1981-01-01

    The results of an experimental analysis (boundary layer wind tunnel test) of the aerodynamic forces resulting from winds acting on flat plate photovoltaic arrays are presented. Local pressure coefficient distributions and normal force coefficients on the arrays are shown and compared to theoretical results. Parameters that were varied when determining the aerodynamic forces included tilt angle, array separation, ground clearance, protective wind barriers, and the effect of the wind velocity profile. Recommended design wind forces and pressures are presented, which envelop the test results for winds perpendicular to the array's longitudinal axis. This wind direction produces the maximum wind loads on the arrays except at the array edge where oblique winds produce larger edge pressure loads. The arrays located at the outer boundary of an array field have a protective influence on the interior arrays of the field. A significant decrease of the array wind loads were recorded in the wind tunnel test on array panels located behind a fence and/or interior to the array field compared to the arrays on the boundary and unprotected from the wind. The magnitude of this decrease was the same whether caused by a fence or upwind arrays.

  10. A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Redman Julia C

    2008-07-01

    Full Text Available Abstract Background Medicago truncatula is a model legume species that is currently the focus of an international genome sequencing effort. Although several different oligonucleotide and cDNA arrays have been produced for genome-wide transcript analysis of this species, intrinsic limitations in the sensitivity of hybridization-based technologies mean that transcripts of genes expressed at low-levels cannot be measured accurately with these tools. Amongst such genes are many encoding transcription factors (TFs, which are arguably the most important class of regulatory proteins. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR is the most sensitive method currently available for transcript quantification, and one that can be scaled up to analyze transcripts of thousands of genes in parallel. Thus, qRT-PCR is an ideal method to tackle the problem of TF transcript quantification in Medicago and other plants. Results We established a bioinformatics pipeline to identify putative TF genes in Medicago truncatula and to design gene-specific oligonucleotide primers for qRT-PCR analysis of TF transcripts. We validated the efficacy and gene-specificity of over 1000 TF primer pairs and utilized these to identify sets of organ-enhanced TF genes that may play important roles in organ development or differentiation in this species. This community resource will be developed further as more genome sequence becomes available, with the ultimate goal of producing validated, gene-specific primers for all Medicago TF genes. Conclusion High-throughput qRT-PCR using a 384-well plate format enables rapid, flexible, and sensitive quantification of all predicted Medicago transcription factor mRNAs. This resource has been utilized recently by several groups in Europe, Australia, and the USA, and we expect that it will become the 'gold-standard' for TF transcript profiling in Medicago truncatula.

  11. Determining the analytical specificity of PCR-based assays for the diagnosis of IA: What is Aspergillus?

    NARCIS (Netherlands)

    Morton, C.O.; White, P.L.; Barnes, R.A.; Klingspor, L.; Cuenca-Estrella, M.; Lagrou, K.; Bretagne, S.; Melchers, W.J.; Mengoli, C.; Caliendo, A.M.; Cogliati, M.; Debets-Ossenkopp, Y.; Gorton, R.; Hagen, F.; Halliday, C.; Hamal, P.; Harvey-Wood, K.; Jaton, K.; Johnson, G.; Kidd, S.; Lengerova, M.; Lass-Florl, C.; Linton, C.; Millon, L.; Morrissey, C.O.; Paholcsek, M.; Talento, A.F.; Ruhnke, M.; Willinger, B.; Donnelly, J.P.; Loeffler, J.

    2017-01-01

    A wide array of PCR tests has been developed to aid the diagnosis of invasive aspergillosis (IA), providing technical diversity but limiting standardisation and acceptance. Methodological recommendations for testing blood samples using PCR exist, based on achieving optimal assay sensitivity to help

  12. Quantitative real-time RT-PCR and chromogenic in situ hybridization

    DEFF Research Database (Denmark)

    Rosa, Fabíola E; Silveira, Sara M; Silveira, Cássia G T

    2009-01-01

    . METHODS: To elucidate the molecular profile of HER-2 status, mRNA and protein expression in 75 invasive breast carcinomas were analyzed by real time quantitative RT-PCR (qRT-PCR) and IHC, respectively. Amplifications were evaluated in 43 of these cases by CISH and in 11 by FISH. RESULTS: The concordance...

  13. Fiber Laser Array

    National Research Council Canada - National Science Library

    Simpson, Thomas

    2002-01-01

    ...., field-dependent, loss within the coupled laser array. During this program, Jaycor focused on the construction and use of an experimental apparatus that can be used to investigate the coherent combination of an array of fiber lasers...

  14. Selection and Validation of Reference Genes for qRT-PCR Expression Analysis of Candidate Genes Involved in Olfactory Communication in the Butterfly Bicyclus anynana

    OpenAIRE

    Arun, Alok; Bauml?, V?ronique; Amelot, Ga?l; Nieberding, Caroline M.

    2015-01-01

    Real-time quantitative reverse transcription PCR (qRT-PCR) is a technique widely used to quantify the transcriptional expression level of candidate genes. qRT-PCR requires the selection of one or several suitable reference genes, whose expression profiles remain stable across conditions, to normalize the qRT-PCR expression profiles of candidate genes. Although several butterfly species (Lepidoptera) have become important models in molecular evolutionary ecology, so far no study aimed at ident...

  15. Spatial normalization of array-CGH data

    Directory of Open Access Journals (Sweden)

    Brennetot Caroline

    2006-05-01

    Full Text Available Abstract Background Array-based comparative genomic hybridization (array-CGH is a recently developed technique for analyzing changes in DNA copy number. As in all microarray analyses, normalization is required to correct for experimental artifacts while preserving the true biological signal. We investigated various sources of systematic variation in array-CGH data and identified two distinct types of spatial effect of no biological relevance as the predominant experimental artifacts: continuous spatial gradients and local spatial bias. Local spatial bias affects a large proportion of arrays, and has not previously been considered in array-CGH experiments. Results We show that existing normalization techniques do not correct these spatial effects properly. We therefore developed an automatic method for the spatial normalization of array-CGH data. This method makes it possible to delineate and to eliminate and/or correct areas affected by spatial bias. It is based on the combination of a spatial segmentation algorithm called NEM (Neighborhood Expectation Maximization and spatial trend estimation. We defined quality criteria for array-CGH data, demonstrating significant improvements in data quality with our method for three data sets coming from two different platforms (198, 175 and 26 BAC-arrays. Conclusion We have designed an automatic algorithm for the spatial normalization of BAC CGH-array data, preventing the misinterpretation of experimental artifacts as biologically relevant outliers in the genomic profile. This algorithm is implemented in the R package MANOR (Micro-Array NORmalization, which is described at http://bioinfo.curie.fr/projects/manor and available from the Bioconductor site http://www.bioconductor.org. It can also be tested on the CAPweb bioinformatics platform at http://bioinfo.curie.fr/CAPweb.

  16. Species Identification of Fox-, Mink-, Dog-, and Rabbit-Derived Ingredients by Multiplex PCR and Real-Time PCR Assay.

    Science.gov (United States)

    Wu, Qingqing; Xiang, Shengnan; Wang, Wenjun; Zhao, Jinyan; Xia, Jinhua; Zhen, Yueran; Liu, Bang

    2018-05-01

    Various detection methods have been developed to date for identification of animal species. New techniques based on PCR approach have raised the hope of developing better identification methods, which can overcome the limitations of the existing methods. PCR-based methods used the mitochondrial DNA (mtDNA) as well as nuclear DNA sequences. In this study, by targeting nuclear DNA, multiplex PCR and real-time PCR methods were developed to assist with qualitative and quantitative analysis. The multiplex PCR was found to simultaneously and effectively distinguish four species (fox, dog, mink, and rabbit) ingredients by the different sizes of electrophoretic bands: 480, 317, 220, and 209 bp. Real-time fluorescent PCR's amplification profiles and standard curves showed good quantitative measurement responses and linearity, as indicated by good repeatability and coefficient of determination R 2  > 0.99. The quantitative results of quaternary DNA mixtures including mink, fox, dog, and rabbit DNA are in line with our expectations: R.D. (relative deviation) varied between 1.98 and 12.23% and R.S.D. (relative standard deviation) varied between 3.06 and 11.51%, both of which are well within the acceptance criterion of ≤ 25%. Combining the two methods is suitable for the rapid identification and accurate quantification of fox-, dog-, mink-, and rabbit-derived ingredients in the animal products.

  17. miRNA Expression Profiles in Cerebrospinal Fluid and Blood of Patients with Acute Ischemic Stroke

    DEFF Research Database (Denmark)

    Sørensen, Sofie Sølvsten; Nygaard, Ann-Britt; Nielsen, Ming-Yuan

    2014-01-01

    in the cell-free fractions of CSF and blood were analyzed by a microarray technique (miRCURY LNA™ microRNA Array, Exiqon A/S, Denmark) using a quantitative PCR (qPCR) platform containing 378 miRNA primers. In total, 183 different miRNAs were detected in the CSF, of which two miRNAs (let-7c and miR-221-3p......The aims of the study were (1) to determine whether miRNAs (microRNAs) can be detected in the cerebrospinal fluid (CSF) and blood of patients with ischemic stroke and (2) to compare these miRNA profiles with corresponding profiles from other neurological patients to address whether the mi......RNA profiles of CSF or blood have potential usefulness as diagnostic biomarkers of ischemic stroke. CSF from patients with acute ischemic stroke (n = 10) and patients with other neurological diseases (n = 10) was collected by lumbar puncture. Blood samples were taken immediately after. Expression profiles...

  18. Methylation-Specific PCR Unraveled

    Directory of Open Access Journals (Sweden)

    Sarah Derks

    2004-01-01

    Full Text Available Methylation‐specific PCR (MSP is a simple, quick and cost‐effective method to analyze the DNA methylation status of virtually any group of CpG sites within a CpG island. The technique comprises two parts: (1 sodium bisulfite conversion of unmethylated cytosine's to uracil under conditions whereby methylated cytosines remains unchanged and (2 detection of the bisulfite induced sequence differences by PCR using specific primer sets for both unmethylated and methylated DNA. This review discusses the critical parameters of MSP and presents an overview of the available MSP variants and the (clinical applications.

  19. pcr

    African Journals Online (AJOL)

    DR. AMINU

    Keywords: Polymerase chain reaction, Diagnosis, Bacteria, Infections. INTRODUCTION ... used to amplify a piece of DNA by in-vitro enzymatic replication (David and .... receiving antimicrobial treatment, or when the causative agents are small ...

  20. Measurement of indicator genes using global complementary DNA (cDNA) amplification, by polyadenylic acid reverse transcriptase polymerase chain reaction (poly A RT-PCR): A feasibility study using paired samples from tissue and ductal juice in patients undergoing pancreatoduodenectomy.

    Science.gov (United States)

    Sanyal, Sudip; Siriwardena, Ajith K; Byers, Richard

    2018-06-01

    The aim of this study is to compare gene expression profiles in RNA isolated from pancreatic ductal juice with the RNA expression profiles of the same genes from matched intra-operative tissue samples from pancreatic tumours. Intra-operative sampling of pancreatic juice and collection of matched tissue samples was undertaken in patients undergoing pancreatoduodenectomy for clinically suspected pancreatic cancer and a precursor lesion, main-duct intraductal papillary mucinous neoplasm. RNA was isolated and Poly A PCR was used to globally amplify the RNA. Real-time polymerase chain reaction (RT-PCR) was used to measure expression levels of 17 genes selected from microarray studies. Spearman's rank correlation test was used to examine the relationship of gene expression between pancreatic juice and tissue. The study was approved by Regional Ethics Committee. Mesothelin (MSLN) showed significant correlation (p cDNA using poly A PCR is technically feasible. Application of the technique to non-invasively obtained pancreatic juice during endoscopic assessment of tumours and the use of gene arrays of cancer indicator genes are the next steps in development of this technique. Copyright © 2018 IAP and EPC. Published by Elsevier B.V. All rights reserved.

  1. Carbon nanotube nanoelectrode arrays

    Science.gov (United States)

    Ren, Zhifeng; Lin, Yuehe; Yantasee, Wassana; Liu, Guodong; Lu, Fang; Tu, Yi

    2008-11-18

    The present invention relates to microelectode arrays (MEAs), and more particularly to carbon nanotube nanoelectrode arrays (CNT-NEAs) for chemical and biological sensing, and methods of use. A nanoelectrode array includes a carbon nanotube material comprising an array of substantially linear carbon nanotubes each having a proximal end and a distal end, the proximal end of the carbon nanotubes are attached to a catalyst substrate material so as to form the array with a pre-determined site density, wherein the carbon nanotubes are aligned with respect to one another within the array; an electrically insulating layer on the surface of the carbon nanotube material, whereby the distal end of the carbon nanotubes extend beyond the electrically insulating layer; a second adhesive electrically insulating layer on the surface of the electrically insulating layer, whereby the distal end of the carbon nanotubes extend beyond the second adhesive electrically insulating layer; and a metal wire attached to the catalyst substrate material.

  2. Josephson junction arrays

    International Nuclear Information System (INIS)

    Bindslev Hansen, J.; Lindelof, P.E.

    1985-01-01

    In this review we intend to cover recent work involving arrays of Josephson junctions. The work on such arrays falls naturally into three main areas of interest: 1. Technical applications of Josephson junction arrays for high-frequency devices. 2. Experimental studies of 2-D model systems (Kosterlitz-Thouless phase transition, commensurate-incommensurate transition in frustrated (flux) lattices). 3. Investigations of phenomena associated with non-equilibrium superconductivity in and around Josephson junctions (with high current density). (orig./BUD)

  3. Phased-array radars

    Science.gov (United States)

    Brookner, E.

    1985-02-01

    The operating principles, technology, and applications of phased-array radars are reviewed and illustrated with diagrams and photographs. Consideration is given to the antenna elements, circuitry for time delays, phase shifters, pulse coding and compression, and hybrid radars combining phased arrays with lenses to alter the beam characteristics. The capabilities and typical hardware of phased arrays are shown using the US military systems COBRA DANE and PAVE PAWS as examples.

  4. Storage array reflection considerations

    International Nuclear Information System (INIS)

    Haire, M.J.; Jordan, W.C.; Taylor, R.G.

    1997-01-01

    The assumptions used for reflection conditions of single containers are fairly well established and consistently applied throughout the industry in nuclear criticality safety evaluations. Containers are usually considered to be either fully water reflected (i.e., surrounded by 6 to 12 in. of water) for safety calculations or reflected by 1 in. of water for nominal (structural material and air) conditions. Tables and figures are usually available for performing comparative evaluations of containers under various loading conditions. Reflection considerations used for evaluating the safety of storage arrays of fissile material are not as well established. When evaluating arrays, it has become more common for analysts to use calculations to demonstrate the safety of the array configuration. In performing these calculations, the analyst has considerable freedom concerning the assumptions made for modeling the reflection of the array. Considerations are given for the physical layout of the array with little or no discussion (or demonstration) of what conditions are bounded by the assumed reflection conditions. For example, an array may be generically evaluated by placing it in a corner of a room in which the opposing walls are far away. Typically, it is believed that complete flooding of the room is incredible, so the array is evaluated for various levels of water mist interspersed among array containers. This paper discusses some assumptions that are made regarding storage array reflection

  5. The EUROBALL array

    International Nuclear Information System (INIS)

    Rossi Alvarez, C.

    1998-01-01

    The quality of the multidetector array EUROBALL is described, with emphasis on the history and formal organization of the related European collaboration. The detector layout is presented together with the electronics and Data Acquisition capabilities. The status of the instrument, its performances and the main features of some recently developed ancillary detectors will also be described. The EUROBALL array is operational in Legnaro National Laboratory (Italy) since April 1997 and is expected to run up to November 1998. The array represents a significant improvement in detector efficiency and sensitivity with respect to the previous generation of multidetector arrays

  6. Rectenna array measurement results

    Science.gov (United States)

    Dickinson, R. M.

    1980-01-01

    The measured performance characteristics of a rectenna array are reviewed and compared to the performance of a single element. It is shown that the performance may be extrapolated from the individual element to that of the collection of elements. Techniques for current and voltage combining were demonstrated. The array performance as a function of various operating parameters is characterized and techniques for overvoltage protection and automatic fault clearing in the array demonstrated. A method for detecting failed elements also exists. Instrumentation for deriving performance effectiveness is described. Measured harmonic radiation patterns and fundamental frequency scattered patterns for a low level illumination rectenna array are presented.

  7. Arrayed waveguide Sagnac interferometer.

    Science.gov (United States)

    Capmany, José; Muñoz, Pascual; Sales, Salvador; Pastor, Daniel; Ortega, Beatriz; Martinez, Alfonso

    2003-02-01

    We present a novel device, an arrayed waveguide Sagnac interferometer, that combines the flexibility of arrayed waveguides and the wide application range of fiber or integrated optics Sagnac loops. We form the device by closing an array of wavelength-selective light paths provided by two arrayed waveguides with a single 2 x 2 coupler in a Sagnac configuration. The equations that describe the device's operation in general conditions are derived. A preliminary experimental demonstration is provided of a fiber prototype in passive operation that shows good agreement with the expected theoretical performance. Potential applications of the device in nonlinear operation are outlined and discussed.

  8. Flat dielectric metasurface lens array for three dimensional integral imaging

    Science.gov (United States)

    Zhang, Jianlei; Wang, Xiaorui; Yang, Yi; Yuan, Ying; Wu, Xiongxiong

    2018-05-01

    In conventional integral imaging, the singlet refractive lens array limits the imaging performance due to its prominent aberrations. Different from the refractive lens array relying on phase modulation via phase change accumulated along the optical paths, metasurfaces composed of nano-scatters can produce phase abrupt over the scale of wavelength. In this letter, we propose a novel lens array consisting of two neighboring flat dielectric metasurfaces for integral imaging system. The aspherical phase profiles of the metasurfaces are optimized to improve imaging performance. The simulation results show that our designed 5 × 5 metasurface-based lens array exhibits high image quality at designed wavelength 865 nm.

  9. Design and optimization of reverse-transcription quantitative PCR experiments.

    Science.gov (United States)

    Tichopad, Ales; Kitchen, Rob; Riedmaier, Irmgard; Becker, Christiane; Ståhlberg, Anders; Kubista, Mikael

    2009-10-01

    Quantitative PCR (qPCR) is a valuable technique for accurately and reliably profiling and quantifying gene expression. Typically, samples obtained from the organism of study have to be processed via several preparative steps before qPCR. We estimated the errors of sample withdrawal and extraction, reverse transcription (RT), and qPCR that are introduced into measurements of mRNA concentrations. We performed hierarchically arranged experiments with 3 animals, 3 samples, 3 RT reactions, and 3 qPCRs and quantified the expression of several genes in solid tissue, blood, cell culture, and single cells. A nested ANOVA design was used to model the experiments, and relative and absolute errors were calculated with this model for each processing level in the hierarchical design. We found that intersubject differences became easily confounded by sample heterogeneity for single cells and solid tissue. In cell cultures and blood, the noise from the RT and qPCR steps contributed substantially to the overall error because the sampling noise was less pronounced. We recommend the use of sample replicates preferentially to any other replicates when working with solid tissue, cell cultures, and single cells, and we recommend the use of RT replicates when working with blood. We show how an optimal sampling plan can be calculated for a limited budget. .

  10. Microfabricated hollow microneedle array using ICP etcher

    Science.gov (United States)

    Ji, Jing; Tay, Francis E. H.; Miao, Jianmin

    2006-04-01

    This paper presents a developed process for fabrication of hollow silicon microneedle arrays. The inner hollow hole and the fluidic reservoir are fabricated in deep reactive ion etching. The profile of outside needles is achieved by the developed fabrication process, which combined isotropic etching and anisotropic etching with inductively coupled plasma (ICP) etcher. Using the combination of SF6/O2 isotropic etching chemistry and Bosch process, the high aspect ratio 3D and high density microneedle arrays are fabricated. The generated needle external geometry can be controlled by etching variables in the isotropic and anisotropic cases.

  11. Microfabricated hollow microneedle array using ICP etcher

    International Nuclear Information System (INIS)

    Ji Jing; Tay, Francis E H; Miao Jianmin

    2006-01-01

    This paper presents a developed process for fabrication of hollow silicon microneedle arrays. The inner hollow hole and the fluidic reservoir are fabricated in deep reactive ion etching. The profile of outside needles is achieved by the developed fabrication process, which combined isotropic etching and anisotropic etching with inductively coupled plasma (ICP) etcher. Using the combination of SF 6 /O 2 isotropic etching chemistry and Bosch process, the high aspect ratio 3D and high density microneedle arrays are fabricated. The generated needle external geometry can be controlled by etching variables in the isotropic and anisotropic cases

  12. Microfabricated hollow microneedle array using ICP etcher

    Energy Technology Data Exchange (ETDEWEB)

    Ji Jing [Mechanical Engineering National University of Singapore, 119260, Singapore (Singapore); Tay, Francis E H [Mechanical Engineering National University of Singapore, 119260, Singapore (Singapore); Miao Jianmin [MicroMachines Center, School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 (Singapore)

    2006-04-01

    This paper presents a developed process for fabrication of hollow silicon microneedle arrays. The inner hollow hole and the fluidic reservoir are fabricated in deep reactive ion etching. The profile of outside needles is achieved by the developed fabrication process, which combined isotropic etching and anisotropic etching with inductively coupled plasma (ICP) etcher. Using the combination of SF{sub 6}/O{sub 2} isotropic etching chemistry and Bosch process, the high aspect ratio 3D and high density microneedle arrays are fabricated. The generated needle external geometry can be controlled by etching variables in the isotropic and anisotropic cases.

  13. Use of PCR-Based Methods for Rapid Differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis

    Science.gov (United States)

    Torriani, Sandra; Zapparoli, Giacomo; Dellaglio, Franco

    1999-01-01

    Two PCR-based methods, specific PCR and randomly amplified polymorphic DNA PCR (RAPD-PCR), were used for rapid and reliable differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis. PCR with a single combination of primers which targeted the proline iminopeptidase (pepIP) gene of L. delbrueckii subsp. bulgaricus allowed amplification of genomic fragments specific for the two subspecies when either DNA from a single colony or cells extracted from dairy products were used. A numerical analysis of the RAPD-PCR patterns obtained with primer M13 gave results that were consistent with the results of specific PCR for all strains except L. delbrueckii subsp. delbrueckii LMG 6412T, which clustered with L. delbrueckii subsp. lactis strains. In addition, RAPD-PCR performed with primer 1254 provided highly polymorphic profiles and thus was superior for distinguishing individual L. delbrueckii strains. PMID:10508059

  14. Use of PCR-based methods for rapid differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis.

    Science.gov (United States)

    Torriani, S; Zapparoli, G; Dellaglio, F

    1999-10-01

    Two PCR-based methods, specific PCR and randomly amplified polymorphic DNA PCR (RAPD-PCR), were used for rapid and reliable differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis. PCR with a single combination of primers which targeted the proline iminopeptidase (pepIP) gene of L. delbrueckii subsp. bulgaricus allowed amplification of genomic fragments specific for the two subspecies when either DNA from a single colony or cells extracted from dairy products were used. A numerical analysis of the RAPD-PCR patterns obtained with primer M13 gave results that were consistent with the results of specific PCR for all strains except L. delbrueckii subsp. delbrueckii LMG 6412(T), which clustered with L. delbrueckii subsp. lactis strains. In addition, RAPD-PCR performed with primer 1254 provided highly polymorphic profiles and thus was superior for distinguishing individual L. delbrueckii strains.

  15. Quantitative PCR high-resolution melting (qPCR-HRM) curve analysis, a new approach to simultaneously screen point mutations and large rearrangements: application to MLH1 germline mutations in Lynch syndrome.

    Science.gov (United States)

    Rouleau, Etienne; Lefol, Cédrick; Bourdon, Violaine; Coulet, Florence; Noguchi, Tetsuro; Soubrier, Florent; Bièche, Ivan; Olschwang, Sylviane; Sobol, Hagay; Lidereau, Rosette

    2009-06-01

    Several techniques have been developed to screen mismatch repair (MMR) genes for deleterious mutations. Until now, two different techniques were required to screen for both point mutations and large rearrangements. For the first time, we propose a new approach, called "quantitative PCR (qPCR) high-resolution melting (HRM) curve analysis (qPCR-HRM)," which combines qPCR and HRM to obtain a rapid and cost-effective method suitable for testing a large series of samples. We designed PCR amplicons to scan the MLH1 gene using qPCR HRM. Seventy-six patients were fully scanned in replicate, including 14 wild-type patients and 62 patients with known mutations (57 point mutations and five rearrangements). To validate the detected mutations, we used sequencing and/or hybridization on a dedicated MLH1 array-comparative genomic hybridization (array-CGH). All point mutations and rearrangements detected by denaturing high-performance liquid chromatography (dHPLC)+multiplex ligation-dependent probe amplification (MLPA) were successfully detected by qPCR HRM. Three large rearrangements were characterized with the dedicated MLH1 array-CGH. One variant was detected with qPCR HRM in a wild-type patient and was located within the reverse primer. One variant was not detected with qPCR HRM or with dHPLC due to its proximity to a T-stretch. With qPCR HRM, prescreening for point mutations and large rearrangements are performed in one tube and in one step with a single machine, without the need for any automated sequencer in the prescreening process. In replicate, its reagent cost, sensitivity, and specificity are comparable to those of dHPLC+MLPA techniques. However, qPCR HRM outperformed the other techniques in terms of its rapidity and amount of data provided.

  16. Force sensitive carbon nanotube arrays for biologically inspired airflow sensing

    Science.gov (United States)

    Maschmann, Matthew R.; Dickinson, Ben; Ehlert, Gregory J.; Baur, Jeffery W.

    2012-09-01

    The compressive electromechanical response of aligned carbon nanotube (CNT) arrays is evaluated for use as an artificial hair sensor (AHS) transduction element. CNT arrays with heights of 12, 75, and 225 µm are examined. The quasi-static and dynamic sensitivity to force, response time, and signal drift are examined within the range of applied stresses predicted by a mechanical model applicable to the conceptual CNT array-based AHS (0-1 kPa). Each array is highly sensitive to compressive loading, with a maximum observed gauge factor of 114. The arrays demonstrate a repeatable response to dynamic cycling after a break-in period of approximately 50 cycles. Utilizing a four-wire measurement electrode configuration, the change in contact resistance between the array and the electrodes is observed to dominate the electromechanical response of the arrays. The response time of the CNT arrays is of the order of 10 ms. When the arrays are subjected to constant stress, mechanical creep is observed that results in a signal drift that generally diminishes the responsiveness of the arrays, particularly at stress approaching 1 kPa. The results of this study serve as a preliminary proof of concept for utilizing CNT arrays as a transduction mechanism for a proposed artificial hair sensor. Such a low profile and light-weight flow sensor is expected to have application in a number of applications including navigation and state awareness of small air vehicles, similar in function to natural hair cell receptors utilized by insects and bats.

  17. Focal plane array with modular pixel array components for scalability

    Science.gov (United States)

    Kay, Randolph R; Campbell, David V; Shinde, Subhash L; Rienstra, Jeffrey L; Serkland, Darwin K; Holmes, Michael L

    2014-12-09

    A modular, scalable focal plane array is provided as an array of integrated circuit dice, wherein each die includes a given amount of modular pixel array circuitry. The array of dice effectively multiplies the amount of modular pixel array circuitry to produce a larger pixel array without increasing die size. Desired pixel pitch across the enlarged pixel array is preserved by forming die stacks with each pixel array circuitry die stacked on a separate die that contains the corresponding signal processing circuitry. Techniques for die stack interconnections and die stack placement are implemented to ensure that the desired pixel pitch is preserved across the enlarged pixel array.

  18. The database of chromosome imbalance regions and genes resided in lung cancer from Asian and Caucasian identified by array-comparative genomic hybridization

    Directory of Open Access Journals (Sweden)

    Lo Fang-Yi

    2012-06-01

    Full Text Available Abstract Background Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. Methods Array-comparative genomic hybridization (array-CGH was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR, chromogenic in situ hybridization (CISH, reverse transcriptase-qPCR (RT-qPCR, and immunohistochemistry (IHC in more patients. Results We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1 functioning in Rho activity control, FRAT2 (10q24.1 involved in Wnt signaling, PAFAH1B1 (17p13.3 functioning in motility control, and ZNF322A (6p22.1 involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (PP=0.06. In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of

  19. The database of chromosome imbalance regions and genes resided in lung cancer from Asian and Caucasian identified by array-comparative genomic hybridization

    International Nuclear Information System (INIS)

    Lo, Fang-Yi; Nandi, Suvobroto; Salgia, Ravi; Wang, Yi-Ching; Chang, Jer-Wei; Chang, I-Shou; Chen, Yann-Jang; Hsu, Han-Shui; Huang, Shiu-Feng Kathy; Tsai, Fang-Yu; Jiang, Shih Sheng; Kanteti, Rajani

    2012-01-01

    Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. Array-comparative genomic hybridization (array-CGH) was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR), chromogenic in situ hybridization (CISH), reverse transcriptase-qPCR (RT-qPCR), and immunohistochemistry (IHC) in more patients. We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1) functioning in Rho activity control, FRAT2 (10q24.1) involved in Wnt signaling, PAFAH1B1 (17p13.3) functioning in motility control, and ZNF322A (6p22.1) involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (P<0.001~P=0.06). In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of PAFAH1B1 protein overexpression was 68

  20. Triggering the GRANDE array

    International Nuclear Information System (INIS)

    Wilson, C.L.; Bratton, C.B.; Gurr, J.; Kropp, W.; Nelson, M.; Sobel, H.; Svoboda, R.; Yodh, G.; Burnett, T.; Chaloupka, V.; Wilkes, R.J.; Cherry, M.; Ellison, S.B.; Guzik, T.G.; Wefel, J.; Gaidos, J.; Loeffler, F.; Sembroski, G.; Goodman, J.; Haines, T.J.; Kielczewska, D.; Lane, C.; Steinberg, R.; Lieber, M.; Nagle, D.; Potter, M.; Tripp, R.

    1990-01-01

    A brief description of the Gamma Ray And Neutrino Detector Experiment (GRANDE) is presented. The detector elements and electronics are described. The trigger logic for the array is then examined. The triggers for the Gamma Ray and the Neutrino portions of the array are treated separately. (orig.)

  1. ISS Solar Array Management

    Science.gov (United States)

    Williams, James P.; Martin, Keith D.; Thomas, Justin R.; Caro, Samuel

    2010-01-01

    The International Space Station (ISS) Solar Array Management (SAM) software toolset provides the capabilities necessary to operate a spacecraft with complex solar array constraints. It monitors spacecraft telemetry and provides interpretations of solar array constraint data in an intuitive manner. The toolset provides extensive situational awareness to ensure mission success by analyzing power generation needs, array motion constraints, and structural loading situations. The software suite consists of several components including samCS (constraint set selector), samShadyTimers (array shadowing timers), samWin (visualization GUI), samLock (array motion constraint computation), and samJet (attitude control system configuration selector). It provides high availability and uptime for extended and continuous mission support. It is able to support two-degrees-of-freedom (DOF) array positioning and supports up to ten simultaneous constraints with intuitive 1D and 2D decision support visualizations of constraint data. Display synchronization is enabled across a networked control center and multiple methods for constraint data interpolation are supported. Use of this software toolset increases flight safety, reduces mission support effort, optimizes solar array operation for achieving mission goals, and has run for weeks at a time without issues. The SAM toolset is currently used in ISS real-time mission operations.

  2. Outbreak of hepatitis E virus infection in Darfur, Sudan: effectiveness of real-time reverse transcription-PCR analysis of dried blood spots.

    Science.gov (United States)

    Mérens, Audrey; Guérin, Philippe Jean; Guthmann, Jean-Paul; Nicand, Elisabeth

    2009-06-01

    Biological samples collected in refugee camps during an outbreak of hepatitis E were used to compare the accuracy of hepatitis E virus RNA amplification by real-time reverse transcription-PCR (RT-PCR) for sera and dried blood spots (concordance of 90.6%). Biological profiles (RT-PCR and serology) of asymptomatic individuals were also analyzed.

  3. High-throughput STR analysis for DNA database using direct PCR.

    Science.gov (United States)

    Sim, Jeong Eun; Park, Su Jeong; Lee, Han Chul; Kim, Se-Yong; Kim, Jong Yeol; Lee, Seung Hwan

    2013-07-01

    Since the Korean criminal DNA database was launched in 2010, we have focused on establishing an automated DNA database profiling system that analyzes short tandem repeat loci in a high-throughput and cost-effective manner. We established a DNA database profiling system without DNA purification using a direct PCR buffer system. The quality of direct PCR procedures was compared with that of conventional PCR system under their respective optimized conditions. The results revealed not only perfect concordance but also an excellent PCR success rate, good electropherogram quality, and an optimal intra/inter-loci peak height ratio. In particular, the proportion of DNA extraction required due to direct PCR failure could be minimized to <3%. In conclusion, the newly developed direct PCR system can be adopted for automated DNA database profiling systems to replace or supplement conventional PCR system in a time- and cost-saving manner. © 2013 American Academy of Forensic Sciences Published 2013. This article is a U.S. Government work and is in the public domain in the U.S.A.

  4. Two-temperature PCR for Microfluidics

    KAUST Repository

    Kodzius, Rimantas

    2010-05-01

    Since its invention in 1983, polymerase chain reaction (PCR) has been the method of choice for DNA amplification. Successful PCR depends on the optimization of several parameters, which is a cumbersome task due to the many variables (conditions and compon

  5. Two-temperature PCR for Microfluidics

    KAUST Repository

    Kodzius, Rimantas; Chang, Donald Choy; Sheng, Ping; Wen, Weijia; Wu, Jinbo; Xiao, Kang; Yu, Vivian

    2010-01-01

    Since its invention in 1983, polymerase chain reaction (PCR) has been the method of choice for DNA amplification. Successful PCR depends on the optimization of several parameters, which is a cumbersome task due to the many variables (conditions and compon

  6. Sensor array signal processing

    CERN Document Server

    Naidu, Prabhakar S

    2009-01-01

    Chapter One: An Overview of Wavefields 1.1 Types of Wavefields and the Governing Equations 1.2 Wavefield in open space 1.3 Wavefield in bounded space 1.4 Stochastic wavefield 1.5 Multipath propagation 1.6 Propagation through random medium 1.7 ExercisesChapter Two: Sensor Array Systems 2.1 Uniform linear array (ULA) 2.2 Planar array 2.3 Distributed sensor array 2.4 Broadband sensor array 2.5 Source and sensor arrays 2.6 Multi-component sensor array2.7 ExercisesChapter Three: Frequency Wavenumber Processing 3.1 Digital filters in the w-k domain 3.2 Mapping of 1D into 2D filters 3.3 Multichannel Wiener filters 3.4 Wiener filters for ULA and UCA 3.5 Predictive noise cancellation 3.6 Exercises Chapter Four: Source Localization: Frequency Wavenumber Spectrum4.1 Frequency wavenumber spectrum 4.2 Beamformation 4.3 Capon's w-k spectrum 4.4 Maximum entropy w-k spectrum 4.5 Doppler-Azimuth Processing4.6 ExercisesChapter Five: Source Localization: Subspace Methods 5.1 Subspace methods (Narrowband) 5.2 Subspace methods (B...

  7. Pathogen Causing Disease of Diagnosis PCR Tecnology

    OpenAIRE

    SEVİNDİK, Emre; KIR, A. Çağrı; BAŞKEMER, Kadir; UZUN, Veysel

    2013-01-01

    Polimerase chain reaction (PCR) with which, the development of recombinant DNA tecnology, a technique commonly used in field of moleculer biology and genetic. Duplication of the target DNA is provided with this technique without the need for cloning. Some fungus species, bacteria, viruses constitutent an important group of pathogenicity in human, animals and plants. There are routinely applied types of PCR in the detection of pathogens infections diseases. These Nested- PCR, Real- Time PCR, M...

  8. Introduction to adaptive arrays

    CERN Document Server

    Monzingo, Bob; Haupt, Randy

    2011-01-01

    This second edition is an extensive modernization of the bestselling introduction to the subject of adaptive array sensor systems. With the number of applications of adaptive array sensor systems growing each year, this look at the principles and fundamental techniques that are critical to these systems is more important than ever before. Introduction to Adaptive Arrays, 2nd Edition is organized as a tutorial, taking the reader by the hand and leading them through the maze of jargon that often surrounds this highly technical subject. It is easy to read and easy to follow as fundamental concept

  9. Piezoelectric transducer array microspeaker

    KAUST Repository

    Carreno, Armando Arpys Arevalo

    2016-12-19

    In this paper we present the fabrication and characterization of a piezoelectric micro-speaker. The speaker is an array of micro-machined piezoelectric membranes, fabricated on silicon wafer using advanced micro-machining techniques. Each array contains 2n piezoelectric transducer membranes, where “n” is the bit number. Every element of the array has a circular shape structure. The membrane is made out four layers: 300nm of platinum for the bottom electrode, 250nm or lead zirconate titanate (PZT), a top electrode of 300nm and a structural layer of 50

  10. Principles and technical aspects of PCR amplification

    National Research Council Canada - National Science Library

    Pelt-Verkuil, Elizabeth van; Belkum, Alex van; Hays, John P

    2008-01-01

    ... to illustrate any particularly important concepts or comments. Indeed, all commercial PCR biotechnology companies offer information about their products on internet sites and in online technical manuals. These online resources will be invaluable for any readers requiring more detailed PCR protocols. The authors have provided references for many PCR co...

  11. The PCR revolution: basic technologies and applications

    National Research Council Canada - National Science Library

    Bustin, Stephen A

    2010-01-01

    ... by leading authorities on the many applications of PCR and how this technology has revolutionized their respective areas of interest. This book conveys the ways in which PCR has overcome many obstacles in life science and clinical research and also charts the PCR's development from time-consuming, low throughput, nonquantitative proced...

  12. MicroRNA profiling in intraocular medulloepitheliomas.

    Directory of Open Access Journals (Sweden)

    Deepak P Edward

    Full Text Available To study the differential expression of microRNA (miRNA profiles between intraocular medulloepithelioma (ME and normal control tissue (CT.Total RNA was extracted from formalin fixed paraffin embedded (FFPE intraocular ME (n=7 and from age matched ciliary body controls (n=8. The clinical history and phenotype was recorded. MiRNA profiles were determined using the Affymetrix GeneChip miRNA Arrays analyzed using expression console 1.3 software. Validation of significantly dysregulated miRNA was confirmed by quantitative real-time PCR. The web-based DNA Intelligent Analysis (DIANA-miRPath v2.0 was used to perform enrichment analysis of differentially expressed (DE miRNA gene targets in Kyoto Encyclopedia of Genes and Genomes (KEGG pathway.The pathologic evaluation revealed one benign (benign non-teratoid, n=1 and six malignant tumors (malignant teratoid, n=2; malignant non-teratoid, n = 4. A total of 88 miRNAs were upregulated and 43 miRNAs were downregulated significantly (P<0.05 in the tumor specimens. Many of these significantly dysregulated miRNAs were known to play various roles in carcinogenesis and tumor behavior. RT-PCR validated three significantly upregulated miRNAs and three significantly downregulated miRNAs namely miR-217, miR-216a, miR-216b, miR-146a, miR-509-3p and miR-211. Many DE miRNAs that were significant in ME tumors showed dysregulation in retinoblastoma, glioblastoma, and precursor, normal and reactive human cartilage. Enriched pathway analysis suggested a significant association of upregulated miRNAs with 15 pathways involved in prion disease and several types of cancer. The pathways involving significantly downregulated miRNAs included the toll-like receptor (TLR (p<4.36E-16 and Nuclear Factor kappa B (NF-κB signaling pathways (p<9.00E-06.We report significantly dysregulated miRNAs in intraocular ME tumors, which exhibited abnormal profiles in other cancers as well such as retinoblastoma and glioblastoma. Pathway analysis

  13. MicroRNA expression profiling to identify and validate reference genes for relative quantification in colorectal cancer.

    LENUS (Irish Health Repository)

    Chang, Kah Hoong

    2010-01-01

    BACKGROUND: Advances in high-throughput technologies and bioinformatics have transformed gene expression profiling methodologies. The results of microarray experiments are often validated using reverse transcription quantitative PCR (RT-qPCR), which is the most sensitive and reproducible method to quantify gene expression. Appropriate normalisation of RT-qPCR data using stably expressed reference genes is critical to ensure accurate and reliable results. Mi(cro)RNA expression profiles have been shown to be more accurate in disease classification than mRNA expression profiles. However, few reports detailed a robust identification and validation strategy for suitable reference genes for normalisation in miRNA RT-qPCR studies. METHODS: We adopt and report a systematic approach to identify the most stable reference genes for miRNA expression studies by RT-qPCR in colorectal cancer (CRC). High-throughput miRNA profiling was performed on ten pairs of CRC and normal tissues. By using the mean expression value of all expressed miRNAs, we identified the most stable candidate reference genes for subsequent validation. As such the stability of a panel of miRNAs was examined on 35 tumour and 39 normal tissues. The effects of normalisers on the relative quantity of established oncogenic (miR-21 and miR-31) and tumour suppressor (miR-143 and miR-145) target miRNAs were assessed. RESULTS: In the array experiment, miR-26a, miR-345, miR-425 and miR-454 were identified as having expression profiles closest to the global mean. From a panel of six miRNAs (let-7a, miR-16, miR-26a, miR-345, miR-425 and miR-454) and two small nucleolar RNA genes (RNU48 and Z30), miR-16 and miR-345 were identified as the most stably expressed reference genes. The combined use of miR-16 and miR-345 to normalise expression data enabled detection of a significant dysregulation of all four target miRNAs between tumour and normal colorectal tissue. CONCLUSIONS: Our study demonstrates that the top six most

  14. MicroRNA expression profiling to identify and validate reference genes for relative quantification in colorectal cancer

    LENUS (Irish Health Repository)

    Chang, Kah Hoong

    2010-04-29

    Abstract Background Advances in high-throughput technologies and bioinformatics have transformed gene expression profiling methodologies. The results of microarray experiments are often validated using reverse transcription quantitative PCR (RT-qPCR), which is the most sensitive and reproducible method to quantify gene expression. Appropriate normalisation of RT-qPCR data using stably expressed reference genes is critical to ensure accurate and reliable results. Mi(cro)RNA expression profiles have been shown to be more accurate in disease classification than mRNA expression profiles. However, few reports detailed a robust identification and validation strategy for suitable reference genes for normalisation in miRNA RT-qPCR studies. Methods We adopt and report a systematic approach to identify the most stable reference genes for miRNA expression studies by RT-qPCR in colorectal cancer (CRC). High-throughput miRNA profiling was performed on ten pairs of CRC and normal tissues. By using the mean expression value of all expressed miRNAs, we identified the most stable candidate reference genes for subsequent validation. As such the stability of a panel of miRNAs was examined on 35 tumour and 39 normal tissues. The effects of normalisers on the relative quantity of established oncogenic (miR-21 and miR-31) and tumour suppressor (miR-143 and miR-145) target miRNAs were assessed. Results In the array experiment, miR-26a, miR-345, miR-425 and miR-454 were identified as having expression profiles closest to the global mean. From a panel of six miRNAs (let-7a, miR-16, miR-26a, miR-345, miR-425 and miR-454) and two small nucleolar RNA genes (RNU48 and Z30), miR-16 and miR-345 were identified as the most stably expressed reference genes. The combined use of miR-16 and miR-345 to normalise expression data enabled detection of a significant dysregulation of all four target miRNAs between tumour and normal colorectal tissue. Conclusions Our study demonstrates that the top six most

  15. Protein Functionalized Nanodiamond Arrays

    Directory of Open Access Journals (Sweden)

    Liu YL

    2010-01-01

    Full Text Available Abstract Various nanoscale elements are currently being explored for bio-applications, such as in bio-images, bio-detection, and bio-sensors. Among them, nanodiamonds possess remarkable features such as low bio-cytotoxicity, good optical property in fluorescent and Raman spectra, and good photostability for bio-applications. In this work, we devise techniques to position functionalized nanodiamonds on self-assembled monolayer (SAMs arrays adsorbed on silicon and ITO substrates surface using electron beam lithography techniques. The nanodiamond arrays were functionalized with lysozyme to target a certain biomolecule or protein specifically. The optical properties of the nanodiamond-protein complex arrays were characterized by a high throughput confocal microscope. The synthesized nanodiamond-lysozyme complex arrays were found to still retain their functionality in interacting with E. coli.

  16. Photonic Crystal Nanocavity Arrays

    National Research Council Canada - National Science Library

    Altug, Hatice; Vuckovic, Jelena

    2006-01-01

    We recently proposed two-dimensional coupled photonic crystal nanocavity arrays as a route to achieve a slow-group velocity of light in all crystal directions, thereby enabling numerous applications...

  17. Carbon nanotube array actuators

    International Nuclear Information System (INIS)

    Geier, S; Mahrholz, T; Wierach, P; Sinapius, M

    2013-01-01

    Experimental investigations of highly vertically aligned carbon nanotubes (CNTs), also known as CNT-arrays, are the main focus of this paper. The free strain as result of an active material behavior is analyzed via a novel experimental setup. Previous test experiences of papers made of randomly oriented CNTs, also called Bucky-papers, reveal comparably low free strain. The anisotropy of aligned CNTs promises better performance. Via synthesis techniques like chemical vapor deposition (CVD) or plasma enhanced CVD (PECVD), highly aligned arrays of multi-walled carbon nanotubes (MWCNTs) are synthesized. Two different types of CNT-arrays are analyzed, morphologically first, and optically tested for their active characteristics afterwards. One type of the analyzed arrays features tube lengths of 750–2000 μm with a large variety of diameters between 20 and 50 nm and a wave-like CNT-shape. The second type features a maximum, almost uniform, length of 12 μm and a constant diameter of 50 nm. Different CNT-lengths and array types are tested due to their active behavior. As result of the presented tests, it is reported that the quality of orientation is the most decisive property for excellent active behavior. Due to their alignment, CNT-arrays feature the opportunity to clarify the actuation mechanism of architectures made of CNTs. (paper)

  18. Metabolic profiling of nuciferine in rat urine, plasma, bile and feces after oral administration using ultra-high performance liquid chromatography-diode array detection-quadrupole time-of-flight mass spectrometry.

    Science.gov (United States)

    Wu, Xiao-Lei; Wu, Ming-Jiang; Chen, Xin-Ze; Ma, Hao-Ling; Ding, Li-Qin; Qiu, Feng; Pan, Qin; Zhang, De-Qin

    2017-06-05

    Nuciferine, a major alkaloid found in Nelumbinis Folium, exhibits a broad spectrum of bioactivities, such as antiobesity, anti-diabetes and anti-inflammatory. However, many research regarding nuciferine focused on the extraction, isolation and biological activity, the metabolism is not comprehensively explained in vivo. Thence, the present of this paper is to establish a simple method for speculating metabolites of nuciferine. A total of 15 metabolites were detected and tentatively identified through ultra high performance liquid chromatography-diode array detection-quadrupole time-of-flight mass spectrometry (UHPLC-DAD-QTOF-MS), including 7 new metabolites. Among them, we also discovered a previously unmentioned metabolically active site at the C 1 -OCH 3 position. These metabolites suggested that demethylation, oxidation, glucuronidation and sulfation were major metabolic pathways. This study provided significant experiment basis for its safety estimate and valuable information about the metabolism of nuciferine, which will be advantageous for new drug development. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Detection of adenoviruses in shellfish by means of conventional-PCR, nested-PCR, and integrated cell culture PCR (ICC/PCR).

    Science.gov (United States)

    Rigotto, C; Sincero, T C M; Simões, C M O; Barardi, C R M

    2005-01-01

    We tested three PCR based methodologies to detect adenoviruses associated with cultivated oysters. Conventional-PCR, nested-PCR, and integrated cell culture-PCR (ICC/PCR) were first optimized using oysters seeded with know amounts of Adenovirus serotype 5 (Ad5). The maximum sensitivity for Ad5 detection was determined for each method, and then used to detect natural adenovirus contamination in oysters from three aquiculture farms in Florianopolis, Santa Catarina State, Brazil, over a period of 6 months. The results showed that the nested-PCR was more sensitive (limit of detection: 1.2 PFU/g of tissue) than conventional-PCR and ICC-PCR (limit of detection for both: 1.2 x 10(2)PFU/g of tissue) for detection of Ad5 in oyster extracts. Nested-PCR was able to detect 90% of Ad5 contamination in harvested oyster samples, while conventional-PCR was unable to detect Ad5 in any of the samples. The present work suggests that detection of human adenoviruses can be used as a tool to monitor the presence of human viruses in marine environments where shellfish grow, and that nested-PCR is the method of choice.

  20. Analysis of Chemokines and Receptors Expression Profile in the Myelin Mutant Taiep Rat

    Directory of Open Access Journals (Sweden)

    Guadalupe Soto-Rodriguez

    2015-01-01

    Full Text Available Taiep rat has a failure in myelination and remyelination processes leading to a state of hypomyelination throughout its life. Chemokines, which are known to play a role in inflammation, are also involved in the remyelination process. We aimed to demonstrate that remyelination-stimulating factors are altered in the brainstem of 1- and 6-month-old taiep rats. We used a Rat RT2 Profiler PCR Array to assess mRNA expression of 84 genes coding for cytokines, chemokines, and their receptors. We also evaluated protein levels of CCL2, CCR1, CCR2, CCL5, CCR5, CCR8, CXCL1, CXCR2, CXCR4, FGF2, and VEGFA by ELISA. Sprague-Dawley rats were used as a control. PCR Array procedure showed that proinflammatory cytokines were not upregulated in the taiep rat. In contrast, some mRNA levels of beta and alpha chemokines were upregulated in 1-month-old rats, but CXCR4 was downregulated at their 6 months of age. ELISA results showed that CXCL1, CCL2, CCR2, CCR5, CCR8, and CXCR4 protein levels were decreased in brainstem at the age of 6 months. These results suggest the presence of a chronic neuroinflammation process with deficiency of remyelination-stimulating factors (CXCL1, CXCR2, and CXCR4, which might account for the demyelination in the taiep rat.

  1. [Gene Expression Profile of Apoptosis in Leukemia Cells Induced by Hsp90 Selective inhibitor 17-AAG].

    Science.gov (United States)

    Wang, Na-Na; Li, Zhi-Heng; Tao, Yan-Fang; Xu, Li-Xiao; Pan, Jian; Hu, Shao-Yan

    2016-06-01

    To investigate the apoptotic effects of Hsp90 selective inhibitor 17-AAG on human leukemia HL-60 and NB4 cells and analyse its possible mechanism. CCK-8 assay was used to quantify the growth inhibition of cells after exposure to 17-AAG for 24 hours. Flow cytometrve with annexin V/propidium iodide staining was used to detect apoptosis of leukemia cells. Then Western blot was used to detect the activation of apoptosis related protein caspase-3 and PARP level. Gene expression profile of NB4 cells treated with 17-AAG was analyzed with real-time PCR arrays. The inhibition of leukemia cell proliferation displayed a dose-dependent manner. Annexin V assay, cell cycle analysis and activation of PARP demonstrate that 17-AAG induced apoptosis leukemia cells. Real-time PCR array analysis showed that expression of 56 genes significantly up-regulated and expression of 23 genes were significantly down-regulated after 17-AAG treatment. The 17-AAG can inhibit the proliferation and induce the apoptosis of leukemia cells. After leukemia cells are treated with 17-AAG, the significant changes of apoptosis-related genes occured, and the cell apoptosis occurs via activating apoptosis related signaling pathway.

  2. Detecting Outlier Microarray Arrays by Correlation and Percentage of Outliers Spots

    Directory of Open Access Journals (Sweden)

    Song Yang

    2006-01-01

    Full Text Available We developed a quality assurance (QA tool, namely microarray outlier filter (MOF, and have applied it to our microarray datasets for the identification of problematic arrays. Our approach is based on the comparison of the arrays using the correlation coefficient and the number of outlier spots generated on each array to reveal outlier arrays. For a human universal reference (HUR dataset, which is used as a technical control in our standard hybridization procedure, 3 outlier arrays were identified out of 35 experiments. For a human blood dataset, 12 outlier arrays were identified from 185 experiments. In general, arrays from human blood samples displayed greater variation in their gene expression profiles than arrays from HUR samples. As a result, MOF identified two distinct patterns in the occurrence of outlier arrays. These results demonstrate that this methodology is a valuable QA practice to identify questionable microarray data prior to downstream analysis.

  3. Human minisatellite alleles detectable only after PCR amplification.

    Science.gov (United States)

    Armour, J A; Crosier, M; Jeffreys, A J

    1992-01-01

    We present evidence that a proportion of alleles at two human minisatellite loci is undetected by standard Southern blot hybridization. In each case the missing allele(s) can be identified after PCR amplification and correspond to tandem arrays too short to detect by hybridization. At one locus, there is only one undetected allele (population frequency 0.3), which contains just three repeat units. At the second locus, there are at least five undetected alleles (total population frequency 0.9) containing 60-120 repeats; they are not detected because these tandem repeats give very poor signals when used as a probe in standard Southern blot hybridization, and also cross-hybridize with other sequences in the genome. Under these circumstances only signals from the longest tandemly repeated alleles are detectable above the nonspecific background. The structures of these loci have been compared in human and primate DNA, and at one locus the short human allele containing three repeat units is shown to be an intermediate state in the expansion of a monomeric precursor allele in primates to high copy number in the longer human arrays. We discuss the implications of such loci for studies of human populations, minisatellite isolation by cloning, and the evolution of highly variable tandem arrays.

  4. Technical aspects and recommendations for single-cell qPCR.

    Science.gov (United States)

    Ståhlberg, Anders; Kubista, Mikael

    2018-02-01

    Single cells are basic physiological and biological units that can function individually as well as in groups in tissues and organs. It is central to identify, characterize and profile single cells at molecular level to be able to distinguish different kinds, to understand their functions and determine how they interact with each other. During the last decade several technologies for single-cell profiling have been developed and used in various applications, revealing many novel findings. Quantitative PCR (qPCR) is one of the most developed methods for single-cell profiling that can be used to interrogate several analytes, including DNA, RNA and protein. Single-cell qPCR has the potential to become routine methodology but the technique is still challenging, as it involves several experimental steps and few molecules are handled. Here, we discuss technical aspects and provide recommendation for single-cell qPCR analysis. The workflow includes experimental design, sample preparation, single-cell collection, direct lysis, reverse transcription, preamplification, qPCR and data analysis. Detailed reporting and sharing of experimental details and data will promote further development and make validation studies possible. Efforts aiming to standardize single-cell qPCR open up means to move single-cell analysis from specialized research settings to standard research laboratories. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Suitability of PCR fingerprinting, infrequent-restriction-site PCR, and pulsed-field gel electrophoresis, combined with computerized gel analysis, in library typing of Salmonella enterica serovar enteritidis

    DEFF Research Database (Denmark)

    Garaizar, J.; Lopez-Molina, N.; Laconcha, I.

    2000-01-01

    Strains of Salmonella enterica (n = 212) of different serovars and phage types were used to establish a library typing computerized system for serovar Enteritidis on the basis of PCR fingerprinting, infrequent-restriction-site PCR (IRS-PCR), or pulsed-field gel electrophoresis (PFGE). The rate...... showed an intercenter reproducibility value of 93.3%. The high reproducibility of PFGE combined with the previously determined high discrimination directed its use for library typing. The use of PFGE with enzymes XbaI, BlnI, and SpeI for library typing of serovar Enteritidis was assessed with GelCompar 4.......0 software, Three computer libraries of PFGE DNA profiles were constructed, and their ability to recognize new DNA profiles was analyzed. The results obtained pointed out that the combination of PFGE with computerized analysis could be suitable in long-term epidemiological comparison and surveillance...

  6. See Also:Mechanics of Cohesive-frictional MaterialsCopyright © 2004 John Wiley & Sons, Ltd.Get Sample CopyFree Online Trial -->Recommend to Your LibrarianSave Title to My ProfileSet E-Mail Alert var homepagelinks = new Array(new Array("Journal Home","/cgi-bin/jhome/3312",""),new Array("Issues","/cgi-bin/jtoc/3312/",""),new Array("Early View","/cgi-bin/jeview/3312/",""),new Array("News","/cgi-bin/jabout/3312/News.html","e"),new Array("","","s"),new Array("Product Information","/cgi-bin/jabout/3312/ProductInformation.html",""),new Array("Editorial Board","/cgi-bin/jabout/3312/EditorialBoard.html",""),new Array("For Authors","/cgi-bin/jabout/3312/ForAuthors.html",""),new Array("Subscribe","http://jws-edcv.wiley.com/jcatalog/JournalsCatalogOrder/JournalOrder?PRINT_ISSN=0363-9061",""),new Array("Advertise","/cgi-bin/jabout/3312/Advertise.html",""),new Array("Contact","/cgi-bin/jabout/3312/Contact.html",""),new Array("","","x"));writeJournalLinks("", "3312"); Previous Issue | Next Issue >Volume 29, Issue1 (January 2005)Articles in the Current Issue:Research ArticleHomogenization framework for three-dimensional elastoplastic finite element analysis of a grouted pipe-roofing reinforcement method for tunnelling

    Science.gov (United States)

    Bae, G. J.; Shin, H. S.; Sicilia, C.; Choi, Y. G.; Lim, J. J.

    2005-01-01

    This paper deals with the grouted pipe-roofing reinforcement method that is used in the construction of tunnels through weak grounds. This system consists on installing, prior to the excavation of a length of tunnel, an array of pipes forming a kind of umbrella above the area to be excavated. In some cases, these pipes are later used to inject grout to strengthen the ground and connect the pipes.This system has proven to be very efficient in reducing tunnel convergence and water inflow when tunnelling through weak grounds. However, due to the geometrical and mechanical complexity of the problem, existing finite element frameworks are inappropriate to simulate tunnelling using this method.In this paper, a mathematical framework based on a homogenization technique to simulate grouted pipe-roofing reinforced ground and its implementation into a 3-D finite element programme that can consider stage construction situations are presented. The constitutive model developed allows considering the main design parameters of the problem and only requires geometrical and mechanical properties of the constituents. Additionally, the use of a homogenization approach implies that the generation of the finite element mesh can be easily produced and that re-meshing is not required as basic geometrical parameters such as the orientation of the pipes are changed.The model developed is used to simulate tunnelling with the grouted pipe-roofing reinforcement method. From the analyses, the effects of the main design parameters on the elastic and the elastoplastic analyses are considered. Copyright

  7. Testing of focal plane arrays

    International Nuclear Information System (INIS)

    Merriam, J.D.

    1988-01-01

    Problems associated with the testing of focal plane arrays are briefly examined with reference to the instrumentation and measurement procedures. In particular, the approach and instrumentation used as the Naval Ocean Systems Center is presented. Most of the measurements are made with flooded illumination on the focal plane array. The array is treated as an ensemble of individual pixels, data being taken on each pixel and array averages and standard deviations computed for the entire array. Data maps are generated, showing the pixel data in the proper spatial position on the array and the array statistics

  8. Detection of growth hormone doping by gene expression profiling of peripheral blood.

    Science.gov (United States)

    Mitchell, Christopher J; Nelson, Anne E; Cowley, Mark J; Kaplan, Warren; Stone, Glenn; Sutton, Selina K; Lau, Amie; Lee, Carol M Y; Ho, Ken K Y

    2009-12-01

    GH abuse is a significant problem in many sports, and there is currently no robust test that allows detection of doping beyond a short window after administration. Our objective was to evaluate gene expression profiling in peripheral blood leukocytes in-vivo as a test for GH doping in humans. Seven men and thirteen women were administered GH, 2 mg/d sc for 8 wk. Blood was collected at baseline and at 8 wk. RNA was extracted from the white cell fraction. Microarray analysis was undertaken using Agilent 44K G4112F arrays using a two-color design. Quantitative RT-PCR using TaqMan gene expression assays was performed for validation of selected differentially expressed genes. GH induced an approximately 2-fold increase in circulating IGF-I that was maintained throughout the 8 wk of the study. GH induced significant changes in gene expression with 353 in women and 41 in men detected with a false discovery rate of less than 5%. None of the differentially expressed genes were common between men and women. The maximal changes were a doubling for up-regulated or halving for down-regulated genes, similar in magnitude to the variation between individuals. Quantitative RT-PCR for seven target genes showed good concordance between microarray and quantitative PCR data in women but not in men. Gene expression analysis of peripheral blood leukocytes is unlikely to be a viable approach for the detection of GH doping.

  9. Application of reverse transcription-PCR and real-time PCR in nanotoxicity research.

    Science.gov (United States)

    Mo, Yiqun; Wan, Rong; Zhang, Qunwei

    2012-01-01

    Reverse transcription-polymerase chain reaction (RT-PCR) is a relatively simple and inexpensive technique to determine the expression level of target genes and is widely used in biomedical science research including nanotoxicology studies for semiquantitative analysis. Real-time PCR allows for the detection of PCR amplification in the exponential growth phase of the reaction and is much more quantitative than traditional RT-PCR. Although a number of kits and reagents for RT-PCR and real-time PCR are commercially available, the basic principles are the same. Here, we describe the procedures for total RNA isolation by using TRI Reagent, for reverse transcription (RT) by M-MLV reverse transcriptase, and for PCR by GoTaq(®) DNA Polymerase. And real-time PCR will be performed on an iQ5 multicolor real-time PCR detection system by using iQ™ SYBR Green Supermix.

  10. Wire Array Photovoltaics

    Science.gov (United States)

    Turner-Evans, Dan

    Over the past five years, the cost of solar panels has dropped drastically and, in concert, the number of installed modules has risen exponentially. However, solar electricity is still more than twice as expensive as electricity from a natural gas plant. Fortunately, wire array solar cells have emerged as a promising technology for further lowering the cost of solar. Si wire array solar cells are formed with a unique, low cost growth method and use 100 times less material than conventional Si cells. The wires can be embedded in a transparent, flexible polymer to create a free-standing array that can be rolled up for easy installation in a variety of form factors. Furthermore, by incorporating multijunctions into the wire morphology, higher efficiencies can be achieved while taking advantage of the unique defect relaxation pathways afforded by the 3D wire geometry. The work in this thesis shepherded Si wires from undoped arrays to flexible, functional large area devices and laid the groundwork for multijunction wire array cells. Fabrication techniques were developed to turn intrinsic Si wires into full p-n junctions and the wires were passivated with a-Si:H and a-SiNx:H. Single wire devices yielded open circuit voltages of 600 mV and efficiencies of 9%. The arrays were then embedded in a polymer and contacted with a transparent, flexible, Ni nanoparticle and Ag nanowire top contact. The contact connected >99% of the wires in parallel and yielded flexible, substrate free solar cells featuring hundreds of thousands of wires. Building on the success of the Si wire arrays, GaP was epitaxially grown on the material to create heterostructures for photoelectrochemistry. These cells were limited by low absorption in the GaP due to its indirect bandgap, and poor current collection due to a diffusion length of only 80 nm. However, GaAsP on SiGe offers a superior combination of materials, and wire architectures based on these semiconductors were investigated for multijunction

  11. Pitfalls in PCR troubleshooting: Expect the unexpected?

    Directory of Open Access Journals (Sweden)

    Livia Schrick

    2016-01-01

    Full Text Available PCR is a well-understood and established laboratory technique often used in molecular diagnostics. Huge experience has been accumulated over the last years regarding the design of PCR assays and their set-up, including in-depth troubleshooting to obtain the optimal PCR assay for each purpose. Here we report a PCR troubleshooting that came up with a surprising result never observed before. With this report we hope to sensitize the reader to this peculiar problem and to save troubleshooting efforts in similar situations, especially in time-critical and ambitious diagnostic settings.

  12. Absolute quantification by droplet digital PCR versus analog real-time PCR

    Science.gov (United States)

    Hindson, Christopher M; Chevillet, John R; Briggs, Hilary A; Gallichotte, Emily N; Ruf, Ingrid K; Hindson, Benjamin J; Vessella, Robert L; Tewari, Muneesh

    2014-01-01

    Nanoliter-sized droplet technology paired with digital PCR (ddPCR) holds promise for highly precise, absolute nucleic acid quantification. Our comparison of microRNA quantification by ddPCR and real-time PCR revealed greater precision (coefficients of variation decreased by 37–86%) and improved day-to-day reproducibility (by a factor of seven) of ddPCR but with comparable sensitivity. When we applied ddPCR to serum microRNA biomarker analysis, this translated to superior diagnostic performance for identifying individuals with cancer. PMID:23995387

  13. Expression profile of immune response genes in patients with Severe Acute Respiratory Syndrome

    Directory of Open Access Journals (Sweden)

    Tai Dessmon

    2005-01-01

    Full Text Available Abstract Background Severe acute respiratory syndrome (SARS emerged in later February 2003, as a new epidemic form of life-threatening infection caused by a novel coronavirus. However, the immune-pathogenesis of SARS is poorly understood. To understand the host response to this pathogen, we investigated the gene expression profiles of peripheral blood mononuclear cells (PBMCs derived from SARS patients, and compared with healthy controls. Results The number of differentially expressed genes was found to be 186 under stringent filtering criteria of microarray data analysis. Several genes were highly up-regulated in patients with SARS, such as, the genes coding for Lactoferrin, S100A9 and Lipocalin 2. The real-time PCR method verified the results of the gene array analysis and showed that those genes that were up-regulated as determined by microarray analysis were also found to be comparatively up-regulated by real-time PCR analysis. Conclusions This differential gene expression profiling of PBMCs from patients with SARS strongly suggests that the response of SARS affected patients seems to be mainly an innate inflammatory response, rather than a specific immune response against a viral infection, as we observed a complete lack of cytokine genes usually triggered during a viral infection. Our study shows for the first time how the immune system responds to the SARS infection, and opens new possibilities for designing new diagnostics and treatments for this new life-threatening disease.

  14. A review of array radars

    Science.gov (United States)

    Brookner, E.

    1981-10-01

    Achievements in the area of array radars are illustrated by such activities as the operational deployment of the large high-power, high-range-resolution Cobra Dane; the operational deployment of two all-solid-state high-power, large UHF Pave Paws radars; and the development of the SAM multifunction Patriot radar. This paper reviews the following topics: array radars steered in azimuth and elevation by phase shifting (phase-phase steered arrays); arrays steered + or - 60 deg, limited scan arrays, hemispherical coverage, and omnidirectional coverage arrays; array radars steering electronically in only one dimension, either by frequency or by phase steering; and array radar antennas which use no electronic scanning but instead use array antennas for achieving low antenna sidelobes.

  15. Ultra-high performance liquid chromatography coupled with photo-diode array and quadrupole/time-of-flight mass spectrometry based chemical profiling approach to evaluate the influence of preparation methods on the holistic quality of Qiong-Yu-Gao, a traditional complex herbal medicine.

    Science.gov (United States)

    Xu, Jin-Di; Mao, Qian; Shen, Hong; Zhu, Ling-Ying; Li, Song-Lin; Yan, Ru

    2013-08-23

    Qiong-Yu-Gao (QYG), consisting of Rehmanniae Radix (RR), Poriae (PO) and Ginseng Radix (GR), is a commonly used tonic traditional complex herbal medicine (CHM). So far, three different methods have been documented for preparation of QYG, i.e. method 1 (M1): mixing powders of GR and PO with decoction of RR; method 2 (M2): combining the decoction of RR and PO with the decoction of GR; method 3 (M3): decocting the mixture of RR, GR and PO. In present study, an ultra-high performance liquid chromatography coupled with photo-diode array and quadrupole/time-of-flight mass spectrometry (UHPLC-PDA-QTOF-MS/MS) based chemical profiling approach was developed to investigate the influence of the three preparation methods on the holistic quality of QYG. All detected peaks were unambiguously identified by comparing UV spectra, accurate mass data/characteristic mass fragments and retention times with those of reference compounds, and/or tentatively assigned by matching empirical molecular formula with that of known compounds, and/or elucidating quasi-molecular ions and fragment ions referring to information available in literature. A total of 103 components, mainly belonging to ginsenosides, phenethylalcohol glycosides, iridoid glycosides and triterpenoid acids, were identified, of which 5 degraded ginsenosides were putatively determined to be newly generated during preparation procedures of QYG samples. Triterpenoid acids and malonyl-ginsenosides were detected only in M1 samples, while degraded ginsenosides were merely detectable in M2/M3 samples. The possible reasons for the difference among chemical profiles of QYG samples prepared with three methods were also discussed. It could be concluded that preparation method do significantly affect the holistic quality of QYG. The influence of the altered chemical profiles on the bioactivity of QYG needs further investigation. The present study demonstrated that UHPLC-PDA-QTOF-MS/MS based chemical profiling approach is efficient and

  16. Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology.

    Science.gov (United States)

    Smith, Cindy J; Osborn, A Mark

    2009-01-01

    Quantitative PCR (Q-PCR or real-time PCR) approaches are now widely applied in microbial ecology to quantify the abundance and expression of taxonomic and functional gene markers within the environment. Q-PCR-based analyses combine 'traditional' end-point detection PCR with fluorescent detection technologies to record the accumulation of amplicons in 'real time' during each cycle of the PCR amplification. By detection of amplicons during the early exponential phase of the PCR, this enables the quantification of gene (or transcript) numbers when these are proportional to the starting template concentration. When Q-PCR is coupled with a preceding reverse transcription reaction, it can be used to quantify gene expression (RT-Q-PCR). This review firstly addresses the theoretical and practical implementation of Q-PCR and RT-Q-PCR protocols in microbial ecology, highlighting key experimental considerations. Secondly, we review the applications of (RT)-Q-PCR analyses in environmental microbiology and evaluate the contribution and advances gained from such approaches. Finally, we conclude by offering future perspectives on the application of (RT)-Q-PCR in furthering understanding in microbial ecology, in particular, when coupled with other molecular approaches and more traditional investigations of environmental systems.

  17. Detector array and method

    International Nuclear Information System (INIS)

    Timothy, J.G.; Bybee, R.L.

    1978-01-01

    A detector array and method are described in which sets of electrode elements are provided. Each set consists of a number of linear extending parallel electrodes. The sets of electrode elements are disposed at an angle (preferably orthogonal) with respect to one another so that the individual elements intersect and overlap individual elements of the other sets. Electrical insulation is provided between the overlapping elements. The detector array is exposed to a source of charged particles which in accordance with one embodiment comprise electrons derived from a microchannel array plate exposed to photons. Amplifier and discriminator means are provided for each individual electrode element. Detection means are provided to sense pulses on individual electrode elements in the sets, with coincidence of pulses on individual intersecting electrode elements being indicative of charged particle impact at the intersection of the elements. Electronic readout means provide an indication of coincident events and the location where the charged particle or particles impacted. Display means are provided for generating appropriate displays representative of the intensity and locaton of charged particles impacting on the detector array

  18. Diode lasers and arrays

    International Nuclear Information System (INIS)

    Streifer, W.

    1988-01-01

    This paper discusses the principles of operation of III-V semiconductor diode lasers, the use of distributed feedback, and high power laser arrays. The semiconductor laser is a robust, miniature, versatile device, which directly converts electricity to light with very high efficiency. Applications to pumping solid-state lasers and to fiber optic and point-to-point communications are reviewed

  19. Array Theory and Nial

    DEFF Research Database (Denmark)

    Falster, Peter; Jenkins, Michael

    1999-01-01

    This report is the result of collaboration between the authors during the first 8 months of 1999 when M. Jenkins was visiting professor at DTU. The report documents the development of a tool for the investigation of array theory concepts and in particular presents various approaches to choose...

  20. Piezoelectric transducer array microspeaker

    KAUST Repository

    Carreno, Armando Arpys Arevalo; Conchouso Gonzalez, David; Castro, David; Kosel, Jü rgen; Foulds, Ian G.

    2016-01-01

    contains 2n piezoelectric transducer membranes, where “n” is the bit number. Every element of the array has a circular shape structure. The membrane is made out four layers: 300nm of platinum for the bottom electrode, 250nm or lead zirconate titanate (PZT

  1. Calibration strategies for the Cherenkov Telescope Array

    Science.gov (United States)

    Gaug, Markus; Berge, David; Daniel, Michael; Doro, Michele; Förster, Andreas; Hofmann, Werner; Maccarone, Maria C.; Parsons, Dan; de los Reyes Lopez, Raquel; van Eldik, Christopher

    2014-08-01

    The Central Calibration Facilities workpackage of the Cherenkov Telescope Array (CTA) observatory for very high energy gamma ray astronomy defines the overall calibration strategy of the array, develops dedicated hardware and software for the overall array calibration and coordinates the calibration efforts of the different telescopes. The latter include LED-based light pulsers, and various methods and instruments to achieve a calibration of the overall optical throughput. On the array level, methods for the inter-telescope calibration and the absolute calibration of the entire observatory are being developed. Additionally, the atmosphere above the telescopes, used as a calorimeter, will be monitored constantly with state-of-the-art instruments to obtain a full molecular and aerosol profile up to the stratosphere. The aim is to provide a maximal uncertainty of 10% on the reconstructed energy-scale, obtained through various independent methods. Different types of LIDAR in combination with all-sky-cameras will provide the observatory with an online, intelligent scheduling system, which, if the sky is partially covered by clouds, gives preference to sources observable under good atmospheric conditions. Wide-field optical telescopes and Raman Lidars will provide online information about the height-resolved atmospheric extinction, throughout the field-of-view of the cameras, allowing for the correction of the reconstructed energy of each gamma-ray event. The aim is to maximize the duty cycle of the observatory, in terms of usable data, while reducing the dead time introduced by calibration activities to an absolute minimum.

  2. Data Profiling

    OpenAIRE

    Hladíková, Radka

    2010-01-01

    Title: Data Profiling Author: Radka Hladíková Department: Department of Software Engineering Supervisor: Ing. Vladimír Kyjonka Supervisor's e-mail address: Abstract: This thesis puts mind on problems with data quality and data profiling. This Work analyses and summarizes problems of data quality, data defects, process of data quality, data quality assessment and data profiling. The main topic is data profiling as a process of researching data available in existing...

  3. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

    reaction (PCR), oligo hybridization and DNA sequencing. Proper primer design is actually one of the most important factors/steps in successful DNA sequencing. Various bioinformatics programs are available for selection of primer pairs from a template sequence. The plethora programs for PCR primer design reflects the.

  4. [E-MTAB-587] PCR_artifacts

    NARCIS (Netherlands)

    Muino Acuna, J.M.

    2011-01-01

    WARNING: This library was yield low amount of material and it was over-amplified by PCR. This libraries are used study the robustness of several statitical methods against PCR artifacts. ChIP experiments were performed on Arabidopsis wildtype inflorescences using an antibody raised against a

  5. Digital PCR for detection of citrus pathogens

    Science.gov (United States)

    Citrus trees are often infected with multiple pathogens of economic importance, especially those with insect or mite vectors. Real-time/quantitative PCR (qPCR) has been used for high-throughput detection and relative quantification of pathogens; however, target reference or standards are required. I...

  6. Testing for Genetically Modified Foods Using PCR

    Science.gov (United States)

    Taylor, Ann; Sajan, Samin

    2005-01-01

    The polymerase chain reaction (PCR) is a Nobel Prize-winning technique that amplifies a specific segment of DNA and is commonly used to test for the presence of genetic modifications. Students use PCR to test corn meal and corn-muffin mixes for the presence of a promoter commonly used in genetically modified foods, the cauliflower mosaic virus 35S…

  7. Validation of RNAi by real time PCR

    DEFF Research Database (Denmark)

    Josefsen, Knud; Lee, Ying Chiu

    2011-01-01

    Real time PCR is the analytic tool of choice for quantification of gene expression, while RNAi is concerned with downregulation of gene expression. Together, they constitute a powerful approach in any loss of function studies of selective genes. We illustrate here the use of real time PCR to verify...

  8. PCR specific for Actinobacillus pleuropneumoniae serotype 3

    DEFF Research Database (Denmark)

    Zhou, L.; Jones, S.C.P.; Angen, Øystein

    2008-01-01

    , but the method has liminations, for example, cross-reactions between serotypes 3, 6, and 8. This study describes the development of a serotype 3-specific PCR, based on the capsule locus, which can be used in a multiplex format with the organism's specific gene apxIV. The PCR test was evaluated on 266 strains...

  9. Force sensitive carbon nanotube arrays for biologically inspired airflow sensing

    International Nuclear Information System (INIS)

    Maschmann, Matthew R; Ehlert, Gregory J; Baur, Jeffery W; Dickinson, Ben

    2012-01-01

    The compressive electromechanical response of aligned carbon nanotube (CNT) arrays is evaluated for use as an artificial hair sensor (AHS) transduction element. CNT arrays with heights of 12, 75, and 225 µm are examined. The quasi-static and dynamic sensitivity to force, response time, and signal drift are examined within the range of applied stresses predicted by a mechanical model applicable to the conceptual CNT array-based AHS (0–1 kPa). Each array is highly sensitive to compressive loading, with a maximum observed gauge factor of 114. The arrays demonstrate a repeatable response to dynamic cycling after a break-in period of approximately 50 cycles. Utilizing a four-wire measurement electrode configuration, the change in contact resistance between the array and the electrodes is observed to dominate the electromechanical response of the arrays. The response time of the CNT arrays is of the order of 10 ms. When the arrays are subjected to constant stress, mechanical creep is observed that results in a signal drift that generally diminishes the responsiveness of the arrays, particularly at stress approaching 1 kPa. The results of this study serve as a preliminary proof of concept for utilizing CNT arrays as a transduction mechanism for a proposed artificial hair sensor. Such a low profile and light-weight flow sensor is expected to have application in a number of applications including navigation and state awareness of small air vehicles, similar in function to natural hair cell receptors utilized by insects and bats. (paper)

  10. Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays

    DEFF Research Database (Denmark)

    Nielsen, Henrik Bjørn; Knudsen, Steen

    2002-01-01

    PROBEWIZ designs PCR primers for amplifying probes for cDNA arrays. The probes are designed to have minimal homology to other expressed sequences from a given organism. The primer selection is based on user-defined penalties for homology, primer quality, and proximity to the 3' end.......PROBEWIZ designs PCR primers for amplifying probes for cDNA arrays. The probes are designed to have minimal homology to other expressed sequences from a given organism. The primer selection is based on user-defined penalties for homology, primer quality, and proximity to the 3' end....

  11. Polymerase chain reaction methods (PCR in agrobiotechnology

    Directory of Open Access Journals (Sweden)

    Taški-Ajduković Ksenija

    2006-01-01

    Full Text Available The agricultural biotechnology applies polymerase chain reaction (PCR technology at numerous steps throughout product development. The major uses of PCR technology during product development include gene discovery and cloning, vector construction, transformant identification, screening and characterization as well as seed quality control. Commodity and food companies as well as testing laboratories rely on PCR technology to verify the presence or absence of genetically modification (GM in a product or to quantify the amount of GM material present in the product. This article describes the fundamental elements of PCR analysis and its application to the testing of grains and highlights some of areas to which attention must be paid in order to produce reliable test results. The article also discuses issues related to the analysis of different matrixes and the effect they may have on the accuracy of the PCR analytical results.

  12. Cymbal and BB underwater transducers and arrays

    Energy Technology Data Exchange (ETDEWEB)

    Newnham, R.E.; Zhang, J.; Alkoy, S.; Meyer, R.; Hughes, W.J.; Hladky-Hennion, A.C.; Cochran, J.; Markley, D. [Materials Research Laboratory, Penn State University, University Park, PA 16802 (United States)

    2002-09-01

    The cymbal is a miniaturized class V flextensional transducer that was developed for use as a shallow water sound projector and receiver. Single elements are characterized by high Q, low efficiency, and medium power output capability. Its low cost and thin profile allow the transducer to be assembled into large flexible arrays. Efforts were made to model both single elements and arrays using the ATILA code and the integral equation formulation (EQI).Millimeter size microprobe hydrophones (BBs) have been designed and fabricated from miniature piezoelectric hollow ceramic spheres for underwater applications such as mapping acoustic fields of projectors, and flow noise sensors for complex underwater structures. Green spheres are prepared from soft lead zirconate titanate powders using a coaxial nozzle slurry process. A compact hydrophone with a radially-poled sphere is investigated using inside and outside electrodes. Characterization of these hydrophones is done through measurement of hydrostatic piezoelectric charge coefficients, free field voltage sensitivities and directivity beam patterns. (orig.)

  13. Real-time PCR in virology.

    Science.gov (United States)

    Mackay, Ian M; Arden, Katherine E; Nitsche, Andreas

    2002-03-15

    The use of the polymerase chain reaction (PCR) in molecular diagnostics has increased to the point where it is now accepted as the gold standard for detecting nucleic acids from a number of origins and it has become an essential tool in the research laboratory. Real-time PCR has engendered wider acceptance of the PCR due to its improved rapidity, sensitivity, reproducibility and the reduced risk of carry-over contamination. There are currently five main chemistries used for the detection of PCR product during real-time PCR. These are the DNA binding fluorophores, the 5' endonuclease, adjacent linear and hairpin oligoprobes and the self-fluorescing amplicons, which are described in detail. We also discuss factors that have restricted the development of multiplex real-time PCR as well as the role of real-time PCR in quantitating nucleic acids. Both amplification hardware and the fluorogenic detection chemistries have evolved rapidly as the understanding of real-time PCR has developed and this review aims to update the scientist on the current state of the art. We describe the background, advantages and limitations of real-time PCR and we review the literature as it applies to virus detection in the routine and research laboratory in order to focus on one of the many areas in which the application of real-time PCR has provided significant methodological benefits and improved patient outcomes. However, the technology discussed has been applied to other areas of microbiology as well as studies of gene expression and genetic disease.

  14. Trypanosoma rangeli: RAPD-PCR and LSSP-PCR analyses of isolates from southeast Brazil and Colombia and their relation with KPI minicircles.

    Science.gov (United States)

    Marquez, D S; Ramírez, L E; Moreno, J; Pedrosa, A L; Lages-Silva, E

    2007-09-01

    This study presents the first genetic characterization of five Trypanosoma rangeli isolates from Minas Gerais, in the southeast of Brazil and their comparison with Colombian populations by minicircle classification, RAPD-PCR and LSSP-PCR analyses. Our results demonstrated a homogenous T. rangeli population circulating among Didelphis albiventris as reservoir host in Brazil while heterogeneous populations were found in different regions of Colombia. KP1(+) minicircles were found in 100% isolates from Brazil and in 36.4% of the Colombian samples, whereas the KP2 and KP3 minicircles were detected in both groups. RAPD-PCR and LSSP-PCR profiles revealed a polymorphism within KP1(+) and KP1(-) T. rangeli populations and allowed the division of T. rangeli in two branches. The Brazilian KP1(+) isolates were more homogenous than the KP1(+) isolates from Colombia. The RAPD-PCR were entirely consistent with the distribution of KP1 minicircles while those obtained by LSSP-PCR were associated in 88.9% and 71.4% with KP1(+) and KP1(-) populations, respectively.

  15. Chemical profiling approach to evaluate the influence of traditional and simplified decoction methods on the holistic quality of Da-Huang-Xiao-Shi decoction using high-performance liquid chromatography coupled with diode-array detection and time-of-flight mass spectrometry.

    Science.gov (United States)

    Yan, Xuemei; Zhang, Qianying; Feng, Fang

    2016-04-01

    Da-Huang-Xiao-Shi decoction, consisting of Rheum officinale Baill, Mirabilitum, Phellodendron amurense Rupr. and Gardenia jasminoides Ellis, is a traditional Chinese medicine used for the treatment of jaundice. As described in "Jin Kui Yao Lue", a traditional multistep decoction of Da-Huang-Xiao-Shi decoction was required while simplified one-step decoction was used in recent repsorts. To investigate the chemical difference between the decoctions obtained by the traditional and simplified preparations, a sensitive and reliable approach of high-performance liquid chromatography coupled with diode-array detection and electrospray ionization time-of-flight mass spectrometry was established. As a result, a total of 105 compounds were detected and identified. Analysis of the chromatogram profiles of the two decoctions showed that many compounds in the decoction of simplified preparation had changed obviously compared with those in traditional preparation. The changes of constituents would be bound to cause the differences in the therapeutic effects of the two decoctions. The present study demonstrated that certain preparation methods significantly affect the holistic quality of traditional Chinese medicines and the use of a suitable preparation method is crucial for these medicines to produce special clinical curative effect. This research results elucidated the scientific basis of traditional preparation methods in Chinese medicines. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Concurrent array-based queue

    Science.gov (United States)

    Heidelberger, Philip; Steinmacher-Burow, Burkhard

    2015-01-06

    According to one embodiment, a method for implementing an array-based queue in memory of a memory system that includes a controller includes configuring, in the memory, metadata of the array-based queue. The configuring comprises defining, in metadata, an array start location in the memory for the array-based queue, defining, in the metadata, an array size for the array-based queue, defining, in the metadata, a queue top for the array-based queue and defining, in the metadata, a queue bottom for the array-based queue. The method also includes the controller serving a request for an operation on the queue, the request providing the location in the memory of the metadata of the queue.

  17. Fast detection of deletion breakpoints using quantitative PCR

    Directory of Open Access Journals (Sweden)

    Gulshara Abildinova

    2016-01-01

    Full Text Available Abstract The routine detection of large and medium copy number variants (CNVs is well established. Hemizygotic deletions or duplications in the large Duchenne muscular dystrophy DMD gene responsible for Duchenne and Becker muscular dystrophies are routinely identified using multiple ligation probe amplification and array-based comparative genomic hybridization. These methods only map deleted or duplicated exons, without providing the exact location of breakpoints. Commonly used methods for the detection of CNV breakpoints include long-range PCR and primer walking, their success being limited by the deletion size, GC content and presence of DNA repeats. Here, we present a strategy for detecting the breakpoints of medium and large CNVs regardless of their size. The hemizygous deletion of exons 45-50 in the DMD gene and the large autosomal heterozygous PARK2 deletion were used to demonstrate the workflow that relies on real-time quantitative PCR to narrow down the deletion region and Sanger sequencing for breakpoint confirmation. The strategy is fast, reliable and cost-efficient, making it amenable to widespread use in genetic laboratories.

  18. Radar techniques using array antennas

    CERN Document Server

    Wirth, Wulf-Dieter

    2013-01-01

    Radar Techniques Using Array Antennas is a thorough introduction to the possibilities of radar technology based on electronic steerable and active array antennas. Topics covered include array signal processing, array calibration, adaptive digital beamforming, adaptive monopulse, superresolution, pulse compression, sequential detection, target detection with long pulse series, space-time adaptive processing (STAP), moving target detection using synthetic aperture radar (SAR), target imaging, energy management and system parameter relations. The discussed methods are confirmed by simulation stud

  19. Enhancing transformer dynamic rating through grid application of photovoltaic arrays

    International Nuclear Information System (INIS)

    El-Gasseir, M.M.; Sayer, M.A.; Alteneder, K.P.; McCulla, G.A.; Bigger, J.

    1993-01-01

    This paper demonstrates that exact matching between the substation's peak-day load profile and the profile of coincident net output generation of the PV array is unjustifiable and will unduly lead to overlooking many investment deferment opportunities that would otherwise be major components of high value applications of PV arrays. Further, the paper shows how and to what extent the load matchability requirement could be relaxed. Because of the thermal inertia of transformers, the output of an adequately sized and located photovoltaic array can both delay and reduce transformer temperature rise even in cases where load peak occurs after sunset. The time lag due to thermal inertia and ambient temperature decline allow overloading of the transformer beyond its normal rating without significant loss of life. Simulations depicting the interplay between PV array capacity, ambient temperature, transformer size, oil and winding temperature rise, peak load magnitude, load profile and loss of life, have been conducted. Tradeoffs between PV array capacity and transformer over-rating gains have been assessed. The impacts of PV generation on the over-rating potential of an actual 22.4-MVA bank transformer of a Salt River Project (SRP) distribution substation in Phoenix, Arizona were evaluated

  20. Complementary techniques: validation of gene expression data by quantitative real time PCR.

    Science.gov (United States)

    Provenzano, Maurizio; Mocellin, Simone

    2007-01-01

    Microarray technology can be considered the most powerful tool for screening gene expression profiles of biological samples. After data mining, results need to be validated with highly reliable biotechniques allowing for precise quantitation of transcriptional abundance of identified genes. Quantitative real time PCR (qrt-PCR) technology has recently reached a level of sensitivity, accuracy and practical ease that support its use as a routine bioinstrumentation for gene level measurement. Currently, qrt-PCR is considered by most experts the most appropriate method to confirm or confute microarray-generated data. The knowledge of the biochemical principles underlying qrt-PCR as well as some related technical issues must be beard in mind when using this biotechnology.

  1. Karolinske psychodynamic profile (KAPP)

    DEFF Research Database (Denmark)

    Mathiesen, Birgit Bork; Søgaard, Ulf

    2006-01-01

    psykologiske testmetoder, assesment, Karolinska psychodynamic profile (KAPP), psykodynamisk profil......psykologiske testmetoder, assesment, Karolinska psychodynamic profile (KAPP), psykodynamisk profil...

  2. The Big Optical Array

    International Nuclear Information System (INIS)

    Mozurkewich, D.; Johnston, K.J.; Simon, R.S.

    1990-01-01

    This paper describes the design and the capabilities of the Naval Research Laboratory Big Optical Array (BOA), an interferometric optical array for high-resolution imaging of stars, stellar systems, and other celestial objects. There are four important differences between the BOA design and the design of Mark III Optical Interferometer on Mount Wilson (California). These include a long passive delay line which will be used in BOA to do most of the delay compensation, so that the fast delay line will have a very short travel; the beam combination in BOA will be done in triplets, to allow measurement of closure phase; the same light will be used for both star and fringe tracking; and the fringe tracker will use several wavelength channels

  3. A 4 probe array

    Energy Technology Data Exchange (ETDEWEB)

    Fernando, C E [CEGB, Marchwood Engineering Laboratories, Marchwood, Southampton, Hampshire (United Kingdom)

    1980-11-01

    A NDT system is described which moves away from the present manual method using a single send/receive transducer combination and uses instead an array of four transducers. Four transducers are shown sufficient to define a point reflector with a resolution of m{lambda}z/R where m{lambda} is the minimum detectable path difference in the system (corresponding to a m cycle time resolution), z the range and R the radius of the array. Signal averaging with an input ADC rate of 100 MHz is used with voice output for the range data. Typical resolution measurements in a water tank are presented. We expect a resolution of the order of mm in steel at a range of 80 mm. The system is expected to have applications in automated, high resolution, sizing of defects and in the inspection of austenitic stainless steel welds. (author)

  4. MicroRNA Expression Profiling to Identify and Validate Reference Genes for the Relative Quantification of microRNA in Rectal Cancer

    DEFF Research Database (Denmark)

    Eriksen, Anne Haahr Mellergaard; Andersen, Rikke Fredslund; Pallisgaard, Niels

    2016-01-01

    the miRNA profiling experiment, miR-645, miR-193a-5p, miR-27a and let-7g were identified as stably expressed, both in malignant and stromal tissue. In addition, NormFinder confirmed high expression stability for the four miRNAs. In the RT-qPCR based validation experiments, no significant difference...... management. Real-time quantitative polymerase chain reaction (RT-qPCR) is commonly used, when measuring miRNA expression. Appropriate normalisation of RT-qPCR data is important to ensure reliable results. The aim of the present study was to identify stably expressed miRNAs applicable as normaliser candidates...... in future studies of miRNA expression in rectal cancer.MATERIALS AND METHODS: We performed high-throughput miRNA profiling (OpenArray®) on ten pairs of laser micro-dissected rectal cancer tissue and adjacent stroma. A global mean expression normalisation strategy was applied to identify the most stably...

  5. Timed arrays wideband and time varying antenna arrays

    CERN Document Server

    Haupt, Randy L

    2015-01-01

    Introduces timed arrays and design approaches to meet the new high performance standards The author concentrates on any aspect of an antenna array that must be viewed from a time perspective. The first chapters briefly introduce antenna arrays and explain the difference between phased and timed arrays. Since timed arrays are designed for realistic time-varying signals and scenarios, the book also reviews wideband signals, baseband and passband RF signals, polarization and signal bandwidth. Other topics covered include time domain, mutual coupling, wideband elements, and dispersion. The auth

  6. Solar collector array

    Science.gov (United States)

    Hall, John Champlin; Martins, Guy Lawrence

    2015-09-06

    A method and apparatus for efficient manufacture, assembly and production of solar energy. In one aspect, the apparatus may include a number of modular solar receiver assemblies that may be separately manufactured, assembled and individually inserted into a solar collector array housing shaped to receive a plurality of solar receivers. The housing may include optical elements for focusing light onto the individual receivers, and a circuit for electrically connecting the solar receivers.

  7. Photovoltaic cell array

    Science.gov (United States)

    Eliason, J. T. (Inventor)

    1976-01-01

    A photovoltaic cell array consisting of parallel columns of silicon filaments is described. Each fiber is doped to produce an inner region of one polarity type and an outer region of an opposite polarity type to thereby form a continuous radial semi conductor junction. Spaced rows of electrical contacts alternately connect to the inner and outer regions to provide a plurality of electrical outputs which may be combined in parallel or in series.

  8. Phased array antenna control

    Science.gov (United States)

    Doland, G. D. (Inventor)

    1978-01-01

    Several new and useful improvements in steering and control of phased array antennas having a small number of elements, typically on the order of 5 to 17 elements are provided. Among the improvements are increasing the number of beam steering positions, reducing the possibility of phase transients in signals received or transmitted with the antennas, and increasing control and testing capacity with respect to the antennas.

  9. Seismometer array station processors

    International Nuclear Information System (INIS)

    Key, F.A.; Lea, T.G.; Douglas, A.

    1977-01-01

    A description is given of the design, construction and initial testing of two types of Seismometer Array Station Processor (SASP), one to work with data stored on magnetic tape in analogue form, the other with data in digital form. The purpose of a SASP is to detect the short period P waves recorded by a UK-type array of 20 seismometers and to edit these on to a a digital library tape or disc. The edited data are then processed to obtain a rough location for the source and to produce seismograms (after optimum processing) for analysis by a seismologist. SASPs are an important component in the scheme for monitoring underground explosions advocated by the UK in the Conference of the Committee on Disarmament. With digital input a SASP can operate at 30 times real time using a linear detection process and at 20 times real time using the log detector of Weichert. Although the log detector is slower, it has the advantage over the linear detector that signals with lower signal-to-noise ratio can be detected and spurious large amplitudes are less likely to produce a detection. It is recommended, therefore, that where possible array data should be recorded in digital form for input to a SASP and that the log detector of Weichert be used. Trial runs show that a SASP is capable of detecting signals down to signal-to-noise ratios of about two with very few false detections, and at mid-continental array sites it should be capable of detecting most, if not all, the signals with magnitude above msub(b) 4.5; the UK argues that, given a suitable network, it is realistic to hope that sources of this magnitude and above can be detected and identified by seismological means alone. (author)

  10. Array processor architecture

    Science.gov (United States)

    Barnes, George H. (Inventor); Lundstrom, Stephen F. (Inventor); Shafer, Philip E. (Inventor)

    1983-01-01

    A high speed parallel array data processing architecture fashioned under a computational envelope approach includes a data base memory for secondary storage of programs and data, and a plurality of memory modules interconnected to a plurality of processing modules by a connection network of the Omega gender. Programs and data are fed from the data base memory to the plurality of memory modules and from hence the programs are fed through the connection network to the array of processors (one copy of each program for each processor). Execution of the programs occur with the processors operating normally quite independently of each other in a multiprocessing fashion. For data dependent operations and other suitable operations, all processors are instructed to finish one given task or program branch before all are instructed to proceed in parallel processing fashion on the next instruction. Even when functioning in the parallel processing mode however, the processors are not locked-step but execute their own copy of the program individually unless or until another overall processor array synchronization instruction is issued.

  11. Material Biocompatibility for PCR Microfluidic Chips

    KAUST Repository

    Kodzius, Rimantas; Chang, Donald Choy; Gong, Xiuqing; Wen, Weijia; Wu, Jinbo; Xiao, Kang; Yi, Xin

    2010-01-01

    As part of the current miniaturization trend, biological reactions and processes are being adapted to microfluidics devices. PCR is the primary method employed in DNA amplification, its miniaturization is central to efforts to develop portable devices for diagnostics and testing purposes. A problem is the PCR-inhibitory effect due to interaction between PCR reagents and the surrounding environment, which effect is increased in high-surface-are-to-volume ration microfluidics. In this study, we evaluated the biocompatibility of various common materials employed in the fabrication of microfluidic chips, including silicon, several kinds of silicon oxide, glasses, plastics, wax, and adhesives. Two-temperature PCR was performed with these materials to determine their PCR-inhibitory effect. In most of the cases, addition of bovine serum albumin effectively improved the reaction yield. We also studied the individual PCR components from the standpoint of adsorption. Most of the materials did not inhibit the DNA, whereas they did show noticeable interaction with the DNA polymerase. Our test, instead of using microfluidic devices, can be easily conducted in common PCR tubes using a standard bench thermocycler. Our data supports an overview of the means by which the materials most bio-friendly to microfluidics can be selected.

  12. Material Biocompatibility for PCR Microfluidic Chips

    KAUST Repository

    Kodzius, Rimantas

    2010-04-23

    As part of the current miniaturization trend, biological reactions and processes are being adapted to microfluidics devices. PCR is the primary method employed in DNA amplification, its miniaturization is central to efforts to develop portable devices for diagnostics and testing purposes. A problem is the PCR-inhibitory effect due to interaction between PCR reagents and the surrounding environment, which effect is increased in high-surface-are-to-volume ration microfluidics. In this study, we evaluated the biocompatibility of various common materials employed in the fabrication of microfluidic chips, including silicon, several kinds of silicon oxide, glasses, plastics, wax, and adhesives. Two-temperature PCR was performed with these materials to determine their PCR-inhibitory effect. In most of the cases, addition of bovine serum albumin effectively improved the reaction yield. We also studied the individual PCR components from the standpoint of adsorption. Most of the materials did not inhibit the DNA, whereas they did show noticeable interaction with the DNA polymerase. Our test, instead of using microfluidic devices, can be easily conducted in common PCR tubes using a standard bench thermocycler. Our data supports an overview of the means by which the materials most bio-friendly to microfluidics can be selected.

  13. Comparison between digital PCR and real-time PCR in detection of Salmonella typhimurium in milk.

    Science.gov (United States)

    Wang, Meng; Yang, Junjie; Gai, Zhongtao; Huo, Shengnan; Zhu, Jianhua; Li, Jun; Wang, Ranran; Xing, Sheng; Shi, Guosheng; Shi, Feng; Zhang, Lei

    2018-02-02

    As a kind of zero-tolerance foodborne pathogens, Salmonella typhimurium poses a great threat to quality of food products and public health. Hence, rapid and efficient approaches to identify Salmonella typhimurium are urgently needed. Combined with PCR and fluorescence technique, real-time PCR (qPCR) and digital PCR (ddPCR) are regarded as suitable tools for detecting foodborne pathogens. To compare the effect between qPCR and ddPCR in detecting Salmonella typhimurium, a series of nucleic acid, pure strain culture and spiking milk samples were applied and the resistance to inhibitors referred in this article as well. Compared with qPCR, ddPCR exhibited more sensitive (10 -4 ng/μl or 10 2 cfu/ml) and less pre-culturing time (saving 2h). Moreover, ddPCR had stronger resistance to inhibitors than qPCR, yet absolute quantification hardly performed when target's concentration over 1ng/μl or 10 6 cfu/ml. This study provides an alternative strategy in detecting foodborne Salmonella typhimurium. Copyright © 2018 Elsevier B.V. All rights reserved.

  14. Development of Gene Expression Fingerprints for Identification of Environmental Contaminants Using cDNA Arrays

    National Research Council Canada - National Science Library

    Inouye, L

    2004-01-01

    ...) to develop cDNA array-based assays that map gene expression from contaminant exposures. Results substantiate that distinct gene expression profiles exist for major contaminant classes such as PARs, PCBs, and PCDD/Fs...

  15. UARS Cryogenic Limb Array Etalon Spectrometer (CLAES) Level 3AT V001

    Data.gov (United States)

    National Aeronautics and Space Administration — The Cryogenic Limb Array Etalon Spectrometer (CLAES) Level 3AT data product consists of daily, 65.536 second interval time-ordered vertical profiles of temperature...

  16. UARS Cryogenic Limb Array Etalon Spectrometer (CLAES) Level 3AL V001

    Data.gov (United States)

    National Aeronautics and Space Administration — The Cryogenic Limb Array Etalon Spectrometer (CLAES) Level 3AL data product consists of daily, 4 degree increment latitude-ordered vertical profiles of temperature...

  17. Real-time PCR in virology

    OpenAIRE

    Mackay, Ian M.; Arden, Katherine E.; Nitsche, Andreas

    2002-01-01

    The use of the polymerase chain reaction (PCR) in molecular diagnostics has increased to the point where it is now accepted as the gold standard for detecting nucleic acids from a number of origins and it has become an essential tool in the research laboratory. Real-time PCR has engendered wider acceptance of the PCR due to its improved rapidity, sensitivity, reproducibility and the reduced risk of carry-over contamination. There are currently five main chemistries used for the detection of P...

  18. Precision Measurements of Wind Turbine Noise using a Large Aperture Microphone Array

    DEFF Research Database (Denmark)

    Bradley, Stuart; Mikkelsen, Torben Krogh; Hünerbein, Sabine Von

    2016-01-01

    Experiments are described with a large microphone array (40 m scale) recording wind turbine noise. The array comprised 42 purpose-designed low-noise microphones simultaneously sampled at 20 kHz. Very high quality, fast, meteorological profile data was available from nearby 80 m masts and from the...

  19. Integration of Antibody Array Technology into Drug Discovery and Development.

    Science.gov (United States)

    Huang, Wei; Whittaker, Kelly; Zhang, Huihua; Wu, Jian; Zhu, Si-Wei; Huang, Ruo-Pan

    Antibody arrays represent a high-throughput technique that enables the parallel detection of multiple proteins with minimal sample volume requirements. In recent years, antibody arrays have been widely used to identify new biomarkers for disease diagnosis or prognosis. Moreover, many academic research laboratories and commercial biotechnology companies are starting to apply antibody arrays in the field of drug discovery. In this review, some technical aspects of antibody array development and the various platforms currently available will be addressed; however, the main focus will be on the discussion of antibody array technologies and their applications in drug discovery. Aspects of the drug discovery process, including target identification, mechanisms of drug resistance, molecular mechanisms of drug action, drug side effects, and the application in clinical trials and in managing patient care, which have been investigated using antibody arrays in recent literature will be examined and the relevance of this technology in progressing this process will be discussed. Protein profiling with antibody array technology, in addition to other applications, has emerged as a successful, novel approach for drug discovery because of the well-known importance of proteins in cell events and disease development.

  20. Calibrated user-friendly reverse transcriptase-PCR assay

    DEFF Research Database (Denmark)

    Bor, M V; Sørensen, B S; Rammer, P

    1998-01-01

    We report a competitive reverse transcriptase-PCR (RT-PCR) assay and a calibrated user-friendly RT-PCR assay (CURT-PCR) for epidermal growth factor receptor (EGFR) mRNA. A calibrator was prepared from isolated rat liver RNA, and the amount of EGFR mRNA was determined by competitive RT-PCR. In CUR...

  1. Gene array and real time PCR analysis of the adrenal sensitivity to adrenocorticotropic hormone in pig

    Directory of Open Access Journals (Sweden)

    SanCristobal Magali

    2008-02-01

    Full Text Available Abstract Background Variability in hypothalamic-pituitary-adrenal (HPA axis activity has been shown to be influenced by genetic factors and related to great metabolic differences such as obesity. The aim of this study was to investigate molecular bases of genetic variability of the adrenal sensitivity to ACTH, a major source of variability, in Meishan (MS and Large White (LW pigs, MS being reported to exhibit higher basal cortisol levels, response to ACTH and fatness than LW. A pig cDNA microarray was used to identify changes in gene expression in basal conditions and in response to ACTH stimulation. Results Genotype and/or ACTH affected the expression of 211 genes related to transcription, cell growth/maintenance, signal transduction, cell structure/adhesion/extra cellular matrix and protein kinase/phosphatase activity. No change in the expression of known key regulator proteins of the ACTH signaling pathway or of steroidogenic enzymes was found. However, Mdh2, Sdha, Suclg2, genes involved in the tricarboxylic acid (TCA pathway, were over-expressed in MS pigs. Higher TCA cycle activity in MS than in LW may thus result in higher steroidogenic activity and thus explain the typically higher cortisol levels in MS compared to LW. Moreover, up-regulation of Star and Ldlr genes in MS and/or in response to ACTH suggest that differences in the adrenal function between MS and LW may also involve mechanisms requisite for cholesterol supply to steroidogenesis. Conclusion The present study provides new potential candidate genes to explain genetic variations in the adrenal sensitivity to ACTH and better understand relationship between HPA axis activity and obesity.

  2. Rice8987 Array: PCR check - RMOS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available There are independent 8979 cDNA clones that were selected from about 40,000 cDNA clones isolated in the first research... stage of the rice genome research project. Those 8979 cDNA clones were

  3. Denaturation strategies for detection of double stranded PCR products on GMR magnetic biosensor array

    DEFF Research Database (Denmark)

    Rizzi, Giovanni; Lee, Jung-Rok; Guldberg, Per

    2017-01-01

    Microarrays and other surface-based nucleic acid detection schemes rely on the hybridization of the target to surface-bound detection probes. We present the first comparison of two strategies to detect DNA using a giant magnetoresistive (GMR) biosensor platform starting from an initially double...

  4. In-phased second harmonic wave array generation with intra-Talbot-cavity frequency-doubling.

    Science.gov (United States)

    Hirosawa, Kenichi; Shohda, Fumio; Yanagisawa, Takayuki; Kannari, Fumihiko

    2015-03-23

    The Talbot cavity is one promising method to synchronize the phase of a laser array. However, it does not achieve the lowest array mode with the same phase but the highest array mode with the anti-phase between every two adjacent lasers, which is called out-phase locking. Consequently, their far-field images exhibit 2-peak profiles. We propose intra-Talbot-cavity frequency-doubling. By placing a nonlinear crystal in a Talbot cavity, the Talbot cavity generates an out-phased fundamental wave array, which is converted into an in-phase-locked second harmonic wave array at the nonlinear crystal. We demonstrate numerical calculations and experiments on intra-Talbot-cavity frequency-doubling and obtain an in-phase-locked second harmonic wave array for a Nd:YVO₄ array laser.

  5. Diagnosis of trichomonas vaginalis infection by PCR

    International Nuclear Information System (INIS)

    Issa, R.M.; Shalaby, M.A.

    2007-01-01

    To compare the sensitivity of PCR, wet preparation and culture in detecting Trichomonas vaginalis in urine and vaginal fluid. A PCR targeting the beta-tubulin genes of T. vaginalis was used for the detection of the organism in both vaginal swab and urine specimens from infected patients. Random urine samples were collected from 30 patients (23 females and 7 males), and tested for T. vaginalis by wet preparation and the Inpouch T. vaginalis culture systeme. Two vaginal swabs were collected by each woman. PCR detection. was carried out on samples negative by first methods. The positive result was found in 28.57% in male urine and 39.13% in female urine samples, 65.21% in 1st swab and 78.26 % in 2nd swab by wet preparation. By culture, the male urine samples showed 42.85% positive, female urine 69.56% while 1st swab showed 86.95% positive and 2nd swab 91.30% positive. All negative cases by culture in urine and vaginal samples were tested by PCR, which showed 2 cases to be positive in male urine samples and 5 cases positive in female urine sample. PCR assay was as good as or more sensitive than wet preparation and culture and resulted in practical advantage of providing results in shorter time. However, PCR test is still very expensive. (author)

  6. Educational Cosmic Ray Arrays

    International Nuclear Information System (INIS)

    Soluk, R. A.

    2006-01-01

    In the last decade a great deal of interest has arisen in using sparse arrays of cosmic ray detectors located at schools as a means of doing both outreach and physics research. This approach has the unique advantage of involving grade school students in an actual ongoing experiment, rather then a simple teaching exercise, while at the same time providing researchers with the basic infrastructure for installation of cosmic ray detectors. A survey is made of projects in North America and Europe and in particular the ALTA experiment at the University of Alberta which was the first experiment operating under this paradigm

  7. Storage array reflection considerations

    International Nuclear Information System (INIS)

    Haire, M.J.; Jordan, W.C.; Taylor, R.G.

    1997-01-01

    The assumptions used for reflection conditions of single containers are fairly well established and consistently applied throughout the industry in nuclear criticality safety evaluations. Containers are usually considered to be either fully water-reflected (i.e. surrounded by 6 to 12 in. of water) for safety calculations or reflected by 1 in. of water for nominal (structural material and air) conditions. Tables and figures are usually available for performing comparative evaluations of containers under various loading conditions. Reflection considerations used for evaluating the safety of storage arrays of fissile material are not as well established

  8. Rapid identification of dairy lactic acid bacteria by M13-generated, RAPD-PCR fingerprint databases.

    Science.gov (United States)

    Rossetti, Lia; Giraffa, Giorgio

    2005-11-01

    About a thousand lactic acid bacteria (LAB) isolated from dairy products, especially cheeses, were identified and typed by species-specific PCR and RAPD-PCR, respectively. RAPD-PCR profiles, which were obtained by using the M13 sequence as a primer, allowed us to implement a large database of different fingerprints, which were analysed by BioNumerics software. Cluster analysis of the combined RAPD-PCR fingerprinting profiles enabled us to implement a library, which is a collection of library units, which in turn is a selection of representative database entries. A library unit, in this case, can be considered to be a definable taxon. The strains belonged to 11 main RAPD-PCR fingerprinting library units identified as Lactobacillus casei/paracasei, Lactobacillus plantarum, Lactobacillus rhamnosus, Lactobacillus helveticus, Lactobacillus delbrueckii, Lactobacillus fermentum, Lactobacillus brevis, Enterococcus faecium, Enterococcus faecalis, Streptococcus thermophilus and Lactococcus lactis. The possibility to routinely identify newly typed, bacterial isolates by consulting the library of the software was valued. The proposed method could be suggested to refine previous strain identifications, eliminate redundancy and dispose of a technologically useful LAB strain collection. The same approach could also be applied to identify LAB strains isolated from other food ecosystems.

  9. Selecting Sums in Arrays

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Jørgensen, Allan Grønlund

    2008-01-01

    In an array of n numbers each of the \\binomn2+nUnknown control sequence '\\binom' contiguous subarrays define a sum. In this paper we focus on algorithms for selecting and reporting maximal sums from an array of numbers. First, we consider the problem of reporting k subarrays inducing the k largest...... sums among all subarrays of length at least l and at most u. For this problem we design an optimal O(n + k) time algorithm. Secondly, we consider the problem of selecting a subarray storing the k’th largest sum. For this problem we prove a time bound of Θ(n · max {1,log(k/n)}) by describing...... an algorithm with this running time and by proving a matching lower bound. Finally, we combine the ideas and obtain an O(n· max {1,log(k/n)}) time algorithm that selects a subarray storing the k’th largest sum among all subarrays of length at least l and at most u....

  10. Programmable cellular arrays. Faults testing and correcting in cellular arrays

    International Nuclear Information System (INIS)

    Cercel, L.

    1978-03-01

    A review of some recent researches about programmable cellular arrays in computing and digital processing of information systems is presented, and includes both combinational and sequential arrays, with full arbitrary behaviour, or which can realize better implementations of specialized blocks as: arithmetic units, counters, comparators, control systems, memory blocks, etc. Also, the paper presents applications of cellular arrays in microprogramming, in implementing of a specialized computer for matrix operations, in modeling of universal computing systems. The last section deals with problems of fault testing and correcting in cellular arrays. (author)

  11. Molecular characterization of Salmonella isolates by REP-PCR and RAPD analysis.

    Science.gov (United States)

    Albufera, U; Bhugaloo-Vial, P; Issack, M I; Jaufeerally-Fakim, Y

    2009-05-01

    Eighteen Salmonella isolates from both human and food (non-human) sources (fish, meat, and poultry) were characterized using conventional culture methods, biochemical, serological, and molecular analyses. REP-PCR and RAPD produced DNA profiles for differentiation purposes. Enterobacterial repetitive intergenic consensus (ERIC), repetitive extragenic palindronic (REP) and BOXAIR primers were selected for REP-PCR and two arbitrary primers, namely OPP-16 and OPS-11 were used for RAPD to generate DNA fingerprints from the Salmonella isolates. REP-PCR method showed greater discriminatory power in differentiating closely related strains of the related strains of Salmonella and produced more complex banding patterns as compared with RAPD. A dendogram was constructed with both sets of profiles using SPSS Version 13.0 computer software and showed that most human isolates were separately clustered from the non-human isolates. Two of the human isolates were closely related to some of the non-human isolates. A good correlation was also observed between the serogrouping of the O antigen and the molecular profiles obtained from REP-PCR and RAPD data of the Salmonella isolates. The results of a principal coordinate analysis (PCA) corresponded to the clustering in the dendrogram.

  12. High-resolution melt PCR analysis for genotyping of Ureaplasma parvum isolates directly from clinical samples.

    Science.gov (United States)

    Payne, Matthew S; Tabone, Tania; Kemp, Matthew W; Keelan, Jeffrey A; Spiller, O Brad; Newnham, John P

    2014-02-01

    Ureaplasma sp. infection in neonates and adults underlies a variety of disease pathologies. Of the two human Ureaplasma spp., Ureaplasma parvum is clinically the most common. We have developed a high-resolution melt (HRM) PCR assay for the differentiation of the four serovars of U. parvum in a single step. Currently U. parvum strains are separated into four serovars by sequencing the promoter and coding region of the multiple-banded antigen (MBA) gene. We designed primers to conserved sequences within this region for PCR amplification and HRM analysis to generate reproducible and distinct melt profiles that distinguish clonal representatives of serovars 1, 3, 6, and 14. Furthermore, our HRM PCR assay could classify DNA extracted from 74 known (MBA-sequenced) test strains with 100% accuracy. Importantly, HRM PCR was also able to identify U. parvum serovars directly from 16 clinical swabs. HRM PCR performed with DNA consisting of mixtures of combined known serovars yielded profiles that were easily distinguished from those for single-serovar controls. These profiles mirrored clinical samples that contained mixed serovars. Unfortunately, melt curve analysis software is not yet robust enough to identify the composition of mixed serovar samples, only that more than one serovar is present. HRM PCR provides a single-step, rapid, cost-effective means to differentiate the four serovars of U. parvum that did not amplify any of the known 10 serovars of Ureaplasma urealyticum tested in parallel. Choice of reaction reagents was found to be crucial to allow sufficient sensitivity to differentiate U. parvum serovars directly from clinical swabs rather than requiring cell enrichment using microbial culture techniques.

  13. Report for Detection of Biothreat Agents and Environmental Samples using the LLNL Virulence Array for DHS

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, Crystal [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gardner, Shea [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); McLoughlin, Kevin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Thissen, James [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Jackson, Paul [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2011-04-18

    The objective of this project is to provide DHS a comprehensive evaluation of the current genomic technologies including genotyping, Taqman PCR, multiple locus variable tandem repeat analysis (MLVA), microarray and high-throughput DNA sequencing in the analysis of biothreat agents from complex environmental samples. This report focuses on the design, testing and results of samples on the Virulence Array.

  14. Dynamics of vaginal bacterial communities in women developing bacterial vaginosis, candidiasis, or no infection, analyzed by PCR-denaturing gradient gel electrophoresis and real-time PCR.

    Science.gov (United States)

    Vitali, Beatrice; Pugliese, Ciro; Biagi, Elena; Candela, Marco; Turroni, Silvia; Bellen, Gert; Donders, Gilbert G G; Brigidi, Patrizia

    2007-09-01

    The microbial flora of the vagina plays a major role in preventing genital infections, including bacterial vaginosis (BV) and candidiasis (CA). An integrated approach based on PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR was used to study the structure and dynamics of bacterial communities in vaginal fluids of healthy women and patients developing BV and CA. Universal eubacterial primers and Lactobacillus genus-specific primers, both targeted at 16S rRNA genes, were used in DGGE and real-time PCR analysis, respectively. The DGGE profiles revealed that the vaginal flora was dominated by Lactobacillus species under healthy conditions, whereas several potentially pathogenic bacteria were present in the flora of women with BV. Lactobacilli were the predominant bacterial population in the vagina for patients affected by CA, but changes in the composition of Lactobacillus species were observed. Real-time PCR analysis allowed the quantitative estimation of variations in lactobacilli associated with BV and CA diseases. A statistically significant decrease in the relative abundance of lactobacilli was found in vaginal fluids of patients with BV compared to the relative abundance of lactobacilli in the vaginal fluids of healthy women and patients with CA.

  15. SASqPCR: robust and rapid analysis of RT-qPCR data in SAS.

    Directory of Open Access Journals (Sweden)

    Daijun Ling

    Full Text Available Reverse transcription quantitative real-time PCR (RT-qPCR is a key method for measurement of relative gene expression. Analysis of RT-qPCR data requires many iterative computations for data normalization and analytical optimization. Currently no computer program for RT-qPCR data analysis is suitable for analytical optimization and user-controllable customization based on data quality, experimental design as well as specific research aims. Here I introduce an all-in-one computer program, SASqPCR, for robust and rapid analysis of RT-qPCR data in SAS. This program has multiple macros for assessment of PCR efficiencies, validation of reference genes, optimization of data normalizers, normalization of confounding variations across samples, and statistical comparison of target gene expression in parallel samples. Users can simply change the macro variables to test various analytical strategies, optimize results and customize the analytical processes. In addition, it is highly automatic and functionally extendable. Thus users are the actual decision-makers controlling RT-qPCR data analyses. SASqPCR and its tutorial are freely available at http://code.google.com/p/sasqpcr/downloads/list.

  16. Magnetic properties of strip-like Josephson-junction arrays

    International Nuclear Information System (INIS)

    Chen, D.-X; Moreno, J.J.; Hernando, A.; Sanchez, A.

    2000-01-01

    Zero-field-cooled (ZFC) and field-cooled (FC) magnetic properties of strip-like Josephson-junction (JJ) arrays with very strong demagnetizing effects are calculated from basic laws. Similar to slab-like JJ arrays without considering demagnetizing effects, a vortex state evolves to a critical state (CS) with increasing maximum JJ currents in the ZFC case, and a vortex state always remains with a negative low-field susceptibility in the FC case. However, the strong demagnetizing effects cause qualitative changes in the CS, where the overall feature of the field and current profiles turns out to be similar to that in type-II superconducting strips, but not like the ordinary Bean CS in slab-like JJ arrays, the CS current profile is never flat and the critical current is no longer a step function of the maximum JJ current as in slab-like JJ arrays. The calculated results of different types of JJ arrays indicate that although the intergranular CS in granular superconductors may have a common origin, the discovered paramagnetic Meissner effect in them is still difficult to explain. (author)

  17. Permanganate-assisted removal of PCR inhibitors during the DNA Chelex extraction from stained denim samples.

    Science.gov (United States)

    Pîrlea, Sorina; Puiu, Mihaela; Răducan, Adina; Oancea, Dumitru

    2017-03-01

    In this study, it was demonstrated that the DNA Chelex extraction combined with the permanganate assisted-oxidation is highly efficient in removing the PCR inhibitors often found in clothing materials, such as phthalocyanine. The extraction assays were conducted in saliva, blood and epithelial cells samples mixed with three oxidation-resistant dye copper(II) α-phthalocyanine, copper(II) β-phthalocyanine and tetrasulfonated copper(II) β-phthalocyanine. After DNA amplification, all samples were able to provide full DNA profiles. The permanganate/Chelex system was tested further on denim-stained samples and displayed the same ability to remove the PCR inhibitors from the commercial textile materials.

  18. Identification of clinically relevant viridans streptococci by an oligonucleotide array.

    Science.gov (United States)

    Chen, Chao Chien; Teng, Lee Jene; Kaiung, Seng; Chang, Tsung Chain

    2005-04-01

    Viridans streptococci (VS) are common etiologic agents of subacute infective endocarditis and are capable of causing a variety of pyogenic infections. Many species of VS are difficult to differentiate by phenotypic traits. An oligonucleotide array based on 16S-23S rRNA gene intergenic spacer (ITS) sequences was developed to identify 11 clinically relevant VS. These 11 species were Streptococcus anginosus, S. constellatus, S. gordonii, S. intermedius, S. mitis, S. mutans, S. oralis, S. parasanguinis, S. salivarius, S. sanguinis, and S. uberis. The method consisted of PCR amplification of the ITS regions by using a pair of universal primers, followed by hybridization of the digoxigenin-labeled PCR products to a panel of species-specific oligonucleotides immobilized on a nylon membrane. After 120 strains of the 11 species of VG and 91 strains of other bacteria were tested, the sensitivity and specificity of the oligonucleotide array were found to be 100% (120 of 120 strains) and 95.6% (87 of 91 strains), respectively. S. pneumoniae cross-hybridized to the probes used for the identification of S. mitis, and simple biochemical tests such as optochin susceptibility or bile solubility should be used to differentiate S. pneumoniae from S. mitis. In conclusion, identification of species of VS by use of the present oligonucleotide array is accurate and could be used as an alternative reliable method for species identification of strains of VS.

  19. Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution.

    Science.gov (United States)

    Ishii, Satoshi; Sadowsky, Michael J

    2009-04-01

    A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence-based PCR or rep-PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or 'fingerprints' of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep-PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep-PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep-PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution.

  20. Combinatorial aspects of covering arrays

    Directory of Open Access Journals (Sweden)

    Charles J. Colbourn

    2004-11-01

    Full Text Available Covering arrays generalize orthogonal arrays by requiring that t -tuples be covered, but not requiring that the appearance of t -tuples be balanced.Their uses in screening experiments has found application in software testing, hardware testing, and a variety of fields in which interactions among factors are to be identified. Here a combinatorial view of covering arrays is adopted, encompassing basic bounds, direct constructions, recursive constructions, algorithmic methods, and applications.

  1. Silicon Micromachined Microlens Array for THz Antennas

    Science.gov (United States)

    Lee, Choonsup; Chattopadhyay, Goutam; Mehdi, IImran; Gill, John J.; Jung-Kubiak, Cecile D.; Llombart, Nuria

    2013-01-01

    5 5 silicon microlens array was developed using a silicon micromachining technique for a silicon-based THz antenna array. The feature of the silicon micromachining technique enables one to microfabricate an unlimited number of microlens arrays at one time with good uniformity on a silicon wafer. This technique will resolve one of the key issues in building a THz camera, which is to integrate antennas in a detector array. The conventional approach of building single-pixel receivers and stacking them to form a multi-pixel receiver is not suited at THz because a single-pixel receiver already has difficulty fitting into mass, volume, and power budgets, especially in space applications. In this proposed technique, one has controllability on both diameter and curvature of a silicon microlens. First of all, the diameter of microlens depends on how thick photoresist one could coat and pattern. So far, the diameter of a 6- mm photoresist microlens with 400 m in height has been successfully microfabricated. Based on current researchers experiences, a diameter larger than 1-cm photoresist microlens array would be feasible. In order to control the curvature of the microlens, the following process variables could be used: 1. Amount of photoresist: It determines the curvature of the photoresist microlens. Since the photoresist lens is transferred onto the silicon substrate, it will directly control the curvature of the silicon microlens. 2. Etching selectivity between photoresist and silicon: The photoresist microlens is formed by thermal reflow. In order to transfer the exact photoresist curvature onto silicon, there needs to be etching selectivity of 1:1 between silicon and photoresist. However, by varying the etching selectivity, one could control the curvature of the silicon microlens. The figure shows the microfabricated silicon microlens 5 x5 array. The diameter of the microlens located in the center is about 2.5 mm. The measured 3-D profile of the microlens surface has a

  2. PCR+ In Diesel Fuels and Emissions Research

    Energy Technology Data Exchange (ETDEWEB)

    McAdams, H.T.

    2002-04-15

    In past work for the U.S. Department of Energy (DOE) and Oak Ridge National Laboratory (ORNL), PCR+ was developed as an alternative methodology for building statistical models. PCR+ is an extension of Principal Components Regression (PCR), in which the eigenvectors resulting from Principal Components Analysis (PCA) are used as predictor variables in regression analysis. The work was motivated by the observation that most heavy-duty diesel (HDD) engine research was conducted with test fuels that had been ''concocted'' in the laboratory to vary selected fuel properties in isolation from each other. This approach departs markedly from the real world, where the reformulation of diesel fuels for almost any purpose leads to changes in a number of interrelated properties. In this work, we present new information regarding the problems encountered in the conventional approach to model-building and how the PCR+ method can be used to improve research on the relationship between fuel characteristics and engine emissions. We also discuss how PCR+ can be applied to a variety of other research problems related to diesel fuels.

  3. Nanoelectrode array for electrochemical analysis

    Energy Technology Data Exchange (ETDEWEB)

    Yelton, William G [Sandia Park, NM; Siegal, Michael P [Albuquerque, NM

    2009-12-01

    A nanoelectrode array comprises a plurality of nanoelectrodes wherein the geometric dimensions of the electrode controls the electrochemical response, and the current density is independent of time. By combining a massive array of nanoelectrodes in parallel, the current signal can be amplified while still retaining the beneficial geometric advantages of nanoelectrodes. Such nanoelectrode arrays can be used in a sensor system for rapid, non-contaminating field analysis. For example, an array of suitably functionalized nanoelectrodes can be incorporated into a small, integrated sensor system that can identify many species rapidly and simultaneously under field conditions in high-resistivity water, without the need for chemical addition to increase conductivity.

  4. Array architectures for iterative algorithms

    Science.gov (United States)

    Jagadish, Hosagrahar V.; Rao, Sailesh K.; Kailath, Thomas

    1987-01-01

    Regular mesh-connected arrays are shown to be isomorphic to a class of so-called regular iterative algorithms. For a wide variety of problems it is shown how to obtain appropriate iterative algorithms and then how to translate these algorithms into arrays in a systematic fashion. Several 'systolic' arrays presented in the literature are shown to be specific cases of the variety of architectures that can be derived by the techniques presented here. These include arrays for Fourier Transform, Matrix Multiplication, and Sorting.

  5. Molecular, Serological And Microbiological Profiling Evidence Of ...

    African Journals Online (AJOL)

    All items that the boy had contact with including a laboratory coat, bunch of keys and shoes were swabbed. Finally samples of all the boy's food and drinks were taken. Microbiological, Serological and Polymerase Chain Reaction (PCR) Profiling Assays. l the samples were cultured on Sorbitol - MacConkey (SMAC) agar, ...

  6. Josephson junctions array resonators

    Energy Technology Data Exchange (ETDEWEB)

    Gargiulo, Oscar; Muppalla, Phani; Mirzaei, Iman; Kirchmair, Gerhard [Institute for Quantum Optics and Quantum Information, Innsbruck (Austria)

    2016-07-01

    We present an experimental analysis of the self- and cross-Kerr effect of extended plasma resonances in Josephson junction chains. The chain consists of 1600 individual junctions and we can measure quality factors in excess of 10000. The Kerr effect manifests itself as a frequency shift that depends linearly on the number of photons in a resonant mode. By changing the input power we are able to measure this frequency shift on a single mode (self-kerr). By changing the input power on another mode while measuring the same one, we are able to evaluate the cross-kerr effect. We can measure the cross-Kerr effect by probing the resonance frequency of one mode while exciting another mode of the array with a microwave drive.

  7. Diagnosable structured logic array

    Science.gov (United States)

    Whitaker, Sterling (Inventor); Miles, Lowell (Inventor); Gambles, Jody (Inventor); Maki, Gary K. (Inventor)

    2009-01-01

    A diagnosable structured logic array and associated process is provided. A base cell structure is provided comprising a logic unit comprising a plurality of input nodes, a plurality of selection nodes, and an output node, a plurality of switches coupled to the selection nodes, where the switches comprises a plurality of input lines, a selection line and an output line, a memory cell coupled to the output node, and a test address bus and a program control bus coupled to the plurality of input lines and the selection line of the plurality of switches. A state on each of the plurality of input nodes is verifiably loaded and read from the memory cell. A trusted memory block is provided. The associated process is provided for testing and verifying a plurality of truth table inputs of the logic unit.

  8. Low Frequency Space Array

    International Nuclear Information System (INIS)

    Dennison, B.; Weiler, K.W.; Johnston, K.J.

    1987-01-01

    The Low Frequency Space Array (LFSA) is a conceptual mission to survey the entire sky and to image individual sources at frequencies between 1.5 and 26 MHz, a frequency range over which the earth's ionosphere transmits poorly or not at all. With high resolution, high sensitivity observations, a new window will be opened in the electromagnetic spectrum for astronomical investigation. Also, extending observations down to such low frequencies will bring astronomy to the fundamental limit below which the galaxy becomes optically thick due to free-free absorption. A number of major scientific goals can be pursued with such a mission, including mapping galactic emission and absorption, studies of individual source spectra in a frequency range where a number of important processes may play a role, high resolution imaging of extended sources, localization of the impulsive emission from Jupiter, and a search for coherent emission processes. 19 references

  9. Scintillator detector array

    International Nuclear Information System (INIS)

    Cusano, D.A.; Dibianca, F.A.

    1981-01-01

    This patent application relates to a scintillator detector array for use in computerized tomography and comprises a housing including a plurality of chambers, the said housing having a front wall transmissive to x-rays and side walls opaque to x-rays, such as of tungsten and tantalum, a liquid scintillation medium including a soluble fluor, the solvent for the fluor being disposed in the chambers. The solvent comprises either an intrinsically high Z solvent or a solvent which has dissolved therein a high Z compound e.g. iodo or bromonaphthalene; or toluene, xylene or trimethylbenzene with a lead or tin alkyl dissolved therein. Also disposed about the chambers are a plurality of photoelectric devices. (author)

  10. Wideband Array for C, X, and Ku-Band Applications with 5.3:1 Bandwidth

    Science.gov (United States)

    Novak, Markus H.; Volakis, John L.; Miranda, Felix A.

    2015-01-01

    Planar arrays that exploit strong intentional coupling between elements have allowed for very wide bandwidths in low-profile configurations. However, such designs also require complex impedance matching networks that must also be very compact. For many space applications, typically occurring at C-, X-, Ku-, and most recently at Ka-band, such designs require specialized and expensive fabrication techniques. To address this issue, a novel ultra-wideband array is presented, using a simplified feed network to reduce fabrication cost. The array operates from 3.5-18.5 GHz with VSWR less than 2.4 at broadside, and is of very low profile, having a total height of lambda/10 at the lowest frequency of operation. Validation is provided using a 64-element prototype array, fabricated using common Printed Circuit Board (PCB) technology. The low size, weight, and cost of this array make it attractive for space-borne applications.

  11. Cascading Constrained 2-D Arrays using Periodic Merging Arrays

    DEFF Research Database (Denmark)

    Forchhammer, Søren; Laursen, Torben Vaarby

    2003-01-01

    We consider a method for designing 2-D constrained codes by cascading finite width arrays using predefined finite width periodic merging arrays. This provides a constructive lower bound on the capacity of the 2-D constrained code. Examples include symmetric RLL and density constrained codes...

  12. Networked Sensor Arrays

    International Nuclear Information System (INIS)

    Tighe, R. J.

    2002-01-01

    A set of independent radiation sensors, coupled with real-time data telemetry, offers the opportunity to run correlation algorithms for the sensor array as well as to incorporate non-radiological data into the system. This may enhance the overall sensitivity of the sensors and provide an opportunity to project the location of a source within the array. In collaboration with Lawrence Livermore National Laboratory (LLNL) and Sandia National Laboratories (SNL), we have conducted field experiments to test a prototype system. Combining the outputs of a set of distributed sensors permits the correlation that the independent sensor outputs. Combined with additional information such as traffic patterns and velocities, this can reduce random/false detections and enhance detection capability. The principle components of such a system include: (1) A set of radiation sensors. These may be of varying type and complexity, including gamma and/or neutron detectors, gross count and spectral-capable sensors, and low to high energy-resolution sensors. (2) A set of non-radiation sensors. These may include sensors such as vehicle presence and imaging sensors. (3) A communications architecture for near real-time telemetry. Depending upon existing infrastructure and bandwidth requirements, this may be a radio or hard-wire based system. (4) A central command console to pole the sensors, correlate their output, and display the data in a meaningful form to the system operator. Both sensitivity and selectivity are important considerations when evaluating the performance of a detection system. Depending on the application, the optimization of sensitivity as well as the rejection of ''nuisance'' radioactive sources may or may not be critical

  13. Printed glycan array

    DEFF Research Database (Denmark)

    Shilova, Nadezhda; Navakouski, Maxim; Khasbiullina, Nailya

    2012-01-01

    usually has to dilute the starting material in order to have sufficient volume for PGA experimentation. The PGA used in this study allows for the use of whole serum without modifications to the protocol, and the background is surprisingly low. Antibodies profiles observed in undiluted serum versus 1......G/IgM ratio corresponds to their titer, whereas at 1:100 dilution the measured ratio corresponds to real molar concentration of IgG and IgM....

  14. Population diversity of ammonium oxidizers investigated by specific PCR amplification

    Science.gov (United States)

    Ward, B.B.; Voytek, M.A.; Witzel, K.-P.

    1997-01-01

    The species composition of ammonia-oxidizing bacteria in aquatic environments was investigated using PCR primers for 16S rRNA genes to amplify specific subsets of the total ammonia-oxidizer population. The specificity of the amplification reactions was determined using total genomic DNA from known nitrifying strains and non-nitrifying strains identified as having similar rDNA sequences. Specificity of amplification was determined both for direct amplification, using the nitrifier specific primers, and with nested amplification, in which the nitrifier primers were used to reamplify a fragment obtained from direct amplification with Eubacterial universal primers. The present level of specificity allows the distinction between Nitrosomonas europaea, Nitrosomonas sp. (marine) and the other known ammonia-oxidizers in the beta subclass of the Proteobacteria. Using total DNA extracted from natural samples, we used direct amplification to determine presence/absence of different species groups. Species composition was found to differ among depths in vertical profiles of lake samples and among samples and enrichments from various other aquatic environments. Nested PCR yielded several more positive reactions, which implies that nitrifier DNA was present in most samples, but often at very low levels.

  15. From the 'PCR' function to the 'PCR' profession; de la fonction 'PCR' au metier 'PCR'

    Energy Technology Data Exchange (ETDEWEB)

    Perrin, L. [CERAP, 91 - Gif sur Yvette (France)

    2008-07-01

    After having recalled the legal context concerning the appointment and training of a radiation protection expert (PCR for 'personne competente en radioprotection'), the author outlines that the PCR's role has notably evolved: his function is now of primary importance in the company and his activity does not correspond to the legal framework any longer. Moreover, with the application of a European directive, some small establishments possessing ionizing radiation sources are disadvantaged, and the PCR is now facing an increasing number of missions and tasks. The author gives a list of them and assesses a needed time of 146 days per year: this means PCRs cannot have an other activity within their company

  16. Profiling cancer

    DEFF Research Database (Denmark)

    Ciro, Marco; Bracken, Adrian P; Helin, Kristian

    2003-01-01

    In the past couple of years, several very exciting studies have demonstrated the enormous power of gene-expression profiling for cancer classification and prediction of patient survival. In addition to promising a more accurate classification of cancer and therefore better treatment of patients......, gene-expression profiling can result in the identification of novel potential targets for cancer therapy and a better understanding of the molecular mechanisms leading to cancer....

  17. Ultrasensitive quantitation of human papillomavirus type 16 E6 oncogene sequences by nested real time PCR

    Directory of Open Access Journals (Sweden)

    López-Revilla Rubén

    2010-05-01

    Full Text Available Abstract Background We have developed an ultrasensitive method based on conventional PCR preamplification followed by nested amplification through real time PCR (qPCR in the presence of the DNA intercalating agent EvaGreen. Results Amplification mixtures calibrated with a known number of pHV101 copies carrying a 645 base pair (bp-long insert of the human papillomavirus type 16 (HPV16 E6 oncogene were used to generate the E6-1 amplicon of 645 bp by conventional PCR and then the E6-2 amplicon of 237 bp by nested qPCR. Direct and nested qPCR mixtures for E6-2 amplification corresponding to 2.5 × 102-2.5 × 106 initial pHV101 copies had threshold cycle (Ct values in the ranges of 18.7-29.0 and 10.0-25.0, respectively. The Ct of qPCR mixtures prepared with 1/50 volumes of preamplified mixtures containing 50 ng of DNA of the SiHa cell line (derived from an invasive cervical cancer with one HPV16 genome per cell was 19.9. Thermal fluorescence extinction profiles of E6-2 amplicons generated from pHV101 and SiHa DNA were identical, with a peak at 85.5°C. Conclusions Our method based on conventional preamplification for 15 cycles increased 10,750 times the sensitivity of nested qPCR for the quantitation of the E6 viral oncogene and confirmed that the SiHa cell line contains one E6-HPV16 copy per cell.

  18. PCR analysis is superior to histology for diagnosis of Whipple's disease mimicking seronegative rheumatic diseases.

    Science.gov (United States)

    Lehmann, P; Ehrenstein, B; Hartung, W; Dragonas, C; Reischl, U; Fleck, M

    2017-03-01

    The diagnosis of Whipple's disease (WD) is commonly confirmed by histology demonstrating Periodic Acid Schiff (PAS)-positive macrophages in the duodenal mucosa. Analysis of intestinal tissue or other specimens using polymerase chain reaction (PCR) is a more sensitive method. However, the relevance of positive PCR findings is still controversial. Therefore, we evaluated the relevance of histology and PCR findings to establishing the diagnosis of WD in a series of WD patients initially presenting with suspected rheumatic diseases. Between 2006 and 2014, 20 patients with seronegative rheumatic diseases tested positive for Tropheryma whipplei (Tw) by PCR and/or histology and were enrolled in a retrospective analysis of the diagnostic value of both procedures. Seven of the 20 cases (35%) were diagnosed with 'classic' WD as indicated by PAS-positive macrophages. In the remaining 13 patients, the presence of Tw was detected by intestinal (n = 10) or synovial PCR analysis (n = 3). Two of the 20 patients (10%) with evidence of Tw did not respond to antibiotic therapy. They were not considered to suffer from WD. Therefore, relying only on histological findings of intestinal biopsies would have missed 11 (61%) of the 18 patients with WD in our cohort. In comparison, PCR of intestinal biopsies detected Tw-DNA in 14 (93%) of the 15 WD patients evaluated. Patients with a positive histology did not differ from PCR-positive patients with regard to sex, age, or duration of disease, but more often presented with gastrointestinal symptoms. A substantial number of WD patients present without typical intestinal histology findings. Additional PCR analysis of intestinal tissue or synovial fluid increased the sensitivity of the diagnostic evaluation and should be considered particularly in patients presenting with atypical seronegative rheumatic diseases and a high-risk profile for WD.

  19. Propidium monoazide reverse transcription PCR and RT-qPCR for detecting infectious enterovirus and norovirus

    Science.gov (United States)

    Presently there is no established cell line or small animal model that allows for the detection of infectious human norovirus. Current methods based on RT-PCR and RT-qPCR detect both infectious and non-infectious virus and thus the conclusions that may be drawn regarding the publ...

  20. Detection of Leishmania infantum in animals and their ectoparasites by conventional PCR and real time PCR.

    Science.gov (United States)

    de Morais, Rayana Carla Silva; Gonçalves, Suênia da Cunha; Costa, Pietra Lemos; da Silva, Kamila Gaudêncio; da Silva, Fernando José; Silva, Rômulo Pessoa E; de Brito, Maria Edileuza Felinto; Brandão-Filho, Sinval Pinto; Dantas-Torres, Filipe; de Paiva-Cavalcanti, Milena

    2013-04-01

    Visceral leishmaniosis (VL) is a parasitic disease caused by Leishmania infantum, which is primarily transmitted by phlebotomine sandflies. However, there has been much speculation on the role of other arthropods in the transmission of VL. Thus, the aim of this study was to assess the presence of L. infantum in cats, dogs and their ectoparasites in a VL-endemic area in northeastern Brazil. DNA was extracted from blood samples and ectoparasites, tested by conventional PCR (cPCR) and quantitative real time PCR (qPCR) targeting the L. infantum kinetoplast DNA. A total of 280 blood samples (from five cats and 275 dogs) and 117 ectoparasites from dogs were collected. Animals were apparently healthy and not previously tested by serological or molecular diagnostic methods. Overall, 213 (76.1 %) animals and 51 (43.6 %) ectoparasites were positive to L. infantum, with mean parasite loads of 795.2, 31.9 and 9.1 fg in dogs, cats and ectoparasites, respectively. Concerning the positivity between dogs and their ectoparasites, 32 (15.3 %) positive dogs were parasitized by positive ectoparasites. The overall concordance between the PCR protocols used was 59.2 %, with qPCR being more efficient than cPCR; 34.1 % of all positive samples were exclusively positive by qPCR. The high number of positive animals and ectoparasites also indicates that they could serve as sentinels or indicators of the circulation of L. infantum in risk areas.

  1. Diagnosis of Cutaneous Leishmaniasis by Multiplex PCR

    Directory of Open Access Journals (Sweden)

    M Heiat

    2010-07-01

    Full Text Available Introduction: Annually, more than 14 million people are reported to be infected with Leishmaniasis all over the world. In Iran, this disease is seen in the form of cutaneous and visceral leishmaniasis, of which the cutaneous form is more wide spread. In recent years, cutaneous leishmaniaisis is diagnosed by PCR utilizing specific primers in order to amplify different parasite genes including ribosomal RNA genes, kinetoplast DNA or tandem repeating sequences. The aim of this research was to detect early stage cutaneous leishmaniasis using Multiplex-PCR technique. Methods: In this study, 67 samples were prepared from patients with cutaneous leishmaniasis. DNA was extracted with phenolchloroform. Each specimen was analyzed using two different pairs of PCR primers. The sensitivity of each PCR was optimized on pure Leishmania DNA prior to use for diagnosis. Two standard parasites L. major and L. tropica were used as positive control. Results: DNA amplification fragments were two 115 bp and 683 bp for AB and UL primers, respectively. The sensitivity of two primers was not equal for detection of L. major and L. tropica. The sensivity of PCR with AB primer was 35 cells, while that for UL primer was 40 cells. Conclusion: The results of this study indicate that PCR is a sensitive diagnostic assay for cutaneous leishmaniasis and could be employed as the new standard for routine diagnosis when species identification is not required. However, the ability to identify species is especially important in prognosis of the disease and in deciding appropriate therapy, especially in regions where more than one type of species and disease are seen by clinicians.

  2. A functional gene array for detection of bacterial virulence elements

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, C

    2007-11-01

    We report our development of the first of a series of microarrays designed to detect pathogens with known mechanisms of virulence and antibiotic resistance. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples. To validate our approach, we developed a first generation array targeting genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for microorganism detection and discrimination, measured the required target concentration, and assessed tolerance for mismatches between probe and target sequences. Mismatch tolerance is a priority for this application, due to DNA sequence variability among members of gene families. Arrays were created using the NimbleGen Maskless Array Synthesizer at Lawrence Livermore National Laboratory. Purified genomic DNA from combinations of one or more of the four target organisms, pure cultures of four related organisms, and environmental aerosol samples with spiked-in genomic DNA were hybridized to the arrays. Based on the success of this prototype, we plan to design further arrays in this series, with the goal of detecting all known virulence and antibiotic resistance gene families in a greatly expanded set of organisms.

  3. Radial microstrip slotline feed network for circular mobile communications array

    Science.gov (United States)

    Simons, Rainee N.; Kelly, Eron S.; Lee, Richard Q.; Taub, Susan R.

    1994-01-01

    In mobile and satellite communications there is a need for low cost and low profile antennas which have a toroidal pattern. Antennas that have been developed for mobile communications include a L-Band electronically steered stripline phased array, a Ka-Band mechanically steered elliptical reflector antenna and a Ka-Band printed dipole. In addition, a L-Band mechanically steered microstrip array, a L-Band microstrip phased array tracking antenna for mounting on a car roof and an X-Band radial line slotted waveguide antenna have been demonstrated. In the above electronically scanned printed arrays, the individual element radiates normally to the plane of the array and hence require a phase shifter to scan the beam towards the horizon. Scanning in the azimuth is by mechanical or electronic steering. An alternate approach is to mount microstrip patch radiators on the surface of a cone to achieve the required elevation angle. The array then scans in the azimuth by beam switching.

  4. Systematic flow manipulation by a deflector-turbine array

    Science.gov (United States)

    Mandre, Shreyas; Mangan, Niall M.

    2017-11-01

    Wind and hydrokinetic turbines are often installed in the wake of upstream turbines that limit the energy incident on the downstream ones. In two-dimensions, we describe how an array can deflect the wake away and redirect more energy to itself. Using inviscid fluid dynamics, we formulate the definitions of ``deflectors'' and ``turbines'' as elements that introduce bound and shed vorticity in the flow, respectively. To illustrate the flow manipulation, we consider a deflector-turbine array constrained to a line segment aligned with the freestream and acting as an internal boundary. We impose profiles of bound and shed vorticity on this segment that parameterize the flow deflection and the wake deficit respectively, and analyze the resulting flow using inviscid fluid dynamics. We find that the power extracted by the array is the product of two components: (i) the deflected kinetic energy incident on the array, and (ii) the array efficiency, or its ability to extract a fraction of the incident energy, both of which vary with deflection strength. The array efficiency decreases slightly with increasing deflection from about 57% at weak deflection to 39% at high deflection. This decrease is outweighed by an increase in the incident kinetic energy due to deflection. Funded by the Advanced Research Projects Agency - Energy.

  5. Reduction of heteroduplex formation in PCR amplification

    Czech Academy of Sciences Publication Activity Database

    Michu, Elleni; Mráčková, Martina; Vyskot, Boris; Žlůvová, Jitka

    2010-01-01

    Roč. 54, č. 1 (2010), s. 173-176 ISSN 0006-3134 R&D Projects: GA AV ČR(CZ) KJB600040801; GA ČR(CZ) GD204/09/H002; GA AV ČR(CZ) IAA600040801; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : polymerase chain reaction * reconditioning PCR * mixed-template PCR Subject RIV: BO - Biophysics Impact factor: 1.582, year: 2010

  6. A naked-eye colorimetric "PCR developer"

    Science.gov (United States)

    Valentini, Paola; Pompa, Pier Paolo

    2016-04-01

    Despite several advances in molecular biology and diagnostics, Polymerase Chain Reaction (PCR) is currently the gold standard for nucleic acids amplification and detection, due to its versatility, low-cost and universality, with estimated genetically modified organisms, and pathogens). The PCR developer proved to be highly specific and ultra-sensitive, discriminating down to few copies of HIV viral DNA, diluted in an excess of interfering human genomic DNA, which is a clinically relevant viral load. Hence, it could be a valuable tool for both academic research and clinical applications.

  7. Comparative analysis of gene expression profiles of OPN signalling ...

    Indian Academy of Sciences (India)

    were orally treated with the high-fat emulsion (10 mL/kg) by gavage once a day ... 4 weeks, and drinking water was offered with 10% ethanol. Drinking water ..... detected by Rat Genome 230 2.0 Array and dark grey colour represents RT-PCR.

  8. Molecular profiling of microbial communities from contaminated sources: Use of subtractive cloning methods and rDNA spacer sequences. 1998 annual progress report

    International Nuclear Information System (INIS)

    Robb, F.T.

    1998-01-01

    'The major objective of the research is to provide appropriate sequences and to assemble a high-density DNA array of oligonucleotides that can be used for rapid profiling of microbial populations from polluted areas. The sequences to be assigned to the DNA array are chosen from from cloned genomic DNA sequences (the ribosomal operon, described below) from groundwater at DOE sites containing organic solvents. The sites, Hanford Nuclear Plant and Lawrence Livermore Site 300, have well characterized pollutant histories, which have been provided by the collaborators. At this mid-point of the project, over 60 unique sequence classes of intergenic spacer region have been identified from the first sample site. The use of these sequences as hybridization probes, and their frequency of occurrence, allow a clear distinction between bacterial communities before and after remediation by acetate/nitrate pumping. The authors have developed the hybridization conditions for identifying PCR products in a 96 well format, a versatile alignment and visualization program (acronym: MALIGN) developed by Dr. Dennis Maeder, has been used to align the ISRs, which are variable in length and sometimes in position of the tRNAs. Finally, in collaboration with Dr. W. Chen and Dr. J. Zhou at ORNL, they have significant evidence that mass spectrometer analysis can be used to determine the lengths of PCR amplified intergenic spacer DNA.'

  9. Cyclotron-Resonance-Maser Arrays

    International Nuclear Information System (INIS)

    Kesar, A.; Lei, L.; Dikhtyar, V.; Korol, M.; Jerby, E.

    1999-01-01

    The cyclotron-resonance-maser (CRM) array [1] is a radiation source which consists of CRM elements coupled together under a common magnetic field. Each CRM-element employs a low-energy electron-beam which performs a cyclotron interaction with the local electromagnetic wave. These waves can be coupled together among the CRM elements, hence the interaction is coherently synchronized in the entire array. The implementation of the CRM-array approach may alleviate several technological difficulties which impede the development of single-beam gyro-devices. Furthermore, it proposes new features, such as the phased-array antenna incorporated in the CRM-array itself. The CRM-array studies may lead to the development of compact, high-power radiation sources operating at low-voltages. This paper introduces new conceptual schemes of CRM-arrays, and presents the progress in related theoretical and experimental studies in our laboratory. These include a multi-mode analysis of a CRM-array, and a first operation of this device with five carbon-fiber cathodes

  10. Submillimeter heterodyne arrays for APEX

    NARCIS (Netherlands)

    Güsten, R.; Baryshev, A.; Bell, A.; Belloche, A.; Graf, U.; Hafok, H.; Heyminck, S.; Hochgürtel, S.; Honingh, C. E.; Jacobs, K.; Kasemann, C.; Klein, B.; Klein, T.; Korn, A.; Krämer, I.; Leinz, C.; Lundgren, A.; Menten, K. M.; Meyer, K.; Muders, D.; Pacek, F.; Rabanus, D.; Schäfer, F.; Schilke, P.; Schneider, G.; Stutzki, J.; Wieching, G.; Wunsch, A.; Wyrowski, F.

    2008-01-01

    We report on developments of submillimeter heterodyne arrays for high resolution spectroscopy with APEX. Shortly, we will operate state-of-the-art instruments in all major atmospheric windows accessible from Llano de Chajnantor. CHAMP+, a dual-color 2×7 element heterodyne array for operation in the

  11. Digital electrostatic acoustic transducer array

    KAUST Repository

    Carreno, Armando Arpys Arevalo

    2016-12-19

    In this paper we present the fabrication and characterization of an array of electrostatic acoustic transducers. The array is micromachined on a silicon wafer using standard micro-machining techniques. Each array contains 2n electrostatic transducer membranes, where “n” is the bit number. Every element of the array has a hexagonal membrane shape structure, which is separated from the substrate by 3µm air gap. The membrane is made out 5µm thick polyimide layer that has a bottom gold electrode on the substrate and a gold top electrode on top of the membrane (250nm). The wafer layout design was diced in nine chips with different array configurations, with variation of the membrane dimensions. The device was tested with 90 V giving and sound output level as high as 35dB, while actuating all the elements at the same time.

  12. Digital electrostatic acoustic transducer array

    KAUST Repository

    Carreno, Armando Arpys Arevalo; Castro, David; Conchouso Gonzalez, David; Kosel, Jü rgen; Foulds, Ian G.

    2016-01-01

    In this paper we present the fabrication and characterization of an array of electrostatic acoustic transducers. The array is micromachined on a silicon wafer using standard micro-machining techniques. Each array contains 2n electrostatic transducer membranes, where “n” is the bit number. Every element of the array has a hexagonal membrane shape structure, which is separated from the substrate by 3µm air gap. The membrane is made out 5µm thick polyimide layer that has a bottom gold electrode on the substrate and a gold top electrode on top of the membrane (250nm). The wafer layout design was diced in nine chips with different array configurations, with variation of the membrane dimensions. The device was tested with 90 V giving and sound output level as high as 35dB, while actuating all the elements at the same time.

  13. Chunking of Large Multidimensional Arrays

    Energy Technology Data Exchange (ETDEWEB)

    Rotem, Doron; Otoo, Ekow J.; Seshadri, Sridhar

    2007-02-28

    Data intensive scientific computations as well on-lineanalytical processing applications as are done on very large datasetsthat are modeled as k-dimensional arrays. The storage organization ofsuch arrays on disks is done by partitioning the large global array intofixed size hyper-rectangular sub-arrays called chunks or tiles that formthe units of data transfer between disk and memory. Typical queriesinvolve the retrieval of sub-arrays in a manner that accesses all chunksthat overlap the query results. An important metric of the storageefficiency is the expected number of chunks retrieved over all suchqueries. The question that immediately arises is "what shapes of arraychunks give the minimum expected number of chunks over a query workload?"In this paper we develop two probabilistic mathematical models of theproblem and provide exact solutions using steepest descent and geometricprogramming methods. Experimental results, using synthetic workloads onreal life data sets, show that our chunking is much more efficient thanthe existing approximate solutions.

  14. Passive microfluidic array card and reader

    Science.gov (United States)

    Dugan, Lawrence Christopher [Modesto, CA; Coleman, Matthew A [Oakland, CA

    2011-08-09

    A microfluidic array card and reader system for analyzing a sample. The microfluidic array card includes a sample loading section for loading the sample onto the microfluidic array card, a multiplicity of array windows, and a transport section or sections for transporting the sample from the sample loading section to the array windows. The microfluidic array card reader includes a housing, a receiving section for receiving the microfluidic array card, a viewing section, and a light source that directs light to the array window of the microfluidic array card and to the viewing section.

  15. Molecular analysis of the genera eremopyrum (ledeb). jaub. and spach and agropyron gaertner (poaceae) by pcr methods

    International Nuclear Information System (INIS)

    Yilmaz, R.; Cabi, E.; Dogan, M.

    2014-01-01

    RAPD-PCR (Random Amplified Polymorphic DNA Polymerase Chain Reaction) and Post PCR (Polymerase Chain Reaction) Melting Curve Analysis (MCA) have been used to investigate the pattern of genetic variation among some species in the genera Eremopyrum (Ledeb.) Jaub. and Spach and Agropyron Gaertner (Poaceae). Thirteen primers have been used in the study based on the RAPD-PCR and MCA analyses. Each species produced a distinct pattern of DNA fragments which have been used as a measure of the degree of relationship between species by means of using the RAPD-PCR results with three primers selected for identifying the genetic similarities. Polymorphic melting profiles have been obtained with Post PCR MCA method using three primers. Genetic similarities are calculated for all the species studied with RAPD-PCR and MCA methods, the dendrograms are obtained with the MVSP (Multi Variate Statistical Package) software using UPGMA (Unweighted Pair Group Method with Arithmetic Averages) and Jaccard's Coefficient. Polymorphism between 18 populations of Eremopyrum and 6 Agropyron populations and within the species are determined by using RAPD-PCR and Post PCR melting curve analysis (MCA) respectively. (author)

  16. Global Expression Patterns of Three Festuca Species Exposed to Different Doses of Glyphosate Using the Affymetrix GeneChip Wheat Genome Array

    Directory of Open Access Journals (Sweden)

    Ozge Cebeci

    2009-01-01

    Full Text Available Glyphosate has been shown to act as an inhibitor of an aromatic amino acid biosynthetic pathway, while other pathways that may be affected by glyphosate are not known. Cross species hybridizations can provide a tool for elucidating biological pathways conserved among organisms. Comparative genome analyses have indicated a high level of colinearity among grass species and Festuca, on which we focus here, and showed rearrangements common to the Pooideae family. Based on sequence conservation among grass species, we selected the Affymetrix GeneChip Wheat Genome Array as a tool for the analysis of expression profiles of three Festuca (fescue species with distinctly different tolerances to varying levels of glyphosate. Differences in transcript expression were recorded upon foliar glyphosate application at 1.58 mM and 6.32 mM, representing 5% and 20%, respectively, of the recommended rate. Differences highlighted categories of general metabolic processes, such as photosynthesis, protein synthesis, stress responses, and a larger number of transcripts responded to 20% glyphosate application. Differential expression of genes encoding proteins involved in the shikimic acid pathway could not be identified by cross hybridization. Microarray data were confirmed by RT-PCR and qRT-PCR analyses. This is the first report to analyze the potential of cross species hybridization in Fescue species and the data and analyses will help extend our knowledge on the cellular processes affected by glyphosate.

  17. SAQC: SNP Array Quality Control

    Directory of Open Access Journals (Sweden)

    Li Ling-Hui

    2011-04-01

    Full Text Available Abstract Background Genome-wide single-nucleotide polymorphism (SNP arrays containing hundreds of thousands of SNPs from the human genome have proven useful for studying important human genome questions. Data quality of SNP arrays plays a key role in the accuracy and precision of downstream data analyses. However, good indices for assessing data quality of SNP arrays have not yet been developed. Results We developed new quality indices to measure the quality of SNP arrays and/or DNA samples and investigated their statistical properties. The indices quantify a departure of estimated individual-level allele frequencies (AFs from expected frequencies via standardized distances. The proposed quality indices followed lognormal distributions in several large genomic studies that we empirically evaluated. AF reference data and quality index reference data for different SNP array platforms were established based on samples from various reference populations. Furthermore, a confidence interval method based on the underlying empirical distributions of quality indices was developed to identify poor-quality SNP arrays and/or DNA samples. Analyses of authentic biological data and simulated data show that this new method is sensitive and specific for the detection of poor-quality SNP arrays and/or DNA samples. Conclusions This study introduces new quality indices, establishes references for AFs and quality indices, and develops a detection method for poor-quality SNP arrays and/or DNA samples. We have developed a new computer program that utilizes these methods called SNP Array Quality Control (SAQC. SAQC software is written in R and R-GUI and was developed as a user-friendly tool for the visualization and evaluation of data quality of genome-wide SNP arrays. The program is available online (http://www.stat.sinica.edu.tw/hsinchou/genetics/quality/SAQC.htm.

  18. Development of portable phased array UT system for real-time flaw imaging

    International Nuclear Information System (INIS)

    Goto, M.

    1995-01-01

    Many functions and features of phased array UT technology must be useful for NDE in the industrial field. Some phased array UT systems have been developed for the inspection of nuclear pressure vessel and turbine components. However, phased array UT is still a special NDE technique and it has not been used widely in the past. The reasons of that are system size, cost, operator performance, equipment design and others. TOSHIBA has newly developed PC controlled portable phased array system to solve those problems. The portable phased array UT system is very compact and light but it is able to drive up to 32-channel linear array probe, to display real-time linear/sector B-scan, to display accumulated B-scan with an encoder and to display profile overlaid B-scan. The first applications were turbine component inspections for precise flaw investigation and flaw image data recording

  19. Circularly Polarized Antenna Array Fed by Air-Bridge Free CPW-Slotline Network

    Directory of Open Access Journals (Sweden)

    Yilin Liu

    2017-01-01

    Full Text Available A novel design of 1×2 and 2×2 circularly polarized (CP microstrip patch antenna arrays is presented in this paper. The two CP antenna arrays are fed by sequentially rotated coplanar waveguide (CPW to slotline networks and are processed on 1 mm thick single-layer FR4 substrates. Both of the two arrays are low-profile and lightweight. An air-bridge free CPW-slotline power splitter is appropriately designed to form the feeding networks and realize the two CP antenna arrays. The mechanism of circular polarization in this design is explained. The simulated and measured impedance bandwidths as well as the 3 dB axial ratio bandwidths and the radiation patterns of the two proposed antenna arrays are presented. This proposed design can be easily extended to form a larger plane array with good performance owing to its simple structure.

  20. Detection of Mycobacterium Tuberculosis by using PCR

    International Nuclear Information System (INIS)

    Suhadi, F; Dadang-Sudrajat; Maria-Lina, R.

    1996-01-01

    Polymerase Chain Reaction (PCR) procedure using three primary set derived from repetitive DNA sequence specific to mycobacteria was used to diagnose pathogenic Mycobacterium tuberculosis. The assay was specific for M. tuberculosis and could be used to detect the amount DNA less than 10 -9 g

  1. PCR detection of potato cyst nematode.

    Science.gov (United States)

    Reid, Alex

    2009-01-01

    Potato cyst nematode (PCN) is responsible for losses in potato production totalling millions of euros every year in the EC. It is important for growers to know which species is present in their land as this determines its subsequent use. The two species Globodera pallida and Globodera rostochiensis can be differentiated using an allele-specific PCR.

  2. Altered retinal microRNA expression profiles in early diabetic retinopathy: an in silico analysis.

    Science.gov (United States)

    Xiong, Fen; Du, Xinhua; Hu, Jianyan; Li, Tingting; Du, Shanshan; Wu, Qiang

    2014-07-01

    MicroRNAs (miRNAs) - as negative regulators of target genes - are associated with various human diseases, but their precise role(s) in diabetic retinopathy (DR) remains to be elucidated. The aim of this study was to elucidate the involvement of miRNAs in early DR using in silico analysis to explore their gene expression patterns. We used the streptozotocin (STZ)-induced diabetic rat to investigate the roles of miRNAs in early DR. Retinal miRNA expression profiles from diabetic versus healthy control rats were examined by miRNA array analysis. Based on several bioinformatic systems, specifically, gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, we identified signatures of the potential pathological processes, gene functions, and signaling pathways that are influenced by dysregulated miRNAs. We used quantitative real-time polymerase chain reaction (qRT-PCR) to validate six (i.e. those with significant changes in expression levels) of the 17 miRNAs that were detected in the miRNA array. We also describe the significant role of the miRNA-gene network, which is based on the interactions between miRNAs and target genes. GO analysis of the 17 miRNAs detected in the miRNA array analysis revealed the most prevalent miRNAs to be those related to biological processes, olfactory bulb development and axonogenesis. These miRNAs also exert significant influence on additional pathways, including the mitogen-activated protein and calcium signaling pathways. Six of the seventeen miRNAs were chosen for qRT-PCR validation. With the exception of a slight difference in miRNA-350, our results are in close agreement with the differential expressions detected by array analysis. This study, which describes miRNA expression during the early developmental phases of DR, revealed extensive miRNA interactions. Based on both their target genes and signaling pathways, we suggest that miRNAs perform critical regulatory functions during the early stages of DR

  3. A survey of tools for the analysis of quantitative PCR (qPCR) data.

    Science.gov (United States)

    Pabinger, Stephan; Rödiger, Stefan; Kriegner, Albert; Vierlinger, Klemens; Weinhäusel, Andreas

    2014-09-01

    Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research. Analysis of qPCR data is a crucial part of the entire experiment, which has led to the development of a plethora of methods. The released tools either cover specific parts of the workflow or provide complete analysis solutions. Here, we surveyed 27 open-access software packages and tools for the analysis of qPCR data. The survey includes 8 Microsoft Windows, 5 web-based, 9 R-based and 5 tools from other platforms. Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR. We report an overview of the functionality, features and specific requirements of the individual software tools, such as data exchange formats, availability of a graphical user interface, included procedures for graphical data presentation, and offered statistical methods. In addition, we provide an overview about quantification strategies, and report various applications of qPCR. Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.

  4. Quantitative Real-Time PCR using the Thermo Scientific Solaris qPCR Assay

    Science.gov (United States)

    Ogrean, Christy; Jackson, Ben; Covino, James

    2010-01-01

    The Solaris qPCR Gene Expression Assay is a novel type of primer/probe set, designed to simplify the qPCR process while maintaining the sensitivity and accuracy of the assay. These primer/probe sets are pre-designed to >98% of the human and mouse genomes and feature significant improvements from previously available technologies. These improvements were made possible by virtue of a novel design algorithm, developed by Thermo Scientific bioinformatics experts. Several convenient features have been incorporated into the Solaris qPCR Assay to streamline the process of performing quantitative real-time PCR. First, the protocol is similar to commonly employed alternatives, so the methods used during qPCR are likely to be familiar. Second, the master mix is blue, which makes setting the qPCR reactions easier to track. Third, the thermal cycling conditions are the same for all assays (genes), making it possible to run many samples at a time and reducing the potential for error. Finally, the probe and primer sequence information are provided, simplifying the publication process. Here, we demonstrate how to obtain the appropriate Solaris reagents using the GENEius product search feature found on the ordering web site (www.thermo.com/solaris) and how to use the Solaris reagents for performing qPCR using the standard curve method. PMID:20567213

  5. Pneumocystis PCR: It Is Time to Make PCR the Test of Choice.

    Science.gov (United States)

    Doyle, Laura; Vogel, Sherilynn; Procop, Gary W

    2017-01-01

    The testing strategy for Pneumocystis at the Cleveland Clinic changed from toluidine blue staining to polymerase chain reaction (PCR). We studied the differences in positivity rates for these assays and compared each with the detection of Pneumocystis in companion specimens by cytology and surgical pathology. We reviewed the results of all Pneumocystis test orders 1 year before and 1 year after the implementation of a Pneumocystis -specific PCR. We also reviewed the corresponding cytology and surgical pathology results, if performed. Finally, we reviewed the medical records of patients with rare Pneumocystis detected by PCR in an effort to differentiate colonization vs true disease. Toluidine blue staining and surgical pathology had similar sensitivities and negative predictive values, both of which were superior to cytology. There was a >4-fold increase in the annual detection of Pneumocystis by PCR compared with toluidine blue staining (toluidine blue staining: 11/1583 [0.69%] vs PCR: 44/1457 [3.0%]; chi-square P < .001). PCR detected 1 more case than surgical pathology and was far more sensitive than cytology. Chart review demonstrated that the vast majority of patients with rare Pneumocystis detected were immunosuppressed, had radiologic findings supportive of this infection, had no other pathogens detected, and were treated for pneumocystosis by the clinical team. PCR was the most sensitive method for the detection of Pneumocystis and should be considered the diagnostic test of choice. Correlation with clinical and radiologic findings affords discrimination of early true disease from the far rarer instances of colonization.

  6. Dependently typed array programs don’t go wrong

    NARCIS (Netherlands)

    Trojahner, K.; Grelck, C.

    2009-01-01

    The array programming paradigm adopts multidimensional arrays as the fundamental data structures of computation. Array operations process entire arrays instead of just single elements. This makes array programs highly expressive and introduces data parallelism in a natural way. Array programming

  7. Dependently typed array programs don't go wrong

    NARCIS (Netherlands)

    Trojahner, K.; Grelck, C.

    2008-01-01

    The array programming paradigm adopts multidimensional arrays as the fundamental data structures of computation. Array operations process entire arrays instead of just single elements. This makes array programs highly expressive and introduces data parallelism in a natural way. Array programming

  8. Digital PCR for direct quantification of viruses without DNA extraction

    OpenAIRE

    Pav?i?, Jernej; ?el, Jana; Milavec, Mojca

    2015-01-01

    DNA extraction before amplification is considered an essential step for quantification of viral DNA using real-time PCR (qPCR). However, this can directly affect the final measurements due to variable DNA yields and removal of inhibitors, which leads to increased inter-laboratory variability of qPCR measurements and reduced agreement on viral loads. Digital PCR (dPCR) might be an advantageous methodology for the measurement of virus concentrations, as it does not depend on any calibration mat...

  9. Detection of Lymnaea columella infection by Fasciola hepatica through Multiplex-PCR

    Directory of Open Access Journals (Sweden)

    Kelly Grace Magalhães

    2004-06-01

    Full Text Available From complete mitochondrial DNA sequence of Fasciola hepatica available in Genbank, specific primers were designed for a conserved and repetitive region of this trematode. A pair of primers was used for diagnosis of infected Lymnaea columella by F. hepatica during the pre-patent period simultaneously with another pair of primers which amplified the internal transcribed spacer (ITS region of rDNA from L. columella in a single Multiplex-PCR. The amplification generated a ladder band profile specific for F. hepatica. This profile was observed in positive molluscs at different times of infection, including adult worms from the trematode. The Multiplex-PCR technique showed to be a fast and safe tool for fascioliasis diagnosis, enabling the detection of F. hepatica miracidia in L. columella during the pre-patent period and identification of transmission areas.

  10. A Simple PCR Method for Rapid Genotype Analysis of Mycobacterium ulcerans

    Science.gov (United States)

    Stinear, Timothy; Davies, John K.; Jenkin, Grant A.; Portaels, Françoise; Ross, Bruce C.; OppEdIsano, Frances; Purcell, Maria; Hayman, John A.; Johnson, Paul D. R.

    2000-01-01

    Two high-copy-number insertion sequences, IS2404 and IS2606, were recently identified in Mycobacterium ulcerans and were shown by Southern hybridization to possess restriction fragment length polymorphism between strains from different geographic origins. We have designed a simple genotyping method that captures these differences by PCR amplification of the region between adjacent copies of IS2404 and IS2606. We have called this system 2426 PCR. The method is rapid, reproducible, sensitive, and specific for M. ulcerans, and it has confirmed previous studies suggesting a clonal population structure of M. ulcerans within a geographic region. M. ulcerans isolates from Australia, Papua New Guinea, Malaysia, Surinam, Mexico, Japan, China, and several countries in Africa were easily differentiated based on an array of 4 to 14 PCR products ranging in size from 200 to 900 bp. Numerical analysis of the banding patterns suggested a close evolutionary link between M. ulcerans isolates from Africa and southeast Asia. The application of 2426 PCR to total DNA, extracted directly from M. ulcerans-infected tissue specimens without culture, demonstrated the sensitivity and specificity of this method and confirmed for the first time that both animal and human isolates from areas of endemicity in southeast Australia have the same genotype. PMID:10747130

  11. Comparison of simultaneous splenic sample PCR with blood sample PCR for diagnosis and treatment of experimental Ehrlichia canis infection.

    Science.gov (United States)

    Harrus, Shimon; Kenny, Martin; Miara, Limor; Aizenberg, Itzhak; Waner, Trevor; Shaw, Susan

    2004-11-01

    This report presents evidence that dogs recover from acute canine monocytic ehrlichiosis (CME) after 16 days of doxycycline treatment (10 mg/kg of body weight every 24 h). Blood PCR was as valuable as splenic aspirate PCR for early diagnosis of acute CME. Splenic aspirate PCR was, however, superior to blood PCR for the evaluation of ehrlichial elimination.

  12. MicroRNAs expression profile in solid and unicystic ameloblastomas

    Science.gov (United States)

    Setién-Olarra, A.; Bediaga, N. G.; Aguirre-Echebarria, P.; Aguirre-Urizar, J. M.; Mosqueda-Taylor, A.

    2017-01-01

    Objectives Odontogenic tumors (OT) represent a specific pathological category that includes some lesions with unpredictable biological behavior. Although most of these lesions are benign, some, such as the ameloblastoma, exhibit local aggressiveness and high recurrence rates. The most common types of ameloblastoma are the solid/multicystic (SA) and the unicystic ameloblastoma (UA); the latter considered a much less aggressive entity as compared to the SA. The microRNA system regulates the expression of many human genes while its deregulation has been associated with neoplastic development. The aim of the current study was to determine the expression profiles of microRNAs present in the two most common types of ameloblastomas. Material & methods MicroRNA expression profiles were assessed using TaqMan® Low Density Arrays (TLDAs) in 24 samples (8 SA, 8 UA and 8 control samples). The findings were validated using quantitative RTqPCR in an independent cohort of 19 SA, 8 UA and 19 dentigerous cysts as controls. Results We identified 40 microRNAs differentially regulated in ameloblastomas, which are related to neoplastic development and differentiation, and with the osteogenic process. Further validation of the top ranked microRNAs revealed significant differences in the expression of 6 of them in relation to UA, 7 in relation to SA and 1 (miR-489) that was related to both types. Conclusion We identified a new microRNA signature for the ameloblastoma and for its main types, which may be useful to better understand the etiopathogenesis of this neoplasm. In addition, we identified a microRNA (miR-489) that is suggestive of differentiating among solid from unicystic ameloblastoma. PMID:29053755

  13. Optimization and analysis of a quantitative real-time PCR-based technique to determine microRNA expression in formalin-fixed paraffin-embedded samples

    Directory of Open Access Journals (Sweden)

    Reis Patricia P

    2010-06-01

    Full Text Available Abstract Background MicroRNAs (miRs are non-coding RNA molecules involved in post-transcriptional regulation, with diverse functions in tissue development, differentiation, cell proliferation and apoptosis. miRs may be less prone to degradation during formalin fixation, facilitating miR expression studies in formalin-fixed paraffin-embedded (FFPE tissue. Results Our study demonstrates that the TaqMan Human MicroRNA Array v1.0 (Early Access platform is suitable for miR expression analysis in FFPE tissue with a high reproducibility (correlation coefficients of 0.95 between duplicates, p 35, we show that reproducibility between technical replicates, equivalent dilutions, and FFPE vs. frozen samples is best in the high abundance stratum. We also demonstrate that the miR expression profiles of FFPE samples are comparable to those of fresh-frozen samples, with a correlation of up to 0.87 (p Conclusion Our study thus demonstrates the utility, reproducibility, and optimization steps needed in miR expression studies using FFPE samples on a high-throughput quantitative PCR-based miR platform, opening up a realm of research possibilities for retrospective studies.

  14. ESPRIT And Uniform Linear Arrays

    Science.gov (United States)

    Roy, R. H.; Goldburg, M.; Ottersten, B. E.; Swindlehurst, A. L.; Viberg, M.; Kailath, T.

    1989-11-01

    Abstract ¬â€?ESPRIT is a recently developed and patented technique for high-resolution estimation of signal parameters. It exploits an invariance structure designed into the sensor array to achieve a reduction in computational requirements of many orders of magnitude over previous techniques such as MUSIC, Burg's MEM, and Capon's ML, and in addition achieves performance improvement as measured by parameter estimate error variance. It is also manifestly more robust with respect to sensor errors (e.g. gain, phase, and location errors) than other methods as well. Whereas ESPRIT only requires that the sensor array possess a single invariance best visualized by considering two identical but other-wise arbitrary arrays of sensors displaced (but not rotated) with respect to each other, many arrays currently in use in various applications are uniform linear arrays of identical sensor elements. Phased array radars are commonplace in high-resolution direction finding systems, and uniform tapped delay lines (i.e., constant rate A/D converters) are the rule rather than the exception in digital signal processing systems. Such arrays possess many invariances, and are amenable to other types of analysis, which is one of the main reasons such structures are so prevalent. Recent developments in high-resolution algorithms of the signal/noise subspace genre including total least squares (TLS) ESPRIT applied to uniform linear arrays are summarized. ESPRIT is also shown to be a generalization of the root-MUSIC algorithm (applicable only to the case of uniform linear arrays of omni-directional sensors and unimodular cisoids). Comparisons with various estimator bounds, including CramerRao bounds, are presented.

  15. Fiber-array based optogenetic prosthetic system for stimulation therapy

    Science.gov (United States)

    Gu, Ling; Cote, Chris; Tejeda, Hector; Mohanty, Samarendra

    2012-02-01

    Recent advent of optogenetics has enabled activation of genetically-targeted neuronal cells using low intensity blue light with high temporal precision. Since blue light is attenuated rapidly due to scattering and absorption in neural tissue, optogenetic treatment of neurological disorders may require stimulation of specific cell types in multiple regions of the brain. Further, restoration of certain neural functions (vision, and auditory etc) requires accurate spatio-temporal stimulation patterns rather than just precise temporal stimulation. In order to activate multiple regions of the central nervous system in 3D, here, we report development of an optogenetic prosthetic comprising of array of fibers coupled to independently-controllable LEDs. This design avoids direct contact of LEDs with the brain tissue and thus does not require electrical and heat isolation, which can non-specifically stimulate and damage the local brain regions. The intensity, frequency, and duty cycle of light pulses from each fiber in the array was controlled independently using an inhouse developed LabView based program interfaced with a microcontroller driving the individual LEDs. While the temporal profile of the light pulses was controlled by varying the current driving the LED, the beam profile emanating from each fiber tip could be sculpted by microfabrication of the fiber tip. The fiber array was used to stimulate neurons, expressing channelrhodopsin-2, in different locations within the brain or retina. Control of neural activity in the mice cortex, using the fiber-array based prosthetic, is evaluated from recordings made with multi-electrode array (MEA). We also report construction of a μLED array based prosthetic for spatio-temporal stimulation of cortex.

  16. PCR-DGGE Analysis of Bacterial Population Attached to the Bovine Rumen Wall

    OpenAIRE

    Lukáš, F. (Filip); Šimůnek, J. (Jiří); Mrázek, J. (Jakub); Kopečný, J. (Jan)

    2010-01-01

    We isolated and amplified by PCR 16S rDNA from bacteria attached to the bovine rumen wall and analyzed it by denaturing gradient gel electrophoresis (DGGE) with subsequent sequence analysis. The attached bacterial community differed from the bacteria of rumen content; however, no differences were observed among the five epithelial sampling sites taken from each animal. The DGGE profile of the bacterial population attached to the rumen wall represented a high inter-animal variation.

  17. A sensor array system for monitoring moisture dynamics inunsaturated soil

    Energy Technology Data Exchange (ETDEWEB)

    Salve, R.; Cook, P.J.

    2007-05-15

    To facilitate investigations of moisture dynamics inunsaturated soil, we have developed a technique to qualitatively monitorpatterns of saturation changes. Field results suggest that this device,the sensor array system (SAS), is suitable for determining changes inrelative wetness along vertical soil profiles. The performance of theseprobes was compared with that of the time domain reflectometry (TDR)technique under controlled and field conditions. Measurements from bothtechniques suggest that by obtaining data at high spatial and temporalresolution, the SAS technique was effective in determining patterns ofsaturation changes along a soil profile. In addition, hardware used inthe SAS technique was significantly cheaper than the TDR system, and thesensor arrays were much easier to install along a soilprofile.

  18. The Owens Valley Millimeter Array

    International Nuclear Information System (INIS)

    Padin, S.; Scott, S.L.; Woody, D.P.; Scoville, N.Z.; Seling, T.V.

    1991-01-01

    The telescopes and signal processing systems of the Owens Valley Millimeter Array are considered, and improvements in the sensitivity and stability of the instrument are characterized. The instrument can be applied to map sources in the 85 to 115 GHz and 218 to 265 GHz bands with a resolution of about 1 arcsec in the higher frequency band. The operation of the array is fully automated. The current scientific programs for the array encompass high-resolution imaging of protoplanetary/protostellar disk structures, observations of molecular cloud complexes associated with spiral structure in nearby galaxies, and observations of molecular structures in the nuclei of spiral and luminous IRAS galaxies. 9 refs

  19. Fundamentals of ultrasonic phased arrays

    CERN Document Server

    Schmerr, Lester W

    2014-01-01

    This book describes in detail the physical and mathematical foundations of ultrasonic phased array measurements.?The book uses linear systems theory to develop a comprehensive model of the signals and images that can be formed with phased arrays. Engineers working in the field of ultrasonic nondestructive evaluation (NDE) will find in this approach a wealth of information on how to design, optimize and interpret ultrasonic inspections with phased arrays. The fundamentals and models described in the book will also be of significant interest to other fields, including the medical ultrasound and

  20. ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization.

    Science.gov (United States)

    Sang, Jian; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Xia, Lin; Zou, Dong; Wang, Fan; Xu, Xingjian; Han, Xiaojiao; Fan, Jinqi; Yang, Ye; Zuo, Wanzhu; Zhang, Yang; Zhao, Wenming; Bao, Yiming; Xiao, Jingfa; Hu, Songnian; Hao, Lili; Zhang, Zhang

    2018-01-04

    Real-time quantitative PCR (RT-qPCR) has become a widely used method for accurate expression profiling of targeted mRNA and ncRNA. Selection of appropriate internal control genes for RT-qPCR normalization is an elementary prerequisite for reliable expression measurement. Here, we present ICG (http://icg.big.ac.cn), a wiki-driven knowledgebase for community curation of experimentally validated internal control genes as well as their associated experimental conditions. Unlike extant related databases that focus on qPCR primers in model organisms (mainly human and mouse), ICG features harnessing collective intelligence in community integration of internal control genes for a variety of species. Specifically, it integrates a comprehensive collection of more than 750 internal control genes for 73 animals, 115 plants, 12 fungi and 9 bacteria, and incorporates detailed information on recommended application scenarios corresponding to specific experimental conditions, which, collectively, are of great help for researchers to adopt appropriate internal control genes for their own experiments. Taken together, ICG serves as a publicly editable and open-content encyclopaedia of internal control genes and accordingly bears broad utility for reliable RT-qPCR normalization and gene expression characterization in both model and non-model organisms. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Detection of hepatitis C virus RNA: comparison of one-stage polymerase chain reaction (PCR) with nested-set PCR.

    OpenAIRE

    Gretch, D R; Wilson, J J; Carithers, R L; dela Rosa, C; Han, J H; Corey, L

    1993-01-01

    We evaluated a new hepatitis C virus RNA assay based on one-stage PCR followed by liquid hybridization with an oligonucleotide probe and compared it with nested-set PCR. The one-stage and nested-set PCR assays had identical sensitivities in analytical experiments and showed 100% concordance when clinical specimens were used. One-stage PCR may be less prone to contamination than nested-set PCR.

  2. Oligonucleotide arrays vs. metaphase-comparative genomic hybridisation and BAC arrays for single-cell analysis: first applications to preimplantation genetic diagnosis for Robertsonian translocation carriers.

    Science.gov (United States)

    Ramos, Laia; del Rey, Javier; Daina, Gemma; García-Aragonés, Manel; Armengol, Lluís; Fernandez-Encinas, Alba; Parriego, Mònica; Boada, Montserrat; Martinez-Passarell, Olga; Martorell, Maria Rosa; Casagran, Oriol; Benet, Jordi; Navarro, Joaquima

    2014-01-01

    Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH) and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈ 20 kb). Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14)(q10;q10). Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers.

  3. Oligonucleotide arrays vs. metaphase-comparative genomic hybridisation and BAC arrays for single-cell analysis: first applications to preimplantation genetic diagnosis for Robertsonian translocation carriers.

    Directory of Open Access Journals (Sweden)

    Laia Ramos

    Full Text Available Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈ 20 kb. Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14(q10;q10. Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers.

  4. Oligonucleotide Arrays vs. Metaphase-Comparative Genomic Hybridisation and BAC Arrays for Single-Cell Analysis: First Applications to Preimplantation Genetic Diagnosis for Robertsonian Translocation Carriers

    Science.gov (United States)

    Ramos, Laia; del Rey, Javier; Daina, Gemma; García-Aragonés, Manel; Armengol, Lluís; Fernandez-Encinas, Alba; Parriego, Mònica; Boada, Montserrat; Martinez-Passarell, Olga; Martorell, Maria Rosa; Casagran, Oriol; Benet, Jordi; Navarro, Joaquima

    2014-01-01

    Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH) and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈20 kb). Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14)(q10;q10). Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers. PMID:25415307

  5. Laser interferometer array for Big Dee

    International Nuclear Information System (INIS)

    Fairbanks, E.S.

    1984-01-01

    A twelve channel interferometer array is planned for obtaining electron density profiles on Big Dee. Three of the channels are vertical; the remainder are radial or diagonal in an azimuthal plane. Each channel consists of coaxial CO/sub 2/ and HeNe laser beams. The reference beam is formed by splitting off half of the laser power at each wavelength by using acousto-optic modulators which introduce a 40 MHz frequency shift in the reference beam. In the radial channels the probe beam passes through a barium fluoride window to a plane metal mirror on the inside wall of the vacuum vessel. The reflected beam passes back out of the vacuum vessel, through the same window, to a beam splitter where the probe beam and the reference beam are again combined

  6. UARS Cryogenic Limb Array Etalon Spectrometer (CLAES) Level 3AL V009 (UARCL3AL) at GES DISC

    Data.gov (United States)

    National Aeronautics and Space Administration — The Cryogenic Limb Array Etalon Spectrometer (CLAES) Level 3AL data product consists of daily, 4 degree increment latitude-ordered vertical profiles of temperature...

  7. UARS Cryogenic Limb Array Etalon Spectrometer (CLAES) Level 3AT V009 (UARCL3AT) at GES DISC

    Data.gov (United States)

    National Aeronautics and Space Administration — The Cryogenic Limb Array Etalon Spectrometer (CLAES) Level 3AT data product consists of daily, 65.536 second interval time-ordered vertical profiles of temperature...

  8. SQIF Arrays as RF Sensors (Briefing Charts)

    National Research Council Canada - National Science Library

    Yukon, Stanford P

    2007-01-01

    ... (Superconducting Quantum Interference Filter) arrays may be employed as sensitive RF sensors. RF SQIF arrays fabricated with high Tc Josephson junctions can be cooled with small Sterling microcoolers...

  9. Development of an open metadata schema for prospective clinical research (openPCR) in China.

    Science.gov (United States)

    Xu, W; Guan, Z; Sun, J; Wang, Z; Geng, Y

    2014-01-01

    In China, deployment of electronic data capture (EDC) and clinical data management system (CDMS) for clinical research (CR) is in its very early stage, and about 90% of clinical studies collected and submitted clinical data manually. This work aims to build an open metadata schema for Prospective Clinical Research (openPCR) in China based on openEHR archetypes, in order to help Chinese researchers easily create specific data entry templates for registration, study design and clinical data collection. Singapore Framework for Dublin Core Application Profiles (DCAP) is used to develop openPCR and four steps such as defining the core functional requirements and deducing the core metadata items, developing archetype models, defining metadata terms and creating archetype records, and finally developing implementation syntax are followed. The core functional requirements are divided into three categories: requirements for research registration, requirements for trial design, and requirements for case report form (CRF). 74 metadata items are identified and their Chinese authority names are created. The minimum metadata set of openPCR includes 3 documents, 6 sections, 26 top level data groups, 32 lower data groups and 74 data elements. The top level container in openPCR is composed of public document, internal document and clinical document archetypes. A hierarchical structure of openPCR is established according to Data Structure of Electronic Health Record Architecture and Data Standard of China (Chinese EHR Standard). Metadata attributes are grouped into six parts: identification, definition, representation, relation, usage guides, and administration. OpenPCR is an open metadata schema based on research registration standards, standards of the Clinical Data Interchange Standards Consortium (CDISC) and Chinese healthcare related standards, and is to be publicly available throughout China. It considers future integration of EHR and CR by adopting data structure and data

  10. Large scale biomimetic membrane arrays

    DEFF Research Database (Denmark)

    Hansen, Jesper Søndergaard; Perry, Mark; Vogel, Jörg

    2009-01-01

    To establish planar biomimetic membranes across large scale partition aperture arrays, we created a disposable single-use horizontal chamber design that supports combined optical-electrical measurements. Functional lipid bilayers could easily and efficiently be established across CO2 laser micro......-structured 8 x 8 aperture partition arrays with average aperture diameters of 301 +/- 5 mu m. We addressed the electro-physical properties of the lipid bilayers established across the micro-structured scaffold arrays by controllable reconstitution of biotechnological and physiological relevant membrane...... peptides and proteins. Next, we tested the scalability of the biomimetic membrane design by establishing lipid bilayers in rectangular 24 x 24 and hexagonal 24 x 27 aperture arrays, respectively. The results presented show that the design is suitable for further developments of sensitive biosensor assays...

  11. Next Generation Microshutter Arrays Project

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose to develop the next generation MicroShutter Array (MSA) as a multi-object field selector for missions anticipated in the next two decades. For many...

  12. Fundamentals of spherical array processing

    CERN Document Server

    Rafaely, Boaz

    2015-01-01

    This book provides a comprehensive introduction to the theory and practice of spherical microphone arrays. It is written for graduate students, researchers and engineers who work with spherical microphone arrays in a wide range of applications.   The first two chapters provide the reader with the necessary mathematical and physical background, including an introduction to the spherical Fourier transform and the formulation of plane-wave sound fields in the spherical harmonic domain. The third chapter covers the theory of spatial sampling, employed when selecting the positions of microphones to sample sound pressure functions in space. Subsequent chapters present various spherical array configurations, including the popular rigid-sphere-based configuration. Beamforming (spatial filtering) in the spherical harmonics domain, including axis-symmetric beamforming, and the performance measures of directivity index and white noise gain are introduced, and a range of optimal beamformers for spherical arrays, includi...

  13. Application of droplet digital PCR for quantitative detection of Spiroplasma citri in comparison with real time PCR.

    Directory of Open Access Journals (Sweden)

    Yogita Maheshwari

    Full Text Available Droplet digital polymerase chain reaction (ddPCR is a method for performing digital PCR that is based on water-oil emulsion droplet technology. It is a unique approach to measure the absolute copy number of nucleic acid targets without the need of external standards. This study evaluated the applicability of ddPCR as a quantitative detection tool for the Spiroplasma citri, causal agent of citrus stubborn disease (CSD in citrus. Two sets of primers, SP1, based on the spiral in housekeeping gene, and a multicopy prophage gene, SpV1 ORF1, were used to evaluate ddPCR in comparison with real time (quantitative PCR (qPCR for S. citri detection in citrus tissues. Standard curve analyses on tenfold dilution series showed that both ddPCR and qPCR exhibited good linearity and efficiency. However, ddPCR had a tenfold greater sensitivity than qPCR and accurately quantified up to one copy of spiralin gene. Receiver operating characteristic analysis indicated that the ddPCR methodology was more robust for diagnosis of CSD and the area under the curve was significantly broader compared to qPCR. Field samples were used to validate ddPCR efficacy and demonstrated that it was equal or better than qPCR to detect S. citri infection in fruit columella due to a higher pathogen titer. The ddPCR assay detected both the S. citri spiralin and the SpV1 ORF1 targets quantitatively with high precision and accuracy compared to qPCR assay. The ddPCR was highly reproducible and repeatable for both the targets and showed higher resilience to PCR inhibitors in citrus tissue extract for the quantification of S. citri compare to qPCR.

  14. Clostridium perfringens isolate typing by multiplex PCR

    Directory of Open Access Journals (Sweden)

    MR Ahsani

    2010-01-01

    Full Text Available Clostridium perfringens is an important pathogen that provokes numerous different diseases. This bacterium is classified into five different types, each of which capable of causing a different disease. There are various methods for the bacterial identification, many are labor-intensive, time-consuming, expensive and also present low sensitivity and specificity. The aim of this research was to identify the different types of C. perfringens using PCR molecular method. In this study, 130 sheep-dung samples were randomly collected from areas around the city of Kerman, southeastern Iran. After processing and culturing of samples, the produced colonies were morphologically studied, gram stain test was also carried out and the genera of these bacteria were identified through biochemical tests. DNA extracted from isolated bacteria for genotyping was tested by multiplex PCR with specific primers. Based on length of synthesized fragments by PCR, toxin types and bacterial strains were detected. C. perfringens isolated types were divided as follows: 17.39% type A, 21.74% type B, 34.78% type C and 26.09% type D. It should be emphasized that, up to the present moment, C. perfringens type A has not been reported in Iran.

  15. Signaling pathway-focused gene expression profiling in pressure overloaded hearts

    Directory of Open Access Journals (Sweden)

    Marco Musumeci

    2011-01-01

    Full Text Available The β-blocker propranolol displays antihypertrophic and antifibrotic properties in the heart subjected to pressure overload. Yet the underlying mechanisms responsible for these important effects remain to be completely understood. The purpose of this study was to determine signaling pathway-focused gene expression profile associated with the antihypertrophic action of propranolol in pressure overloaded hearts. To address this question, a focused real-time PCR array was used to screen left ventricular RNA expression of 84 gene transcripts representative of 18 different signaling pathways in C57BL/6 mice subjected to transverse aortic constriction (TAC or sham surgery. On the surgery day, mice received either propranolol (80 mg/kg/day or vehicle for 14 days. TAC caused a 49% increase in the left ventricular weight-to-body weight (LVW/BW ratio without changing gene expression. Propranolol blunted LVW/BW ratio increase by approximately 50% while causing about a 3-fold increase in the expression of two genes, namely Brca1 and Cdkn2a, belonging to the TGF-beta and estrogen pathways, respectively. In conclusion, after 2 weeks of pressure overload, TAC hearts show a gene expression profile superimposable to that of sham hearts. Conversely, propranolol treatment is associated with an increased expression of genes which negatively regulate cell cycle progression. It remains to be established whether a mechanistic link between gene expression changes and the antihypertrophic action of propranolol occurs.

  16. Dietary Inulin Supplementation Modifies Significantly the Liver Transcriptomic Profile of Broiler Chickens

    Science.gov (United States)

    Sevane, Natalia; Bialade, Federica; Velasco, Susana; Rebolé, Almudena; Rodríguez, Maria Luisa; Ortiz, Luís T.; Cañón, Javier; Dunner, Susana

    2014-01-01

    Inclusion of prebiotics in the diet is known to be advantageous, with positive influences both on health and growth. The current study investigated the differences in the hepatic transcriptome profiles between chickens supplemented with inulin (a storage carbohydrate found in many plants) and controls. Liver is a major metabolic organ and has been previously reported to be involved in the modification of the lipid metabolism in chickens fed with inulin. A nutrigenomic approach through the analysis of liver RNA hybridized to the Affymetrix GeneChip Chicken Genome Array identified 148 differentially expressed genes among both groups: 104 up-regulated (≥1.4-fold) and 44 down-regulated (≤0.6-fold). Quantitative real-time PCR analysis validated the microarray expression results for five out of seven genes tested. The functional annotation analyses revealed a number of genes, processes and pathways with putative involvement in chicken growth and performance, while reinforcing the immune status of animals, and fostering the production of long chain fatty acids in broilers supplemented with 5 g of inulin kg−1 diet. As far as we are aware, this is the first report of a microarray based gene expression study on the effect of dietary inulin supplementation, supporting further research on the use of this prebiotic on chicken diets as a useful alternative to antibiotics for improving performance and general immunity in poultry farming, along with a healthier meat lipid profile. PMID:24915441

  17. Major differences between human atopic dermatitis and murine models, as determined by using global transcriptomic profiling

    DEFF Research Database (Denmark)

    Ewald, David A.; Noda, Shinji; Oliva, Margeaux

    2017-01-01

    , and a comparison of these models with the human AD transcriptomic fingerprint is lacking. Objective We sought to evaluate the transcriptomic profiles of 6 common murine models and determine how they relate to human AD skin. Methods Transcriptomic profiling was performed by using microarrays and quantitative RT......-PCR on biopsy specimens from NC/Nga, flaky tail, Flg-mutated, ovalbumin-challenged, oxazolone-challenged, and IL-23–injected mice. Gene expression data of patients with AD, psoriasis, and contact dermatitis were obtained from previous patient cohorts. Criteria of a fold change of 2 or greater and a false...... discovery rate of 0.05 or less were used for gene arrays. Results IL-23–injected, NC/Nga, and oxazolone-challenged mice show the largest homology with our human meta-analysis–derived AD transcriptome (37%, 18%, 17%, respectively). Similar to human AD, robust TH1, TH2, and also TH17 activation are seen in IL...

  18. Alteration of gene expression profiling including GPR174 and GNG2 is associated with vasovagal syncope.

    Science.gov (United States)

    Huang, Yu-Juan; Zhou, Zai-wei; Xu, Miao; Ma, Qing-wen; Yan, Jing-bin; Wang, Jian-yi; Zhang, Quo-qin; Huang, Min; Bao, Liming

    2015-03-01

    Vasovagal syncope (VVS) causes accidental harm for susceptible patients. However, pathophysiology of this disorder remains largely unknown. In an effort to understanding of molecular mechanism for VVS, genome-wide gene expression profiling analyses were performed on VVS patients at syncope state. A total of 66 Type 1 VVS child patients and the same number healthy controls were enrolled in this study. Peripheral blood RNAs were isolated from all subjects, of which 10 RNA samples were randomly selected from each groups for gene expression profile analysis using Gene ST 1.0 arrays (Affymetrix). The results revealed that 103 genes were differently expressed between the patients and controls. Significantly, two G-proteins related genes, GPR174 and GNG2 that have not been related to VVS were among the differently expressed genes. The microarray results were confirmed by qRT-PCR in all the tested individuals. Ingenuity pathway analysis and gene ontology annotation study showed that the differently expressed genes are associated with stress response and apoptosis, suggesting that the alteration of some gene expression including G-proteins related genes is associated with VVS. This study provides new insight into the molecular mechanism of VVS and would be helpful to further identify new molecular biomarkers for the disease.

  19. Microfabricated microbial fuel cell arrays reveal electrochemically active microbes.

    Directory of Open Access Journals (Sweden)

    Huijie Hou

    Full Text Available Microbial fuel cells (MFCs are remarkable "green energy" devices that exploit microbes to generate electricity from organic compounds. MFC devices currently being used and studied do not generate sufficient power to support widespread and cost-effective applications. Hence, research has focused on strategies to enhance the power output of the MFC devices, including exploring more electrochemically active microbes to expand the few already known electricigen families. However, most of the MFC devices are not compatible with high throughput screening for finding microbes with higher electricity generation capabilities. Here, we describe the development of a microfabricated MFC array, a compact and user-friendly platform for the identification and characterization of electrochemically active microbes. The MFC array consists of 24 integrated anode and cathode chambers, which function as 24 independent miniature MFCs and support direct and parallel comparisons of microbial electrochemical activities. The electricity generation profiles of spatially distinct MFC chambers on the array loaded with Shewanella oneidensis MR-1 differed by less than 8%. A screen of environmental microbes using the array identified an isolate that was related to Shewanella putrefaciens IR-1 and Shewanella sp. MR-7, and displayed 2.3-fold higher power output than the S. oneidensis MR-1 reference strain. Therefore, the utility of the MFC array was demonstrated.

  20. CMOS gate array characterization procedures

    Science.gov (United States)

    Spratt, James P.

    1993-09-01

    Present procedures are inadequate for characterizing the radiation hardness of gate array product lines prior to personalization because the selection of circuits to be used, from among all those available in the manufacturer's circuit library, is usually uncontrolled. (Some circuits are fundamentally more radiation resistant than others.) In such cases, differences in hardness can result between different designs of the same logic function. Hardness also varies because many gate arrays feature large custom-designed megacells (e.g., microprocessors and random access memories-MicroP's and RAM's). As a result, different product lines cannot be compared equally. A characterization strategy is needed, along with standardized test vehicle(s), methodology, and conditions, so that users can make informed judgments on which gate arrays are best suited for their needs. The program described developed preferred procedures for the radiation characterization of gate arrays, including a gate array evaluation test vehicle, featuring a canary circuit, designed to define the speed versus hardness envelope of the gate array. A multiplier was chosen for this role, and a baseline multiplier architecture is suggested that could be incorporated into an existing standard evaluation circuit chip.

  1. CCD and IR array controllers

    Science.gov (United States)

    Leach, Robert W.; Low, Frank J.

    2000-08-01

    A family of controllers has bene developed that is powerful and flexible enough to operate a wide range of CCD and IR focal plane arrays in a variety of ground-based applications. These include fast readout of small CCD and IR arrays for adaptive optics applications, slow readout of large CCD and IR mosaics, and single CCD and IR array operation at low background/low noise regimes as well as high background/high speed regimes. The CCD and IR controllers have a common digital core based on user- programmable digital signal processors that are used to generate the array clocking and signal processing signals customized for each application. A fiber optic link passes image data and commands to VME or PCI interface boards resident in a host computer to the controller. CCD signal processing is done with a dual slope integrator operating at speeds of up to one Megapixel per second per channel. Signal processing of IR arrays is done either with a dual channel video processor or a four channel video processor that has built-in image memory and a coadder to 32-bit precision for operating high background arrays. Recent developments underway include the implementation of a fast fiber optic data link operating at a speed of 12.5 Megapixels per second for fast image transfer from the controller to the host computer, and supporting image acquisition software and device drivers for the PCI interface board for the Sun Solaris, Linux and Windows 2000 operating systems.

  2. Flexible eddy current coil arrays

    International Nuclear Information System (INIS)

    Krampfner, Y.; Johnson, D.P.

    1987-01-01

    A novel approach was devised to overcome certain limitations of conventional eddy current testing. The typical single-element hand-wound probe was replaced with a two dimensional array of spirally wound probe elements deposited on a thin, flexible polyimide substrate. This provides full and reliable coverage of the test area and eliminates the need for scanning. The flexible substrate construction of the array allows the probes to conform to irregular part geometries, such as turbine blades and tubing, thereby eliminating the need for specialized probes for each geometry. Additionally, the batch manufacturing process of the array can yield highly uniform and reproducible coil geometries. The array is driven by a portable computer-based eddy current instrument, smartEDDY/sup TM/, capable of two-frequency operation, and offers a great deal of versatility and flexibility due to its software-based architecture. The array is coupled to the instrument via an 80-switch multiplexer that can be configured to address up to 1600 probes. The individual array elements may be addressed in any desired sequence, as defined by the software

  3. Purification and Concentration of PCR Products Leads to Increased Signal intensities with Fewer Allelic Drop-Outs and Artifacts

    DEFF Research Database (Denmark)

    Maria Irlund Pedersen, Line; Stangegaard, Michael; Mogensen, Helle Smidt

    2011-01-01

    and the quality of the DNA profiles without re-amplification of the sample. We have validated and implemented an automated method to purify and 2-fold concentrate PCR products resulting in allelic peaks with higher intensity (a median height across all loci from 130 to 404 RFU), fewer allelic dropouts...

  4. Microarray gene expression profiling and analysis in renal cell carcinoma

    Directory of Open Access Journals (Sweden)

    Sadhukhan Provash

    2004-06-01

    Full Text Available Abstract Background Renal cell carcinoma (RCC is the most common cancer in adult kidney. The accuracy of current diagnosis and prognosis of the disease and the effectiveness of the treatment for the disease are limited by the poor understanding of the disease at the molecular level. To better understand the genetics and biology of RCC, we profiled the expression of 7,129 genes in both clear cell RCC tissue and cell lines using oligonucleotide arrays. Methods Total RNAs isolated from renal cell tumors, adjacent normal tissue and metastatic RCC cell lines were hybridized to affymatrix HuFL oligonucleotide arrays. Genes were categorized into different functional groups based on the description of the Gene Ontology Consortium and analyzed based on the gene expression levels. Gene expression profiles of the tissue and cell line samples were visualized and classified by singular value decomposition. Reverse transcription polymerase chain reaction was performed to confirm the expression alterations of selected genes in RCC. Results Selected genes were annotated based on biological processes and clustered into functional groups. The expression levels of genes in each group were also analyzed. Seventy-four commonly differentially expressed genes with more than five-fold changes in RCC tissues were identified. The expression alterations of selected genes from these seventy-four genes were further verified using reverse transcription polymerase chain reaction (RT-PCR. Detailed comparison of gene expression patterns in RCC tissue and RCC cell lines shows significant differences between the two types of samples, but many important expression patterns were preserved. Conclusions This is one of the initial studies that examine the functional ontology of a large number of genes in RCC. Extensive annotation, clustering and analysis of a large number of genes based on the gene functional ontology revealed many interesting gene expression patterns in RCC. Most

  5. Molecular profile and copy number analysis of sporadic colorectal cancer in Taiwan

    Directory of Open Access Journals (Sweden)

    Li Ling-Hui

    2011-06-01

    Full Text Available Abstract Background Colorectal cancer (CRC is a major health concern worldwide, and recently becomes the most common cancer in Asia. The case collection of this study is one of the largest sets of CRC in Asia, and serves as representative data for investigating genomic differences between ethnic populations. We took comprehensive and high-resolution approaches to compare the clinicopathologic and genomic profiles of microsatellite instability (MSI vs. microsatellite stability (MSS in Taiwanese sporadic CRCs. Methods 1,173 CRC tumors were collected from the Taiwan population, and sequencing-based microsatellite typing assay was used to determine MSI and MSS. Genome-wide SNP array was used to detect CN alterations in 16 MSI-H and 13 MSS CRCs and CN variations in 424 general controls. Gene expression array was used to evaluate the effects of CN alterations, and quantitative PCR methods were used to replicate the findings in independent clinical samples. Results These 1,173 CRC tumors can be classified into 75 high-frequency MSI (MSI-H (6.4%, 96 low-frequency MSI (8.2% and 1,002 MSS (85.4%. Of the 75 MSI-H tumors, 22 had a BRAF mutation and 51 showed MLH1 promoter hypermethylation. There were distinctive differences in the extent of CN alterations between CRC MSS and MSI-H subtypes (300 Mb vs. 42 Mb per genome, p-value Conclusions Sporadic CRCs with MSI-H displayed distinguishable clinicopathologic features, which differ from those of MSS. Genomic profiling of the two types of sporadic CRCs revealed significant differences in the extent and distribution of CN alterations in the cancer genome. More than half of expressed genes showing CN differences can directly contribute to their expressional diversities, and the biological functions of the genes associated with CN changes in sporadic CRCs warrant further investigation to establish their possible clinical implications.

  6. Laser capture microdissection and cDNA array analysis of endometrium identify CCL16 and CCL21 as epithelial-derived inflammatory mediators associated with endometriosis

    Directory of Open Access Journals (Sweden)

    Jones Rebecca L

    2007-05-01

    Full Text Available Abstract Background Understanding the pathophysiology of chemokine secretion in endometriosis may offer a novel area of therapeutic intervention. This study aimed to identify chemokines differentially expressed in epithelial glands in eutopic endometrium from normal women and those with endometriosis, and to establish the expression profiles of key chemokines in endometriotic lesions. Methods Laser capture microdissection isolated epithelial glands from endometrial eutopic tissue from women with and without endometriosis in the mid-secretory phase of their menstrual cycles. Gene profiling of the excised glands used a human chemokine and receptor cDNA array. Selected chemokines were further examined using real-time PCR and immunohistochemistry. Results 22 chemokine/receptor genes were upregulated and two downregulated in pooled endometrial epithelium of women with endometriosis compared with controls. CCL16 and CCL21 mRNA was confirmed as elevated in some women with endometriosis compared to controls on individual samples. Immunoreactive CCL16 and CCL21 were predominantly confined to glands in eutopic and ectopic endometrium: leukocytes also stained. Immunoreactive CCL16 was overall higher in glands in ectopic vs. eutopic endometrium from the same woman (P Conclusion This study provides novel candidate molecules and suggests a potential local role for CCL16 and CCL21 as mediators contributing to the inflammatory events associated with endometriosis.

  7. Coded aperture imaging with uniformly redundant arrays

    International Nuclear Information System (INIS)

    Fenimore, E.E.; Cannon, T.M.

    1980-01-01

    A system is described which uses uniformly redundant arrays to image non-focusable radiation. The array is used in conjunction with a balanced correlation technique to provide a system with no artifacts so that virtually limitless signal-to-noise ratio is obtained with high transmission characteristics. The array is mosaicked to reduce required detector size over conventional array detectors. 15 claims

  8. Three-dimensionally Functionalized Reverse Phase Glycoprotein Array for Cancer Biomarker Discovery and Validation

    OpenAIRE

    Pan, Li; Aguilar, Hillary Andaluz; Wang, Linna; Iliuk, Anton; Tao, W. Andy

    2016-01-01

    Glycoproteins have vast structural diversity which plays an important role in many biological processes and have great potential as disease biomarkers. Here we report a novel functionalized reverse phase protein array (RPPA), termed polymer-based reverse phase GlycoProtein Array (polyGPA), to specifically capture and profile glycoproteomes, and validate glycoproteins. Nitrocellulose membrane functionalized with globular hydroxyaminodendrimers was used to covalently capture pre-oxidized glycan...

  9. Species identification and quantification in meat and meat products using droplet digital PCR (ddPCR).

    Science.gov (United States)

    Floren, C; Wiedemann, I; Brenig, B; Schütz, E; Beck, J

    2015-04-15

    Species fraud and product mislabelling in processed food, albeit not being a direct health issue, often results in consumer distrust. Therefore methods for quantification of undeclared species are needed. Targeting mitochondrial DNA, e.g. CYTB gene, for species quantification is unsuitable, due to a fivefold inter-tissue variation in mtDNA content per cell resulting in either an under- (-70%) or overestimation (+160%) of species DNA contents. Here, we describe a reliable two-step droplet digital PCR (ddPCR) assay targeting the nuclear F2 gene for precise quantification of cattle, horse, and pig in processed meat products. The ddPCR assay is advantageous over qPCR showing a limit of quantification (LOQ) and detection (LOD) in different meat products of 0.01% and 0.001%, respectively. The specificity was verified in 14 different species. Hence, determining F2 in food by ddPCR can be recommended for quality assurance and control in production systems. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  10. Modeling of a VMJ PV array under Gaussian high intensity laser power beam condition

    Science.gov (United States)

    Eom, Jeongsook; Kim, Gunzung; Park, Yongwan

    2018-02-01

    The high intensity laser power beaming (HILPB) system is one of the most promising systems in the long-rang wireless power transfer field. The vertical multi-junction photovoltaic (VMJ PV) array converts the HILPB into electricity to power the load or charges a battery. The output power of a VMJ PV array depends mainly on irradiance values of each VMJ PV cells. For simulating an entire VMJ PV array, the irradiance profile of the Gaussian HILPB and the irradiance level of the VMJ PV cell are mathematically modeled first. The VMJ PV array is modeled as a network with dimension m*n, where m represents the number of VMJ PV cells in a column, and n represents the number of VMJ PV cells in a row. In order to validate the results obtained in modeling and simulation, a laboratory setup was developed using 55 VMJ PV array. By using the output power model of VMJ PV array, we can establish an optimal power transmission path by the receiver based on the received signal strength. When the laser beam from multiple transmitters aimed at a VMJ PV array at the same time, the received power is the sum of all energy at a VMJ PV array. The transmitter sends its power characteristics as optically coded laser pulses and powers as HILPB. Using the attenuated power model and output power model of VMJ PV array, the receiver can estimate the maximum receivable powers from the transmitters and select optimal transmitters.

  11. Micro/nanosized refractive lens arrays formed by means of conformal thin film deposition

    International Nuclear Information System (INIS)

    Zeng Hongjun; Lajos, Robert; Elzy, Ed; Metlushko, Vitali

    2008-01-01

    We provide a 'growing' method for fabricating a microlens array with lateral size of a few microns or less. Instead of using complicated etching techniques, the method forms a spherical profile of the lens using conformal chemical vapor deposition. We have fabricated two lens arrays. One has a pitch of 1200 nm, a circular aperture 1000 nm in diameter and a sag height of 130 nm. The other array has a pitch of 600 nm, and a square aperture of 600 nm x 600 nm, with a fill factor close to 100%. The maximum profile deviation between the fabricated lens and an ideal sphere is about 11% and 14% respectively. The calculation indicates that the curvature difference of the profile of the square lens in the orthogonal and diagonal direction is 5.5%. The roughness of the lens is measured as approximately 6 nm

  12. The surface detector array of the Telescope Array experiment

    Energy Technology Data Exchange (ETDEWEB)

    Abu-Zayyad, T. [University of Utah, High Energy Astrophysics Institute, Salt Lake City, Utah (United States); Aida, R. [University of Yamanashi, Interdisciplinary Graduate School of Medicine and Engineering, Kofu, Yamanashi (Japan); Allen, M.; Anderson, R. [University of Utah, High Energy Astrophysics Institute, Salt Lake City, Utah (United States); Azuma, R. [Tokyo Institute of Technology, Meguro, Tokyo (Japan); Barcikowski, E.; Belz, J.W.; Bergman, D.R.; Blake, S.A.; Cady, R. [University of Utah, High Energy Astrophysics Institute, Salt Lake City, Utah (United States); Cheon, B.G. [Hanyang University, Seongdong-gu, Seoul (Korea, Republic of); Chiba, J. [Tokyo University of Science, Noda, Chiba (Japan); Chikawa, M. [Kinki University, Higashi Osaka, Osaka (Japan); Cho, E.J. [Hanyang University, Seongdong-gu, Seoul (Korea, Republic of); Cho, W.R. [Yonsei University, Seodaemun-gu, Seoul (Korea, Republic of); Fujii, H. [Institute of Particle and Nuclear Studies, KEK, Tsukuba, Ibaraki (Japan); Fujii, T. [Osaka City University, Osaka, Osaka (Japan); Fukuda, T. [Tokyo Institute of Technology, Meguro, Tokyo (Japan); Fukushima, M. [Institute for Cosmic Ray Research, University of Tokyo, Kashiwa, Chiba (Japan); University of Tokyo, Institute for the Physics and Mathematics of the Universe, Kashiwa, Chiba (Japan); Gorbunov, D. [Institute for Nuclear Research of the Russian Academy of Sciences, Moscow (Russian Federation); and others

    2012-10-11

    The Telescope Array (TA) experiment, located in the western desert of Utah, USA, is designed for the observation of extensive air showers from extremely high energy cosmic rays. The experiment has a surface detector array surrounded by three fluorescence detectors to enable simultaneous detection of shower particles at ground level and fluorescence photons along the shower track. The TA surface detectors and fluorescence detectors started full hybrid observation in March, 2008. In this article we describe the design and technical features of the TA surface detector.

  13. The surface detector array of the Telescope Array experiment

    International Nuclear Information System (INIS)

    Abu-Zayyad, T.; Aida, R.; Allen, M.; Anderson, R.; Azuma, R.; Barcikowski, E.; Belz, J.W.; Bergman, D.R.; Blake, S.A.; Cady, R.; Cheon, B.G.; Chiba, J.; Chikawa, M.; Cho, E.J.; Cho, W.R.; Fujii, H.; Fujii, T.; Fukuda, T.; Fukushima, M.; Gorbunov, D.

    2012-01-01

    The Telescope Array (TA) experiment, located in the western desert of Utah, USA, is designed for the observation of extensive air showers from extremely high energy cosmic rays. The experiment has a surface detector array surrounded by three fluorescence detectors to enable simultaneous detection of shower particles at ground level and fluorescence photons along the shower track. The TA surface detectors and fluorescence detectors started full hybrid observation in March, 2008. In this article we describe the design and technical features of the TA surface detector.

  14. Successive Standardization of Rectangular Arrays

    Directory of Open Access Journals (Sweden)

    Richard A. Olshen

    2012-02-01

    Full Text Available In this note we illustrate and develop further with mathematics and examples, the work on successive standardization (or normalization that is studied earlier by the same authors in [1] and [2]. Thus, we deal with successive iterations applied to rectangular arrays of numbers, where to avoid technical difficulties an array has at least three rows and at least three columns. Without loss, an iteration begins with operations on columns: first subtract the mean of each column; then divide by its standard deviation. The iteration continues with the same two operations done successively for rows. These four operations applied in sequence completes one iteration. One then iterates again, and again, and again, ... In [1] it was argued that if arrays are made up of real numbers, then the set for which convergence of these successive iterations fails has Lebesgue measure 0. The limiting array has row and column means 0, row and column standard deviations 1. A basic result on convergence given in [1] is true, though the argument in [1] is faulty. The result is stated in the form of a theorem here, and the argument for the theorem is correct. Moreover, many graphics given in [1] suggest that except for a set of entries of any array with Lebesgue measure 0, convergence is very rapid, eventually exponentially fast in the number of iterations. Because we learned this set of rules from Bradley Efron, we call it “Efron’s algorithm”. More importantly, the rapidity of convergence is illustrated by numerical examples.

  15. Integrated Array/Metadata Analytics

    Science.gov (United States)

    Misev, Dimitar; Baumann, Peter

    2015-04-01

    Data comes in various forms and types, and integration usually presents a problem that is often simply ignored and solved with ad-hoc solutions. Multidimensional arrays are an ubiquitous data type, that we find at the core of virtually all science and engineering domains, as sensor, model, image, statistics data. Naturally, arrays are richly described by and intertwined with additional metadata (alphanumeric relational data, XML, JSON, etc). Database systems, however, a fundamental building block of what we call "Big Data", lack adequate support for modelling and expressing these array data/metadata relationships. Array analytics is hence quite primitive or non-existent at all in modern relational DBMS. Recognizing this, we extended SQL with a new SQL/MDA part seamlessly integrating multidimensional array analytics into the standard database query language. We demonstrate the benefits of SQL/MDA with real-world examples executed in ASQLDB, an open-source mediator system based on HSQLDB and rasdaman, that already implements SQL/MDA.

  16. Retrieval of Mir Solar Array

    Science.gov (United States)

    Rutledge, Sharon K.; deGroh, Kim K.

    1999-01-01

    A Russian solar array panel removed in November 1997 from the non-articulating photovoltaic array on the Mir core module was returned to Earth on STS-89 in January 1998. The panel had been exposed to low Earth orbit (LEO) for 10 years prior to retrieval. The retrieval provided a unique opportunity to study the effects of the LEO environment on a functional solar array. To take advantage of this opportunity, a team composed of members from RSC-Energia (Russia), the Boeing Company, and the following NASA Centers--Johnson Space Center, Kennedy Space Center, Langley Research Center, Marshall Space Flight Center, and Lewis Research Center--was put together to analyze the array. After post-retrieval inspections at the Spacehab Facility at Kennedy in Florida, the array was shipped to Lewis in Cleveland for electrical performance tests, closeup photodocumentation, and removal of selected solar cells and blanket material. With approval from RSC-Energia, five cell pairs and their accompanying blanket and mesh material, and samples of painted handrail materials were selected for removal on the basis of their ability to provide degradation information. Sites were selected that provided different sizes and shapes of micrometeoroid impacts and different levels of surface contamination. These materials were then distributed among the team for round robin testing.

  17. Dynamics of Josephson junction arrays

    International Nuclear Information System (INIS)

    Hadley, P.

    1989-01-01

    The dynamics of Josephson junction arrays is a topic that lies at the intersection of the fields of nonlinear dynamics and Josephson junction technology. The series arrays considered here consist of several rapidly oscillating Josephson junctions where each junction is coupled equally to every other junction. The purpose of this study is to understand phaselocking and other cooperative dynamics of this system. Previously, little was known about high dimensional nonlinear systems of this sort. Numerical simulations are used to study the dynamics of these arrays. Three distinct types of periodic solutions to the array equations were observed as well as period doubled and chaotic solutions. One of the periodic solutions is the symmetric, in-phase solution where all of the junctions oscillate identically. The other two periodic solutions are symmetry-broken solutions where all of the junction do not oscillate identically. The symmetry-broken solutions are highly degenerate. As many as (N - 1) stable solutions can coexist for an array of N junctions. Understanding the stability of these several solutions and the transitions among them is vital to the design of useful devices

  18. Feasibility study of patient motion monitoring using tactile array sensor

    International Nuclear Information System (INIS)

    Kim, Tae Ho; Kang, Seong Hee; Kim, Dong Su; Cho, Min Seok; Kim, Kyeong Hyeon; Suh, Tae Suk; Kim, Si Yong

    2014-01-01

    The aim of this study is to evaluate patient pretreatment set-up error and intra-fraction motion using the tactile array sensors (Pressure Profile Systems Inc, Los Angeles, CA) which could measure distributed pressure profiles along the contacting surface and to check a feasibility of the sensor (tactile array sensor) in the patient motion monitoring. Laser alignment and optical camera based monitoring system are very useful for reduce patient set-up error but these systems could not monitor the blind area like patient's back position. Actually after patient alignment using laser or optical monitoring system, it was assumed that there is no error in the patient's back position (pressure profile distribution). But if an error occurs in the patient's back position, it will affect the radiation therapy accuracy. In spite of optical motion monitoring or using the immobilization tool, distributed pressure profiles of patient's back position was changed during inter and intra-fraction. For more accurate patient set-up, blind area (patient's back) monitoring was necessary. We expect that the proposed method will be very useful for make up for the weakness of optical monitoring method

  19. Feasibility study of patient motion monitoring using tactile array sensor

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Tae Ho; Kang, Seong Hee; Kim, Dong Su; Cho, Min Seok; Kim, Kyeong Hyeon; Suh, Tae Suk [Dept. of Biomedical Engineering, Research Institute of Biomedical Engineering, the Catholic University of Korea, Seoul (Korea, Republic of); Kim, Si Yong [Dept. of Radiation Oncology, Virginia Commonwealth University, Richmond (United States)

    2014-11-15

    The aim of this study is to evaluate patient pretreatment set-up error and intra-fraction motion using the tactile array sensors (Pressure Profile Systems Inc, Los Angeles, CA) which could measure distributed pressure profiles along the contacting surface and to check a feasibility of the sensor (tactile array sensor) in the patient motion monitoring. Laser alignment and optical camera based monitoring system are very useful for reduce patient set-up error but these systems could not monitor the blind area like patient's back position. Actually after patient alignment using laser or optical monitoring system, it was assumed that there is no error in the patient's back position (pressure profile distribution). But if an error occurs in the patient's back position, it will affect the radiation therapy accuracy. In spite of optical motion monitoring or using the immobilization tool, distributed pressure profiles of patient's back position was changed during inter and intra-fraction. For more accurate patient set-up, blind area (patient's back) monitoring was necessary. We expect that the proposed method will be very useful for make up for the weakness of optical monitoring method.

  20. Analysis of extracellular RNA by digital PCR

    Directory of Open Access Journals (Sweden)

    Kenji eTakahashi

    2014-06-01

    Full Text Available The transfer of extracellular RNA is emerging as an important mechanism for intracellular communication. The ability for the transfer of functionally active RNA molecules from one cell to another within vesicles such as exosomes enables a cell to modulate cellular signaling and biological processes within recipient cells. The study of extracellular RNA requires sensitive methods for the detection of these molecules. In this methods article, we will describe protocols for the detection of such extracellular RNA using sensitive detection technologies such as digital PCR. These protocols should be valuable to researchers interested in the role and contribution of extracellular RNA to tumor cell biology.

  1. An MLC calibration method using a detector array

    International Nuclear Information System (INIS)

    Simon, Thomas A.; Kahler, Darren; Simon, William E.; Fox, Christopher; Li, Jonathan; Palta, Jatinder; Liu, Chihray

    2009-01-01

    Purpose: The authors have developed a quantitative calibration method for a multileaf collimator (MLC) which measures individual leaf positions relative to the MLC backup jaw on an Elekta Synergy linear accelerator. Methods: The method utilizes a commercially available two-axis detector array (Profiler 2; Sun Nuclear Corporation, Melbourne, FL). To calibrate the MLC bank, its backup jaw is positioned at the central axis and the opposing jaw is retracted to create a half-beam configuration. The position of the backup jaws field edge is then measured with the array to obtain what is termed the radiation defined reference line. The positions of the individual leaf ends relative to this reference line are then inferred by the detector response in the leaf end penumbra. Iteratively adjusting and remeasuring the leaf end positions to within specifications completes the calibration. Using the backup jaw as a reference for the leaf end positions is based on three assumptions: (1) The leading edge of an MLC leaf bank is parallel to its backup jaw's leading edge, (2) the backup jaw position is reproducible, and (3) the measured radiation field edge created by each leaf end is representative of that leaf's position. Data from an electronic portal imaging device (EPID) were used in a similar analysis to check the results obtained with the array. Results: The relative leaf end positions measured with the array differed from those measured with the EPID by an average of 0.11 ±0.09 mm per leaf. The maximum leaf positional change measured with the Profiler 2 over a 3 month period was 0.51 mm. A leaf positional accuracy of ±0.4 mm is easily attainable through the iterative calibration process. The method requires an average of 40 min to measure both leaf banks. Conclusions: This work demonstrates that the Profiler 2 is an effective tool for efficient and quantitative MLC quality assurance and calibration.

  2. An MLC calibration method using a detector array

    Energy Technology Data Exchange (ETDEWEB)

    Simon, Thomas A.; Kahler, Darren; Simon, William E.; Fox, Christopher; Li, Jonathan; Palta, Jatinder; Liu, Chihray [Department of Nuclear and Radiological Engineering, University of Florida, 202 Nuclear Science Building, Gainesville, Florida 32611-8300 (United States); Sun Nuclear Corporation, 425-A Pineda Court, Melbourne, Florida 32940 (United States) and Department of Radiation Oncology, Health Science Center, University of Florida, P.O. Box 100385, Gainesville, Florida 32610-0385 (United States); Department of Radiation Oncology, Health Science Center, University of Florida, P.O. Box 100385, Gainesville, Florida 32610-0385 (United States); Sun Nuclear Corporation, 425-A Pineda Court, Melbourne, Florida 32940 (United States); Department of Radiation Oncology, Tulane University, 1415 Tulane Ave, HC65, New Orleans, Louisiana 70112 (United States); Department of Radiation Oncology, Health Science Center, University of Florida, P.O. Box 100385, Gainesville, Florida 32610-0385 (United States)

    2009-10-15

    Purpose: The authors have developed a quantitative calibration method for a multileaf collimator (MLC) which measures individual leaf positions relative to the MLC backup jaw on an Elekta Synergy linear accelerator. Methods: The method utilizes a commercially available two-axis detector array (Profiler 2; Sun Nuclear Corporation, Melbourne, FL). To calibrate the MLC bank, its backup jaw is positioned at the central axis and the opposing jaw is retracted to create a half-beam configuration. The position of the backup jaws field edge is then measured with the array to obtain what is termed the radiation defined reference line. The positions of the individual leaf ends relative to this reference line are then inferred by the detector response in the leaf end penumbra. Iteratively adjusting and remeasuring the leaf end positions to within specifications completes the calibration. Using the backup jaw as a reference for the leaf end positions is based on three assumptions: (1) The leading edge of an MLC leaf bank is parallel to its backup jaw's leading edge, (2) the backup jaw position is reproducible, and (3) the measured radiation field edge created by each leaf end is representative of that leaf's position. Data from an electronic portal imaging device (EPID) were used in a similar analysis to check the results obtained with the array. Results: The relative leaf end positions measured with the array differed from those measured with the EPID by an average of 0.11 {+-}0.09 mm per leaf. The maximum leaf positional change measured with the Profiler 2 over a 3 month period was 0.51 mm. A leaf positional accuracy of {+-}0.4 mm is easily attainable through the iterative calibration process. The method requires an average of 40 min to measure both leaf banks. Conclusions: This work demonstrates that the Profiler 2 is an effective tool for efficient and quantitative MLC quality assurance and calibration.

  3. Generation of miniaturized planar ecombinant antibody arrays using a microcantilever-based printer

    International Nuclear Information System (INIS)

    Petersson, Linn; Dexlin-Mellby, Linda; Borrebaeck, Carl AK; Wingren, Christer; Berthet Duroure, Nathalie; Auger, Angèle; Ait Ikhlef, Ali

    2014-01-01

    Miniaturized (Ø 10 μm), multiplexed (>5-plex), and high-density (>100 000 spots cm −2 ) antibody arrays will play a key role in generating protein expression profiles in health and disease. However, producing such antibody arrays is challenging, and it is the type and range of available spotters which set the stage. This pilot study explored the use of a novel microspotting tool, Bioplume TM —consisting of an array of micromachined silicon cantilevers with integrated microfluidic channels—to produce miniaturized, multiplexed, and high-density planar recombinant antibody arrays for protein expression profiling which targets crude, directly labelled serum. The results demonstrated that 16-plex recombinant antibody arrays could be produced—based on miniaturized spot features (78.5 um 2 , Ø 10 μm) at a 7–125-times increased spot density (250 000 spots cm −2 ), interfaced with a fluorescent-based read-out. This prototype platform was found to display adequate reproducibility (spot-to-spot) and an assay sensitivity in the pM range. The feasibility of the array platform for serum protein profiling was outlined. (paper)

  4. Generation of miniaturized planar ecombinant antibody arrays using a microcantilever-based printer

    Science.gov (United States)

    Petersson, Linn; Berthet Duroure, Nathalie; Auger, Angèle; Dexlin-Mellby, Linda; Borrebaeck, Carl AK; Ait Ikhlef, Ali; Wingren, Christer

    2014-07-01

    Miniaturized (Ø 10 μm), multiplexed (>5-plex), and high-density (>100 000 spots cm-2) antibody arrays will play a key role in generating protein expression profiles in health and disease. However, producing such antibody arrays is challenging, and it is the type and range of available spotters which set the stage. This pilot study explored the use of a novel microspotting tool, BioplumeTM—consisting of an array of micromachined silicon cantilevers with integrated microfluidic channels—to produce miniaturized, multiplexed, and high-density planar recombinant antibody arrays for protein expression profiling which targets crude, directly labelled serum. The results demonstrated that 16-plex recombinant antibody arrays could be produced—based on miniaturized spot features (78.5 um2, Ø 10 μm) at a 7-125-times increased spot density (250 000 spots cm-2), interfaced with a fluorescent-based read-out. This prototype platform was found to display adequate reproducibility (spot-to-spot) and an assay sensitivity in the pM range. The feasibility of the array platform for serum protein profiling was outlined.

  5. Evaluation of the AGCU Expressmarker 16 and 22 PCR Amplification Kits Using Biological Samples Applied to FTA Micro Cards in Reduced Volume Direct PCR Amplification Reactions

    Directory of Open Access Journals (Sweden)

    Samantha J Ogden

    2015-01-01

    /Kruskal-Wallis test was used. Statistical significance was set at P < 0.05. Confidence intervals for mean values were set at 95%. On using reduced volume PCR reactions in combination with dried blood spots applied to FTA sample collection cards, both the EX16 and EX22 kits were shown to generate STR profiles of sufficient quality to allow entry into National DNA databases. The performance of both EX16 and EX22 was comparable to that of the PP21 System. This study demonstrates the successful use of the Wuxi AGCU ScienTech Incorporation EX16 and EX22 kits in reduced PCR reaction volumes with complex biological samples applied to chemically impregnated FTA sample collection cards.

  6. Determining Fungi rRNA Copy Number by PCR

    Science.gov (United States)

    The goal of this project is to improve the quantification of indoor fungal pollutants via the specific application of quantitative PCR (qPCR). Improvement will be made in the controls used in current qPCR applications. This work focuses on the use of two separate controls within ...

  7. Real-Time PCR for Universal Phytoplasma Detection and Quantification

    DEFF Research Database (Denmark)

    Christensen, Nynne Meyn; Nyskjold, Henriette; Nicolaisen, Mogens

    2013-01-01

    Currently, the most efficient detection and precise quantification of phytoplasmas is by real-time PCR. Compared to nested PCR, this method is less sensitive to contamination and is less work intensive. Therefore, a universal real-time PCR method will be valuable in screening programs and in other...

  8. Comparison of a Commercially Available Repetitive-Element PCR System (DiversiLab) with PCR Ribotyping for Typing of Clostridium difficile Strains ▿

    OpenAIRE

    Eckert, C.; Van Broeck, J.; Spigaglia, P.; Burghoffer, B.; Delmée, M.; Mastrantonio, P.; Barbut, F.

    2011-01-01

    This study compared a repetitive-element PCR (rep-PCR) method (DiversiLab system) to PCR ribotyping. The discriminatory power of rep-PCR was 0.997. Among the PCR ribotype 027 isolates tested, different rep types could be distinguished. rep-PCR showed a higher discriminatory power than PCR ribotyping. Nevertheless, this method requires technical skill, and visual interpretation of rep-PCR fingerprint patterns may be difficult.

  9. Automated PCR setup for forensic casework samples using the Normalization Wizard and PCR Setup robotic methods.

    Science.gov (United States)

    Greenspoon, S A; Sykes, K L V; Ban, J D; Pollard, A; Baisden, M; Farr, M; Graham, N; Collins, B L; Green, M M; Christenson, C C

    2006-12-20

    Human genome, pharmaceutical and research laboratories have long enjoyed the application of robotics to performing repetitive laboratory tasks. However, the utilization of robotics in forensic laboratories for processing casework samples is relatively new and poses particular challenges. Since the quantity and quality (a mixture versus a single source sample, the level of degradation, the presence of PCR inhibitors) of the DNA contained within a casework sample is unknown, particular attention must be paid to procedural susceptibility to contamination, as well as DNA yield, especially as it pertains to samples with little biological material. The Virginia Department of Forensic Science (VDFS) has successfully automated forensic casework DNA extraction utilizing the DNA IQ(trade mark) System in conjunction with the Biomek 2000 Automation Workstation. Human DNA quantitation is also performed in a near complete automated fashion utilizing the AluQuant Human DNA Quantitation System and the Biomek 2000 Automation Workstation. Recently, the PCR setup for casework samples has been automated, employing the Biomek 2000 Automation Workstation and Normalization Wizard, Genetic Identity version, which utilizes the quantitation data, imported into the software, to create a customized automated method for DNA dilution, unique to that plate of DNA samples. The PCR Setup software method, used in conjunction with the Normalization Wizard method and written for the Biomek 2000, functions to mix the diluted DNA samples, transfer the PCR master mix, and transfer the diluted DNA samples to PCR amplification tubes. Once the process is complete, the DNA extracts, still on the deck of the robot in PCR amplification strip tubes, are transferred to pre-labeled 1.5 mL tubes for long-term storage using an automated method. The automation of these steps in the process of forensic DNA casework analysis has been accomplished by performing extensive optimization, validation and testing of the

  10. Optimization of PCR Condition: The First Study of High Resolution Melting Technique for Screening of APOA1 Variance.

    Science.gov (United States)

    Wahyuningsih, Hesty; K Cayami, Ferdy; Bahrudin, Udin; A Sobirin, Mochamad; Ep Mundhofir, Farmaditya; Mh Faradz, Sultana; Hisatome, Ichiro

    2017-03-01

    High resolution melting (HRM) is a post-PCR technique for variant screening and genotyping based on the different melting points of DNA fragments. The advantages of this technique are that it is fast, simple, and efficient and has a high output, particularly for screening of a large number of samples. APOA1 encodes apolipoprotein A1 (apoA1) which is a major component of high density lipoprotein cholesterol (HDL-C). This study aimed to obtain an optimal quantitative polymerase chain reaction (qPCR)-HRM condition for screening of APOA1 variance. Genomic DNA was isolated from a peripheral blood sample using the salting out method. APOA1 was amplified using the RotorGeneQ 5Plex HRM. The PCR product was visualized with the HRM amplification curve and confirmed using gel electrophoresis. The melting profile was confirmed by looking at the melting curve. Five sets of primers covering the translated region of APOA1 exons were designed with expected PCR product size of 100-400 bps. The amplified segments of DNA were amplicons 2, 3, 4A, 4B, and 4C. Amplicons 2, 3 and 4B were optimized at an annealing temperature of 60 °C at 40 PCR cycles. Amplicon 4A was optimized at an annealing temperature of 62 °C at 45 PCR cycles. Amplicon 4C was optimized at an annealing temperature of 63 °C at 50 PCR cycles. In addition to the suitable procedures of DNA isolation and quantification, primer design and an estimated PCR product size, the data of this study showed that appropriate annealing temperature and PCR cycles were important factors in optimization of HRM technique for variant screening in APOA1 .

  11. SNPs and real-time quantitative PCR method for constitutional allelic copy number determination, the VPREB1 marker case

    Directory of Open Access Journals (Sweden)

    Costa Elena

    2011-05-01

    Full Text Available Abstract Background 22q11.2 microdeletion is responsible for the DiGeorge Syndrome, characterized by heart defects, psychiatric disorders, endocrine and immune alterations and a 1 in 4000 live birth prevalence. Real-time quantitative PCR (qPCR approaches for allelic copy number determination have recently been investigated in 22q11.2 microdeletions detection. The qPCR method was performed for 22q11.2 microdeletions detection as a first-level screening approach in a genetically unknown series of patients with congenital heart defects. A technical issue related to the VPREB1 qPCR marker was pointed out. Methods A set of 100 unrelated Italian patients with congenital heart defects were tested for 22q11.2 microdeletions by a qPCR method using six different markers. Fluorescence In Situ Hybridization technique (FISH was used for confirmation. Results qPCR identified six patients harbouring the 22q11.2 microdeletion, confirmed by FISH. The VPREB1 gene marker presented with a pattern consistent with hemideletion in one 3 Mb deleted patient, suggestive for a long distal deletion, and in additional five non-deleted patients. The long distal 22q11.2 deletion was not confirmed by Comparative Genomic Hybridization. Indeed, the VPREB1 gene marker generated false positive results in association with the rs1320 G/A SNP, a polymorphism localized within the VPREB1 marker reverse primer sequence. Patients heterozygous for rs1320 SNP, showed a qPCR profile consistent with the presence of a hemideletion. Conclusions Though the qPCR technique showed advantages as a screening approach in terms of cost and time, the VPREB1 marker case revealed that single nucleotide polymorphisms can interfere with qPCR data generating erroneous allelic copy number interpretations.

  12. X-ray detector array

    International Nuclear Information System (INIS)

    Houston, J.M.

    1980-01-01

    The object of the invention (an ionization chamber X-ray detector array for use with high speed computerised tomographic imaging apparatus) is to reduce the time required to produce a tomographic image. The detector array described determines the distribution of X-ray intensities in one or more flat, coplanar X-ray beams. It comprises three flat anode sheets parallel to the X-ray beam, a plurality of rod-like cathodes between the anodes, a detector gas between the electrodes and a means for applying a potential between the electrodes. Each of the X-ray sources is collimated to give a narrow, planar section of X-ray photons. Sets of X-ray sources in the array are pulsed simultaneously to obtain X-ray transmission data for tomographic image reconstruction. (U.K.)

  13. Innovations in IR projector arrays

    Science.gov (United States)

    Cole, Barry E.; Higashi, B.; Ridley, Jeff A.; Holmen, J.; Newstrom, K.; Zins, C.; Nguyen, K.; Weeres, Steven R.; Johnson, Burgess R.; Stockbridge, Robert G.; Murrer, Robert Lee; Olson, Eric M.; Bergin, Thomas P.; Kircher, James R.; Flynn, David S.

    2000-07-01

    In the past year, Honeywell has developed a 512 X 512 snapshot scene projector containing pixels with very high radiance efficiency. The array can operate in both snapshot and raster mode. The array pixels have near black body characteristics, high radiance outputs, broad band performance, and high speed. IR measurements and performance of these pixels will be described. In addition, a vacuum probe station that makes it possible to select the best die for packaging and delivery based on wafer level radiance screening, has been developed and is in operation. This system, as well as other improvements, will be described. Finally, a review of the status of the present projectors and plans for future arrays is included.

  14. Sensitivity of Pulsar Timing Arrays

    Science.gov (United States)

    Siemens, Xavier

    2015-08-01

    For the better part of the last decade, the North American Nanohertz Observatory for Gravitational Waves (NANOGrav) has been using the Green Bank and Arecibo radio telescopes to monitor millisecond pulsars. NANOGrav, along with similar international collaborations, the European Pulsar Timing Array and the Parkes Pulsar Timing Array in Australia, form a consortium of consortia: the International Pulsar Timing Array (IPTA). The goal of the IPTA is to directly detect low-frequency gravitational waves which cause small changes to the times of arrival of radio pulses from millisecond pulsars. In this talk I will discuss the work of NANOGrav and the IPTA as well as our sensitivity to gravitational waves from astrophysical sources. I will show that a detection is possible by the end of the decade.

  15. Comparison of nested PCR and qPCR for the detection and quantitation of BoHV6 DNA.

    Science.gov (United States)

    Kubiś, Piotr; Materniak, Magdalena; Kuźmak, Jacek

    2013-12-01

    Nested PCR and qPCR (quantitative PCR) tests based on glycoprotein B (gB) gene were designed for detecting Bovine herpesvirus 6 (BoHV6) in bovine whole blood samples and wild ruminant blood clots (deer and roe-deer). This virus, commonly known as BLHV (bovine lymphotropic herpesvirus) belongs to the Herpesviridae family, subfamily Gammaherpesvirinae and Macavirus genus. DNA isolated from 92 dairy cow blood samples and 69 wild ruminant clots were examined for the presence of BoHV6 using nested PCR and qPCR tests. Viral DNA was detected by using nested PCR in 59 out of 92 bovine blood samples (64.1%), and by qPCR in 68 out of 92 bovine blood samples (73.9%), but none out of 69 DNA samples isolated from wild ruminant blood clots, was positive in both assays. The specificity of nested PCR and qPCR was confirmed by using BoHV1, BoHV4, BoHV6, BFV, BIV, and BLV DNA. The sensitivity of nested PCR and qPCR was determined using a serially 10-fold diluted vector pCR2.1HgB (2 × 10(0)-2 × 10(6)copies/reaction). In this testing, qPCR was more sensitive than the nested PCR, detecting two copies of BoHV6 whilst the limit of detection for nested PCR was 20 copies. In all qPCR assays, the coefficients of determination (R(2)) ranged between 0.990 and 0.999, and the calculated amplification efficiencies (Eff%) within the range of 89.7-106.9. The intra- and inter-assay CV (coefficient of variation) values did not exceed 4%. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Identification of periodontopathogen microorganisms by PCR technique

    Directory of Open Access Journals (Sweden)

    Milićević Radovan

    2008-01-01

    Full Text Available INTRODUCTION Periodontitis is an inflammatory disease of the supporting tissues of teeth and is a major cause of tooth loss in adults. The onset and progression of periodontal disease is attributed to the presence of elevated levels of a consortium of pathogenic bacteria. Gram negative bacteria, mainly strict anaerobes, play the major role. OBJECTIVE The present study aimed to assess the presence of the main types of microorganisms involved in the aetiopathogenesis of periodontal disease: Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Eikenella corrodens, Treponema denticola, Tanerella forsythia and Prevotella intermedia in different samples collected from the oral cavity of 90 patients diagnosed with periodontitis. METHOD Bacterial DNA detection was performed in diverse biological materials, namely in dental plaque, gingival tissue and saliva, by means of multiplex PCR, a technique that allows simultaneous identification of two different bacterial genomes. RESULTS In the dental plaque of the periodontitis patients, Treponema denticola dominated. In the gingival tissue, Tannerella forsythia and Treponema denticola were the microbiota most frequently detected, whilst in saliva Treponema denticola and Eikenella corrodens were found with the highest percentage. CONCLUSION The identification of microorganisms by multiplex PCR is specific and sensitive. Rapid and precise assessment of different types of periodontopathogens is extremely important for early detection of the infection and consequently for the prevention and treatment of periodontal disease. In everyday clinical practice, for routine bacterial evaluation in patients with periodontal disease, the dental plaque is the most suitable biological material, because it is the richest in periodontal bacteria.

  17. Denoising PCR-amplified metagenome data

    Directory of Open Access Journals (Sweden)

    Rosen Michael J

    2012-10-01

    Full Text Available Abstract Background PCR amplification and high-throughput sequencing theoretically enable the characterization of the finest-scale diversity in natural microbial and viral populations, but each of these methods introduces random errors that are difficult to distinguish from genuine biological diversity. Several approaches have been proposed to denoise these data but lack either speed or accuracy. Results We introduce a new denoising algorithm that we call DADA (Divisive Amplicon Denoising Algorithm. Without training data, DADA infers both the sample genotypes and error parameters that produced a metagenome data set. We demonstrate performance on control data sequenced on Roche’s 454 platform, and compare the results to the most accurate denoising software currently available, AmpliconNoise. Conclusions DADA is more accurate and over an order of magnitude faster than AmpliconNoise. It eliminates the need for training data to establish error parameters, fully utilizes sequence-abundance information, and enables inclusion of context-dependent PCR error rates. It should be readily extensible to other sequencing platforms such as Illumina.

  18. Hybrid Arrays for Chemical Sensing

    Science.gov (United States)

    Kramer, Kirsten E.; Rose-Pehrsson, Susan L.; Johnson, Kevin J.; Minor, Christian P.

    In recent years, multisensory approaches to environment monitoring for chemical detection as well as other forms of situational awareness have become increasingly popular. A hybrid sensor is a multimodal system that incorporates several sensing elements and thus produces data that are multivariate in nature and may be significantly increased in complexity compared to data provided by single-sensor systems. Though a hybrid sensor is itself an array, hybrid sensors are often organized into more complex sensing systems through an assortment of network topologies. Part of the reason for the shift to hybrid sensors is due to advancements in sensor technology and computational power available for processing larger amounts of data. There is also ample evidence to support the claim that a multivariate analytical approach is generally superior to univariate measurements because it provides additional redundant and complementary information (Hall, D. L.; Linas, J., Eds., Handbook of Multisensor Data Fusion, CRC, Boca Raton, FL, 2001). However, the benefits of a multisensory approach are not automatically achieved. Interpretation of data from hybrid arrays of sensors requires the analyst to develop an application-specific methodology to optimally fuse the disparate sources of data generated by the hybrid array into useful information characterizing the sample or environment being observed. Consequently, multivariate data analysis techniques such as those employed in the field of chemometrics have become more important in analyzing sensor array data. Depending on the nature of the acquired data, a number of chemometric algorithms may prove useful in the analysis and interpretation of data from hybrid sensor arrays. It is important to note, however, that the challenges posed by the analysis of hybrid sensor array data are not unique to the field of chemical sensing. Applications in electrical and process engineering, remote sensing, medicine, and of course, artificial

  19. The OncoArray Consortium

    DEFF Research Database (Denmark)

    Amos, Christopher I; Dennis, Joe; Wang, Zhaoming

    2017-01-01

    by Illumina to facilitate efficient genotyping. The consortium developed standard approaches for selecting SNPs for study, for quality control of markers, and for ancestry analysis. The array was genotyped at selected sites and with prespecified replicate samples to permit evaluation of genotyping accuracy...... among centers and by ethnic background. RESULTS: The OncoArray consortium genotyped 447,705 samples. A total of 494,763 SNPs passed quality control steps with a sample success rate of 97% of the samples. Participating sites performed ancestry analysis using a common set of markers and a scoring...

  20. Phased Arrays 1985 Symposium - Proceedings

    Science.gov (United States)

    1985-08-01

    anjl with an1 au~ U lar fy b)eanir. ( mice the 1311 0 ,0 - (a ) ,[ -40.0. -80𔃺 , -90.0 -45.0 0𔃺 45.0 90.0 ANGLE FROM BROADSIDE (DEGREES) aii ia -40,0...Electronic Scanning", RADC-TR-83-128, Dec. 1983. AL) A138808 222 m " ; . . . • " - " - . . . . -" ARRAYS OF COAXIALIY-FED MONOPOLE ELEMENTS IN A PARALLEL...Research Institute Hanscom AFB, MA 01731 Farmingdale, NY 11735 AB ST RAC U Arrays of coaxially-fed monopoles radiating into a parallel plate region

  1. Airborne electronically steerable phased array

    Science.gov (United States)

    1972-01-01

    The results are presented of the second stage of a program for the design and development of a phased array capable of simultaneous and separate transmission and reception of radio frequency signals at S-band frequencies. The design goals of this stage were the development of three major areas of interest required for the final prototype model. These areas are the construction and testing of the low-weight, full-scale 128-element array of antenna elements, the development of the RF manifold feed system, and the construction and testing of a working module containing diplexer and transmit and receive circuits.

  2. Ribotypes and AP-PCR fingerprints of thermophilic campylobacters from marine recreational waters.

    Science.gov (United States)

    Hernández, J; Fayos, A; Alonso, J L; Owen, R J

    1996-02-01

    Thirty-two strains of thermophilic campylobacters isolated from marine recreational water and seven reference strains were biotyped and analysed by chromosomal DNA HaeIII ribopatterns and AP-PCR profiles based on a random 10-mer primer (5'-CAA TCG CCG T-3'). The majority of seawater isolates (90%) were Campylobacter coli, and three strains were Camp. jejuni. Southern blot hybridization analysis showed differences between the strains, and in a numerical analysis three main clusters were formed at the 45% similarity level, that corresponded to Camp. jejuni subsp. jejuni, Camp. coli, and a combination of Camp. coli and Camp. jejuni subsp. doylei. AP-PCR profiles also differentiated between the species but were less discriminatory than ribotyping because six strains (17%) could not be typed by this method. Numerical analysis gave four main clusters at the 45% similarity level, corresponding to Camp. jejuni subsp. jejuni, Camp. coli (two clusters) and Camp. lari. The study shows that strains within each species are diverse genomically. Both molecular methods were highly discriminatory, although some strains with identical ribotypes could be distinguished by AP-PCR, and they are valuable new alternatives to traditional typing in epidemiological studies of environmental campylobacters.

  3. Optimisation of Forensic Genetics Procedures Used in Disputed Paternity Testing: Adjustment of the PCR Reaction Volume

    Directory of Open Access Journals (Sweden)

    Damir Marjanović

    2006-05-01

    Full Text Available Standard molecular techniques, with only a slight modification, are very useful in obtaining and interpreting the final results in the field of forensic genetic. Data obtained through such analysis are highly reliable and can be used as a very powerful tool that produces valuable results. However, success and swiftness of DNA typing of biological evidence either that found at a crime scene or used in disputed paternity testing, depends on the optimization of numerous factors. One of the most important and critical phases that ensures reliability of the whole procedure is the choice of the most suitable volume for the amplification protocol. Buccal swabs were collected from volunteers. DNA was extracted by Qiagen Dnaeasy Tissue Kit. PowerPlex 16 kit was used to simultaneously amplify 15 STR loci by PCR. Amplification was carried out as described previously. The tested total working reaction volumes were 5, 10 and 25 microl. The PCR amplification was carried out in PE Gene Amp PCR System Thermal Cycler (ABI, Foster City, CA. Amplification products were analyzed on an ABI PRISM 377 instrument (ABI, Foster City, CA in 5% bis-acrilamide gel. Amplification was generally successful for all the tested reaction volumes. Lower partial to complete DNA profiles ratio, the quality of obtained STR profiles, significantly reduced amount of reaction's components give advantage to 5 microl reaction volume over other two tested volumes in this case.

  4. Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples.

    Science.gov (United States)

    Mehta, Rohini; Birerdinc, Aybike; Hossain, Noreen; Afendy, Arian; Chandhoke, Vikas; Younossi, Zobair; Baranova, Ancha

    2010-05-21

    Given the epidemic proportions of obesity worldwide and the concurrent prevalence of metabolic syndrome, there is an urgent need for better understanding the underlying mechanisms of metabolic syndrome, in particular, the gene expression differences which may participate in obesity, insulin resistance and the associated series of chronic liver conditions. Real-time PCR (qRT-PCR) is the standard method for studying changes in relative gene expression in different tissues and experimental conditions. However, variations in amount of starting material, enzymatic efficiency and presence of inhibitors can lead to quantification errors. Hence the need for accurate data normalization is vital. Among several known strategies for data normalization, the use of reference genes as an internal control is the most common approach. Recent studies have shown that both obesity and presence of insulin resistance influence an expression of commonly used reference genes in omental fat. In this study we validated candidate reference genes suitable for qRT-PCR profiling experiments using visceral adipose samples from obese and lean individuals. Cross-validation of expression stability of eight selected reference genes using three popular algorithms, GeNorm, NormFinder and BestKeeper found ACTB and RPII as most stable reference genes. We recommend ACTB and RPII as stable reference genes most suitable for gene expression studies of human visceral adipose tissue. The use of these genes as a reference pair may further enhance the robustness of qRT-PCR in this model system.

  5. Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples

    Directory of Open Access Journals (Sweden)

    Afendy Arian

    2010-05-01

    Full Text Available Abstract Background Given the epidemic proportions of obesity worldwide and the concurrent prevalence of metabolic syndrome, there is an urgent need for better understanding the underlying mechanisms of metabolic syndrome, in particular, the gene expression differences which may participate in obesity, insulin resistance and the associated series of chronic liver conditions. Real-time PCR (qRT-PCR is the standard method for studying changes in relative gene expression in different tissues and experimental conditions. However, variations in amount of starting material, enzymatic efficiency and presence of inhibitors can lead to quantification errors. Hence the need for accurate data normalization is vital. Among several known strategies for data normalization, the use of reference genes as an internal control is the most common approach. Recent studies have shown that both obesity and presence of insulin resistance influence an expression of commonly used reference genes in omental fat. In this study we validated candidate reference genes suitable for qRT-PCR profiling experiments using visceral adipose samples from obese and lean individuals. Results Cross-validation of expression stability of eight selected reference genes using three popular algorithms, GeNorm, NormFinder and BestKeeper found ACTB and RPII as most stable reference genes. Conclusions We recommend ACTB and RPII as stable reference genes most suitable for gene expression studies of human visceral adipose tissue. The use of these genes as a reference pair may further enhance the robustness of qRT-PCR in this model system.

  6. Approach to determine the diversity of Legionella species by nested PCR-DGGE in aquatic environments

    Science.gov (United States)

    Huang, Wen-Chien; Tsai, Hsin-Chi; Tao, Chi-Wei; Chen, Jung-Sheng; Shih, Yi-Jia; Kao, Po-Min; Huang, Tung-Yi; Hsu, Bing-Mu

    2017-01-01

    In this study, we describe a nested PCR-DGGE strategy to detect Legionella communities from river water samples. The nearly full-length 16S rRNA gene was amplified using bacterial primer in the first step. After, the amplicons were employed as DNA templates in the second PCR using Legionella specific primer. The third round of gene amplification was conducted to gain PCR fragments apposite for DGGE analysis. Then the total numbers of amplified genes were observed in DGGE bands of products gained with primers specific for the diversity of Legionella species. The DGGE patterns are thus potential for a high-throughput preliminary determination of aquatic environmental Legionella species before sequencing. Comparative DNA sequence analysis of excised DGGE unique band patterns showed the identity of the Legionella community members, including a reference profile with two pathogenic species of Legionella strains. In addition, only members of Legionella pneumophila and uncultured Legionella sp. were detected. Development of three step nested PCR-DGGE tactic is seen as a useful method for studying the diversity of Legionella community. The method is rapid and provided sequence information for phylogenetic analysis. PMID:28166249

  7. Renewable Energy Country Profiles. Caribbean

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-09-15

    IRENA Renewable Energy Country Profiles take stock of the latest developments in the field of renewables at country level around the world. Each profile combines analysis by IRENA's specialists with the latest available country data and additional information from a wide array of sources. The resulting reports provide a brief yet comprehensive picture of the situation with regard to renewable energy, including energy supply, electrical generation and grid capacity, and access. Energy policies, targets and projects are also considered, along with each country's investment climate and endowment with renewable energy resources. The energy statistics presented here span the period from 2009 until 2012, reflecting varying timelines in the source material. Since data availability differs from country to country, wider regional comparisons are possible only for the latest year with figures available for every country included. Despite the time lag in some cases, the evident differences and disparities between countries and regions around the world remain striking. The current package of country profiles is just a starting point. The geographic scope will continue to expand, and existing profiles will be enhanced with new indicators, with the whole series maintained as a live product on the IRENA website (www.irena.org)

  8. Different DNA methylation patterns detected by the Amplified Methylation Polymorphism Polymerase Chain Reaction (AMP PCR) technique among various cell types of bulls

    OpenAIRE

    Phutikanit, Nawapen; Suwimonteerabutr, Junpen; Harrison, Dion; D'Occhio, Michael; Carroll, Bernie; Techakumphu, Mongkol

    2010-01-01

    Abstract Background The purpose of this study was to apply an arbitrarily primed methylation sensitive polymerase chain reaction (PCR) assay called Amplified Methylation Polymorphism Polymerase Chain Reaction (AMP PCR) to investigate the methylation profiles of somatic and germ cells obtained from Holstein bulls. Methods Genomic DNA was extracted from sperm, leukocytes and fibroblasts obtained from three bulls and digested with a methylation sensitive endonuclease (HpaII). The native genomic ...

  9. Accurate quantification of supercoiled DNA by digital PCR

    Science.gov (United States)

    Dong, Lianhua; Yoo, Hee-Bong; Wang, Jing; Park, Sang-Ryoul

    2016-01-01

    Digital PCR (dPCR) as an enumeration-based quantification method is capable of quantifying the DNA copy number without the help of standards. However, it can generate false results when the PCR conditions are not optimized. A recent international comparison (CCQM P154) showed that most laboratories significantly underestimated the concentration of supercoiled plasmid DNA by dPCR. Mostly, supercoiled DNAs are linearized before dPCR to avoid such underestimations. The present study was conducted to overcome this problem. In the bilateral comparison, the National Institute of Metrology, China (NIM) optimized and applied dPCR for supercoiled DNA determination, whereas Korea Research Institute of Standards and Science (KRISS) prepared the unknown samples and quantified them by flow cytometry. In this study, several factors like selection of the PCR master mix, the fluorescent label, and the position of the primers were evaluated for quantifying supercoiled DNA by dPCR. This work confirmed that a 16S PCR master mix avoided poor amplification of the supercoiled DNA, whereas HEX labels on dPCR probe resulted in robust amplification curves. Optimizing the dPCR assay based on these two observations resulted in accurate quantification of supercoiled DNA without preanalytical linearization. This result was validated in close agreement (101~113%) with the result from flow cytometry. PMID:27063649

  10. Method and system for homogenizing diode laser pump arrays

    Science.gov (United States)

    Bayramian, Andy J

    2013-10-01

    An optical amplifier system includes a diode pump array including a plurality of semiconductor diode laser bars disposed in an array configuration and characterized by a periodic distance between adjacent semiconductor diode laser bars. The periodic distance is measured in a first direction perpendicular to each of the plurality of semiconductor diode laser bars. The diode pump array provides a pump output propagating along an optical path and characterized by a first intensity profile measured as a function of the first direction and having a variation greater than 10%. The optical amplifier system also includes a diffractive optic disposed along the optical path. The diffractive optic includes a photo-thermo-refractive glass member. The optical amplifier system further includes an amplifier slab having an input face and position along the optical path and separated from the diffractive optic by a predetermined distance. A second intensity profile measured at the input face of the amplifier slab as a function of the first direction has a variation less than 10%.

  11. Determining the analytical specificity of PCR-based assays for the diagnosis of IA: What is Aspergillus?

    Science.gov (United States)

    Morton, C Oliver; White, P Lewis; Barnes, Rosemary A; Klingspor, Lena; Cuenca-Estrella, Manuel; Lagrou, Katrien; Bretagne, Stéphane; Melchers, Willem; Mengoli, Carlo; Caliendo, Angela M; Cogliati, Massimo; Debets-Ossenkopp, Yvette; Gorton, Rebecca; Hagen, Ferry; Halliday, Catriona; Hamal, Petr; Harvey-Wood, Kathleen; Jaton, Katia; Johnson, Gemma; Kidd, Sarah; Lengerova, Martina; Lass-Florl, Cornelia; Linton, Chris; Millon, Laurence; Morrissey, C Orla; Paholcsek, Melinda; Talento, Alida Fe; Ruhnke, Markus; Willinger, Birgit; Donnelly, J Peter; Loeffler, Juergen

    2017-06-01

    A wide array of PCR tests has been developed to aid the diagnosis of invasive aspergillosis (IA), providing technical diversity but limiting standardisation and acceptance. Methodological recommendations for testing blood samples using PCR exist, based on achieving optimal assay sensitivity to help exclude IA. Conversely, when testing more invasive samples (BAL, biopsy, CSF) emphasis is placed on confirming disease, so analytical specificity is paramount. This multicenter study examined the analytical specificity of PCR methods for detecting IA by blind testing a panel of DNA extracted from a various fungal species to explore the range of Aspergillus species that could be detected, but also potential cross reactivity with other fungal species. Positivity rates were calculated and regression analysis was performed to determine any associations between technical specifications and performance. The accuracy of Aspergillus genus specific assays was 71.8%, significantly greater (P Aspergillus species (47.2%). For genus specific assays the most often missed species were A. lentulus (25.0%), A. versicolor (24.1%), A. terreus (16.1%), A. flavus (15.2%), A. niger (13.4%), and A. fumigatus (6.2%). There was a significant positive association between accuracy and using an Aspergillus genus PCR assay targeting the rRNA genes (P = .0011). Conversely, there was a significant association between rRNA PCR targets and false positivity (P = .0032). To conclude current Aspergillus PCR assays are better suited for detecting A. fumigatus, with inferior detection of most other Aspergillus species. The use of an Aspergillus genus specific PCR assay targeting the rRNA genes is preferential. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. A survey of tools for the analysis of quantitative PCR (qPCR data

    Directory of Open Access Journals (Sweden)

    Stephan Pabinger

    2014-09-01

    Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.

  13. Simultaneous Detection of Ricin and Abrin DNA by Real-Time PCR (qPCR

    Directory of Open Access Journals (Sweden)

    Roman Wölfel

    2012-08-01

    Full Text Available Ricin and abrin are two of the most potent plant toxins known and may be easily obtained in high yield from the seeds using rather simple technology. As a result, both toxins are potent and available toxins for criminal or terrorist acts. However, as the production of highly purified ricin or abrin requires sophisticated equipment and knowledge, it may be more likely that crude extracts would be used by non-governmental perpetrators. Remaining plant-specific nucleic acids in these extracts allow the application of a real-time PCR (qPCR assay for the detection and identification of abrin or ricin genomic material. Therefore, we have developed a duplex real-time PCR assays for simultaneous detection of ricin and abrin DNA based on the OmniMix HS bead PCR reagent mixture. Novel primers and hybridization probes were designed for detection on a SmartCycler instrument by using 5′-nuclease technology. The assay was thoroughly optimized and validated in terms of analytical sensitivity. Evaluation of the assay sensitivity by probit analysis demonstrated a 95% probability of detection at 3 genomes per reaction for ricin DNA and 1.2 genomes per reaction for abrin DNA. The suitability of the assays was exemplified by detection of ricin and abrin contaminations in a food matrix.

  14. Characterization of bovine ruminal epithelial bacterial communities using 16S rRNA sequencing, PCR-DGGE, and qRT-PCR analysis.

    Science.gov (United States)

    Li, Meiju; Zhou, Mi; Adamowicz, Elizabeth; Basarab, John A; Guan, Le Luo

    2012-02-24

    Currently, knowledge regarding the ecology and function of bacteria attached to the epithelial tissue of the rumen wall is limited. In this study, the diversity of the bacterial community attached to the rumen epithelial tissue was compared to the rumen content bacterial community using 16S rRNA gene sequencing, PCR-DGGE, and qRT-PCR analysis. Sequence analysis of 2785 randomly selected clones from six 16S rDNA (∼1.4kb) libraries showed that the community structures of three rumen content libraries clustered together and were separated from the rumen tissue libraries. The diversity index of each library revealed that ruminal content bacterial communities (4.12/4.42/4.88) were higher than ruminal tissue communities (2.90/2.73/3.23), based on 97% similarity. The phylum Firmicutes was predominant in the ruminal tissue communities, while the phylum Bacteroidetes was predominant in the ruminal content communities. The phyla Fibrobacteres, Planctomycetes, and Verrucomicrobia were only detected in the ruminal content communities. PCR-DGGE analysis of the bacterial profiles of the rumen content and ruminal epithelial tissue samples from 22 steers further confirmed that there is a distinct bacterial community that inhibits the rumen epithelium. The distinctive epimural bacterial communities suggest that Firmicutes, together with other epithelial-specific species, may have additional functions other than food digestion. Copyright © 2011 Elsevier B.V. All rights reserved.

  15. Analytical Performance of Four Polymerase Chain Reaction (PCR and Real Time PCR (qPCR Assays for the Detection of Six Leishmania Species DNA in Colombia

    Directory of Open Access Journals (Sweden)

    Cielo M. León

    2017-10-01

    Full Text Available Leishmaniasis comprises a spectrum of parasitic diseases caused by protozoans of the genus Leishmania. Molecular tools have been widely employed for the detection of Leishmania due to its high sensitivity and specificity. However, the analytical performance of molecular platforms as PCR and real time PCR (qPCR including a wide variety of molecular markers has never been evaluated. Herein, the aim was to evaluate the analytical performance of 4 PCR-based assays (designed on four different targets and applied on conventional and real-time PCR platforms. We evaluated the analytical performance of conventional PCR and real time PCR, determining exclusivity and inclusivity, Anticipated Reportable Range (ARR, limit of detection (LoD and accuracy using primers directed to kDNA, HSP70, 18S and ITS-1 targets. We observed that the kDNA was the most sensitive but does not meet the criterion of exclusivity. The HSP70 presented a higher LoD in conventional PCR and qPCR in comparison with the other markers (1 × 101 and 1 × 10-1 equivalent parasites/mL respectively and had a higher coefficient of variation in qPCR. No statistically significant differences were found between the days of the test with the four molecular markers. The present study revealed that the 18S marker presented the best performance in terms of analytical sensitivity and specificity for the qPCR in the species tested (species circulating in Colombia. Therefore, we recommend to explore the analytical and diagnostic performance in future studies using a broader number of species across America.

  16. Analytical Performance of Four Polymerase Chain Reaction (PCR) and Real Time PCR (qPCR) Assays for the Detection of Six Leishmania Species DNA in Colombia

    Science.gov (United States)

    León, Cielo M.; Muñoz, Marina; Hernández, Carolina; Ayala, Martha S.; Flórez, Carolina; Teherán, Aníbal; Cubides, Juan R.; Ramírez, Juan D.

    2017-01-01

    Leishmaniasis comprises a spectrum of parasitic diseases caused by protozoans of the genus Leishmania. Molecular tools have been widely employed for the detection of Leishmania due to its high sensitivity and specificity. However, the analytical performance of molecular platforms as PCR and real time PCR (qPCR) including a wide variety of molecular markers has never been evaluated. Herein, the aim was to evaluate the analytical performance of 4 PCR-based assays (designed on four different targets) and applied on conventional and real-time PCR platforms. We evaluated the analytical performance of conventional PCR and real time PCR, determining exclusivity and inclusivity, Anticipated Reportable Range (ARR), limit of detection (LoD) and accuracy using primers directed to kDNA, HSP70, 18S and ITS-1 targets. We observed that the kDNA was the most sensitive but does not meet the criterion of exclusivity. The HSP70 presented a higher LoD in conventional PCR and qPCR in comparison with the other markers (1 × 101 and 1 × 10-1 equivalent parasites/mL respectively) and had a higher coefficient of variation in qPCR. No statistically significant differences were found between the days of the test with the four molecular markers. The present study revealed that the 18S marker presented the best performance in terms of analytical sensitivity and specificity for the qPCR in the species tested (species circulating in Colombia). Therefore, we recommend to explore the analytical and diagnostic performance in future studies using a broader number of species across America. PMID:29046670

  17. DNA polymerase preference determines PCR priming efficiency.

    Science.gov (United States)

    Pan, Wenjing; Byrne-Steele, Miranda; Wang, Chunlin; Lu, Stanley; Clemmons, Scott; Zahorchak, Robert J; Han, Jian

    2014-01-30

    Polymerase chain reaction (PCR) is one of the most important developments in modern biotechnology. However, PCR is known to introduce biases, especially during multiplex reactions. Recent studies have implicated the DNA polymerase as the primary source of bias, particularly initiation of polymerization on the template strand. In our study, amplification from a synthetic library containing a 12 nucleotide random portion was used to provide an in-depth characterization of DNA polymerase priming bias. The synthetic library was amplified with three commercially available DNA polymerases using an anchored primer with a random 3' hexamer end. After normalization, the next generation sequencing (NGS) results of the amplified libraries were directly compared to the unamplified synthetic library. Here, high throughput sequencing was used to systematically demonstrate and characterize DNA polymerase priming bias. We demonstrate that certain sequence motifs are preferred over others as primers where the six nucleotide sequences at the 3' end of the primer, as well as the sequences four base pairs downstream of the priming site, may influence priming efficiencies. DNA polymerases in the same family from two different commercial vendors prefer similar motifs, while another commercially available enzyme from a different DNA polymerase family prefers different motifs. Furthermore, the preferred priming motifs are GC-rich. The DNA polymerase preference for certain sequence motifs was verified by amplification from single-primer templates. We incorporated the observed DNA polymerase preference into a primer-design program that guides the placement of the primer to an optimal location on the template. DNA polymerase priming bias was characterized using a synthetic library amplification system and NGS. The characterization of DNA polymerase priming bias was then utilized to guide the primer-design process and demonstrate varying amplification efficiencies among three commercially

  18. Molecular quantification of environmental DNA using microfluidics and digital PCR.

    Science.gov (United States)

    Hoshino, Tatsuhiko; Inagaki, Fumio

    2012-09-01

    Real-time PCR has been widely used to evaluate gene abundance in natural microbial habitats. However, PCR-inhibitory substances often reduce the efficiency of PCR, leading to the underestimation of target gene copy numbers. Digital PCR using microfluidics is a new approach that allows absolute quantification of DNA molecules. In this study, digital PCR was applied to environmental samples, and the effect of PCR inhibitors on DNA quantification was tested. In the control experiment using λ DNA and humic acids, underestimation of λ DNA at 1/4400 of the theoretical value was observed with 6.58 ng μL(-1) humic acids. In contrast, digital PCR provided accurate quantification data with a concentration of humic acids up to 9.34 ng μL(-1). The inhibitory effect of paddy field soil extract on quantification of the archaeal 16S rRNA gene was also tested. By diluting the DNA extract, quantified copy numbers from real-time PCR and digital PCR became similar, indicating that dilution was a useful way to remedy PCR inhibition. The dilution strategy was, however, not applicable to all natural environmental samples. For example, when marine subsurface sediment samples were tested the copy number of archaeal 16S rRNA genes was 1.04×10(3) copies/g-sediment by digital PCR, whereas real-time PCR only resulted in 4.64×10(2) copies/g-sediment, which was most likely due to an inhibitory effect. The data from this study demonstrated that inhibitory substances had little effect on DNA quantification using microfluidics and digital PCR, and showed the great advantages of digital PCR in accurate quantifications of DNA extracted from various microbial habitats. Copyright © 2012 Elsevier GmbH. All rights reserved.

  19. Remedy and Recontamination Assessment Array

    Science.gov (United States)

    2017-03-01

    instruments pre-installed from the R/V Ecos during the April 22, 2016 event. .................................................................... 38...Environmental Security Technology Certification Program IBI Index of Benthic Integrity ISMA In situ Microcosm Arrays HOC Hydrophobic Organic Compound...system was successfully designed and constructed based on the goal of providing an integrated technology for assessing the effectiveness of

  20. Solar array flight dynamic experiment

    Science.gov (United States)

    Schock, Richard W.

    1987-01-01

    The purpose of the Solar Array Flight Dynamic Experiment (SAFDE) is to demonstrate the feasibility of on-orbit measurement and ground processing of large space structures' dynamic characteristics. Test definition or verification provides the dynamic characteristic accuracy required for control systems use. An illumination/measurement system was developed to fly on space shuttle flight STS-41D. The system was designed to dynamically evaluate a large solar array called the Solar Array Flight Experiment (SAFE) that had been scheduled for this flight. The SAFDE system consisted of a set of laser diode illuminators, retroreflective targets, an intelligent star tracker receiver and the associated equipment to power, condition, and record the results. In six tests on STS-41D, data was successfully acquired from 18 retroreflector targets and ground processed, post flight, to define the solar array's dynamic characteristic. The flight experiment proved the viability of on-orbit test definition of large space structures dynamic characteristics. Future large space structures controllability should be greatly enhanced by this capability.

  1. Multiwall carbon nanotube microcavity arrays

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, Rajib; Butt, Haider, E-mail: h.butt@bham.ac.uk [Nanotechnology Laboratory, School of Mechanical Engineering, University of Birmingham, Birmingham B15 2TT (United Kingdom); Rifat, Ahmmed A. [Integrated Lightwave Research Group, Department of Electrical Engineering, Faculty of Engineering, University of Malaya, Kuala Lumpur 50603 (Malaysia); Yetisen, Ali K.; Yun, Seok Hyun [Harvard Medical School and Wellman Center for Photomedicine, Massachusetts General Hospital, 65 Landsdowne Street, Cambridge, Massachusetts 02139 (United States); Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Dai, Qing [National Center for Nanoscience and Technology, Beijing 100190 (China)

    2016-03-21

    Periodic highly dense multi-wall carbon nanotube (MWCNT) arrays can act as photonic materials exhibiting band gaps in the visible regime and beyond terahertz range. MWCNT arrays in square arrangement for nanoscale lattice constants can be configured as a microcavity with predictable resonance frequencies. Here, computational analyses of compact square microcavities (≈0.8 × 0.8 μm{sup 2}) in MWCNT arrays were demonstrated to obtain enhanced quality factors (≈170–180) and narrow-band resonance peaks. Cavity resonances were rationally designed and optimized (nanotube geometry and cavity size) with finite element method. Series (1 × 2 and 1 × 3) and parallel (2 × 1 and 3 × 1) combinations of microcavities were modeled and resonance modes were analyzed. Higher order MWCNT microcavities showed enhanced resonance modes, which were red shifted with increasing Q-factors. Parallel microcavity geometries were also optimized to obtain narrow-band tunable filtering in low-loss communication windows (810, 1336, and 1558 nm). Compact series and parallel MWCNT microcavity arrays may have applications in optical filters and miniaturized optical communication devices.

  2. PHARUS : PHased ARray Universal SAR

    NARCIS (Netherlands)

    Paquay, M.H.A.; Vermeulen, B.C.B.; Koomen, P.J.; Hoogeboom, P.; Snoeij, P.; Pouwels, H.

    1996-01-01

    In the Netherlands, a polarimetric C-band aircraft SAR (Synthetic Aperture Radar) has been developed. The project is called PHARUS, an acronm for PHased ARray Universal SAR. This instrument serves remote sensing applications. The antenna system contains 48 active modules (expandable to 96). A module

  3. Gamma-ray array physics

    International Nuclear Information System (INIS)

    Lister, C. J.

    1999-01-01

    In this contribution I am going to discuss the development of large arrays of Compton Suppressed, High Purity Germanium (HpGe) detectors and the physics that has been, that is being, and that will be done with them. These arrays and their science have dominated low-energy nuclear structure research for the last twenty years and will continue to do so in the foreseeable future. John Sharpey Schafer played a visionary role in convincing a skeptical world that the development of these arrays would lead to a path of enlightenment. The extent to which he succeeded can be seen both through the world-wide propagation of ever more sophisticated devices, and through the world-wide propagation of his students. I, personally, would not be working in research if it were not for Johns inspirational leadership. I am eternally grateful to him. Many excellent reviews of array physics have been made in the past which can provide detailed background reading. The review by Paul Nolan, another ex-Sharpey Schafer student, is particularly comprehensive and clear

  4. Directivity of basic linear arrays

    DEFF Research Database (Denmark)

    Bach, Henning

    1970-01-01

    For a linear uniform array ofnelements, an expression is derived for the directivity as a function of the spacing and the phase constants. The cases of isotropic elements, collinear short dipoles, and parallel short dipoles are included. The formula obtained is discussed in some detail and contour...

  5. Micromolding for ceramic microneedle arrays

    NARCIS (Netherlands)

    van Nieuwkasteele-Bystrova, Svetlana Nikolajevna; Lüttge, Regina

    2011-01-01

    The fabrication process of ceramic microneedle arrays (MNAs) is presented. This includes the manufacturing of an SU-8/Si-master, its double replication resulting in a PDMS mold for production by micromolding and ceramic sintering. The robustness of the replicated structures was tested by means of

  6. Optically Controlled Phased Array Antenna

    National Research Council Canada - National Science Library

    Garafalo, David

    1998-01-01

    .... The antenna is a 3-foot by 9 foot phased array capable of a scan angle of 120 degrees. The antenna was designed to be conformal to the cargo door of a large aircraft and is designed to operate in the frequency range of 830 - 1400 MHz with a 30...

  7. TLD array for precise dose measurements in stereotactic radiation techniques

    International Nuclear Information System (INIS)

    Ertl, A.; Kitz, K.; Griffitt, W.; Hartl, R.F.E.; Zehetmayer, M.

    1996-01-01

    We developed a new TLD array for precise dose measurement and verification of the spatial dose distribution in small radiation targets. It consists of a hemicylindrical, tissue-equivalent rod made of polystyrene with 17 parallel moulds for an exact positioning of each TLD. The spatial resolution of the TLD array was evaluated using the Leskell spherical phantom. Dose planning was performed with KULA 4.4 under stereotactic conditions on axial CT images. In the Leksell gamma unit the TLD array was irradiated with a maximal dose of 10 Gy with an unplugged 14 mm collimator. The doses delivered to the TLDs were rechecked by diode detector and film dosimetry and compared to the computer-generated dose profile. We found excellent agreement of our measured values, even at the critical penumbra decline. For the 14 mm and 18 mm collimator and for the 11 mm collimator combination we compared the measured and calculated data at full width at half maximum. This TLD array may be useful for phantom or tissue model studies on the spatial dose distribution in confined radiation targets as used in stereotactic radiotherapy. (author)

  8. Identification of genus Acinetobacter: Standardization of in-house PCR and its comparison with conventional phenotypic methods.

    Science.gov (United States)

    Kulkarni, Sughosh S; Madalgi, Radhika; Ajantha, Ganavalli S; Kulkarni, Raghavendra D

    2017-01-01

    Acinetobacter is grouped under nonfermenting Gram-negative bacilli. It is increasingly isolated from pathological samples. The ability of this genus to acquire drug resistance and spread in the hospital settings is posing a grave problem in healthcare. Specific treatment protocols are advocated for Acinetobacter infections. Hence, rapid identification and drug susceptibility profiling are critical in the management of these infections. To standardize an in-house polymerase chain reaction (PCR) for identification of genus Acinetobacter and to compare PCR with two protocols for its phenotypic identification. A total of 96 clinical isolates of Acinetobacter were included in the study. An in-house PCR for genus level identification of Acinetobacter was standardized. All the isolates were phenotypically identified by two protocols. The results of PCR and phenotypic identification protocols were compared. The in-house PCR standardized was highly sensitive and specific for the genus Acinetobacter . There was 100% agreement between the phenotypic and molecular identification of the genus. The preliminary identification tests routinely used in clinical laboratories were also in complete agreement with phenotypic and molecular identification. The in-house PCR for genus level identification is specific and sensitive. However, it may not be essential for routine identification as the preliminary phenotypic identification tests used in the clinical laboratory reliably identify the genus Acinetobacter .

  9. Multiplex Amplification Refractory Mutation System PCR (ARMS-PCR) provides sequencing independent typing of canine parvovirus.

    Science.gov (United States)

    Chander, Vishal; Chakravarti, Soumendu; Gupta, Vikas; Nandi, Sukdeb; Singh, Mithilesh; Badasara, Surendra Kumar; Sharma, Chhavi; Mittal, Mitesh; Dandapat, S; Gupta, V K

    2016-12-01

    Canine parvovirus-2 antigenic variants (CPV-2a, CPV-2b and CPV-2c) ubiquitously distributed worldwide in canine population causes severe fatal gastroenteritis. Antigenic typing of CPV-2 remains a prime focus of research groups worldwide in understanding the disease epidemiology and virus evolution. The present study was thus envisioned to provide a simple sequencing independent, rapid, robust, specific, user-friendly technique for detecting and typing of presently circulating CPV-2 antigenic variants. ARMS-PCR strategy was employed using specific primers for CPV-2a, CPV-2b and CPV-2c to differentiate these antigenic types. ARMS-PCR was initially optimized with reference positive controls in two steps; where first reaction was used to differentiate CPV-2a from CPV-2b/CPV-2c. The second reaction was carried out with CPV-2c specific primers to confirm the presence of CPV-2c. Initial validation of the ARMS-PCR was carried out with 24 sequenced samples and the results were matched with the sequencing results. ARMS-PCR technique was further used to screen and type 90 suspected clinical samples. Randomly selected 15 suspected clinical samples that were typed with this technique were sequenced. The results of ARMS-PCR and the sequencing matched exactly with each other. The developed technique has a potential to become a sequencing independent method for simultaneous detection and typing of CPV-2 antigenic variants in veterinary disease diagnostic laboratories globally. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq data

    Directory of Open Access Journals (Sweden)

    Perkins James R

    2012-07-01

    Full Text Available Abstract Background Measuring gene transcription using real-time reverse transcription polymerase chain reaction (RT-qPCR technology is a mainstay of molecular biology. Technologies now exist to measure the abundance of many transcripts in parallel. The selection of the optimal reference gene for the normalisation of this data is a recurring problem, and several algorithms have been developed in order to solve it. So far nothing in R exists to unite these methods, together with other functions to read in and normalise the data using the chosen reference gene(s. Results We have developed two R/Bioconductor packages, ReadqPCR and NormqPCR, intended for a user with some experience with high-throughput data analysis using R, who wishes to use R to analyse RT-qPCR data. We illustrate their potential use in a workflow analysing a generic RT-qPCR experiment, and apply this to a real dataset. Packages are available from http://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.htmland http://www.bioconductor.org/packages/release/bioc/html/NormqPCR.html Conclusions These packages increase the repetoire of RT-qPCR analysis tools available to the R user and allow them to (amongst other things read their data into R, hold it in an ExpressionSet compatible R object, choose appropriate reference genes, normalise the data and look for differential expression between samples.

  11. Numerical study of the properties of optical vortex array laser tweezers.

    Science.gov (United States)

    Kuo, Chun-Fu; Chu, Shu-Chun

    2013-11-04

    Chu et al. constructed a kind of Ince-Gaussian modes (IGM)-based vortex array laser beams consisting of p x p embedded optical vortexes from Ince-Gaussian modes, IG(e)(p,p) modes [Opt. Express 16, 19934 (2008)]. Such an IGM-based vortex array laser beams maintains its vortex array profile during both propagation and focusing, and is applicable to optical tweezers. This study uses the discrete dipole approximation (DDA) method to study the properties of the IGM-based vortex array laser tweezers while it traps dielectric particles. This study calculates the resultant force exerted on the spherical dielectric particles of different sizes situated at the IGM-based vortex array laser beam waist. Numerical results show that the number of trapping spots of a structure light (i.e. IGM-based vortex laser beam), is depended on the relation between the trapped particle size and the structure light beam size. While the trapped particle is small comparing to the beam size of the IGM-based vortex array laser beams, the IGM-based vortex array laser beams tweezers are suitable for multiple traps. Conversely, the tweezers is suitable for single traps. The results of this study is useful to the future development of the vortex array laser tweezers applications.

  12. Rapid molecular characterization of Acinetobacter baumannii clones with rep-PCR and evaluation of carbapenemase genes by new multiplex PCR in Hospital District of Helsinki and Uusimaa.

    Directory of Open Access Journals (Sweden)

    Tanja Pasanen

    Full Text Available Multidrug-resistant Acinetobacter baumannii (MDRAB is an increasing problem worldwide. Prevalence of carbapenem resistance in Acinetobacter spp. due to acquired carbapenemase genes is not known in Finland. The purpose of this study was to examine prevalence and clonal spread of multiresistant A. baumannii group species, and their carbapenemase genes. A total of 55 Acinetobacter isolates were evaluated with repetitive PCR (DiversiLab to analyse clonality of isolates, in conjunction with antimicrobial susceptibility profile for ampicillin/sulbactam, colistin, imipenem, meropenem, rifampicin and tigecycline. In addition, a new real-time PCR assay, detecting most clinically important carbapenemase genes just in two multiplex reactions, was developed. The assay detects genes for KPC, VIM, IMP, GES-1/-10, OXA-48, NDM, GIM-1, SPM-1, IMI/NMC-A, SME, CMY-10, SFC-1, SIM-1, OXA-23-like, OXA-24/40-like, OXA-58 and ISAbaI-OXA-51-like junction, and allows confident detection of isolates harbouring acquired carbapenemase genes. There was a time-dependent, clonal spread of multiresistant A. baumannii strongly correlating with carbapenamase gene profile, at least in this geographically restricted study material. The new carbapenemase screening assay was able to detect all the genes correctly suggesting it might be suitable for epidemiologic screening purposes in clinical laboratories.

  13. Improved 2-D resistivity imaging of features in covered karst terrain with arrays of implanted electrodes

    Science.gov (United States)

    Kiflu, H. G.; Kruse, S. E.; Harro, D.; Loke, M. H.; Wilkinson, P. B.

    2013-12-01

    28-electrode arrays with electrodes 2-5 meters apart, and the deep arrays buried at 4-8 meters depth. Ground penetrating radar surveys, SPT borings and coring data provide selected 'ground truthing'. The case studies show that inclusion of the deep electrode array permits karst features such as undulations at the top of limestone and raveling zones within surficial sediments to be imaged. These features are not accessible from surface arrays with equivalent surface footprints. The method also has better resolution at depth at the ends of the lines, where surface arrays are typically plotted with a trapezoidal truncation due to poor resolution at the lower corners of the profile.

  14. Digital PCR as a tool to measure HIV persistence.

    Science.gov (United States)

    Rutsaert, Sofie; Bosman, Kobus; Trypsteen, Wim; Nijhuis, Monique; Vandekerckhove, Linos

    2018-01-30

    Although antiretroviral therapy is able to suppress HIV replication in infected patients, the virus persists and rebounds when treatment is stopped. In order to find a cure that can eradicate the latent reservoir, one must be able to quantify the persisting virus. Traditionally, HIV persistence studies have used real-time PCR (qPCR) to measure the viral reservoir represented by HIV DNA and RNA. Most recently, digital PCR is gaining popularity as a novel approach to nucleic acid quantification as it allows for absolute target quantification. Various commercial digital PCR platforms are nowadays available that implement the principle of digital PCR, of which Bio-Rad's QX200 ddPCR is currently the most used platform in HIV research. Quantification of HIV by digital PCR is proving to be a valuable improvement over qPCR as it is argued to have a higher robustness to mismatches between the primers-probe set and heterogeneous HIV, and forfeits the need for a standard curve, both of which are known to complicate reliable quantification. However, currently available digital PCR platforms occasionally struggle with unexplained false-positive partitions, and reliable segregation between positive and negative droplets remains disputed. Future developments and advancements of the digital PCR technology are promising to aid in the accurate quantification and characterization of the persistent HIV reservoir.

  15. Wideband Low Side Lobe Aperture Coupled Patch Phased Array Antennas

    Science.gov (United States)

    Poduval, Dhruva

    Low profile printed antenna arrays with wide bandwidth, high gain, and low Side Lobe Level (SLL) are in great demand for current and future commercial and military communication systems and radar. Aperture coupled patch antennas have been proposed to obtain wide impedance bandwidths in the past. Aperture coupling is preferred particularly for phased arrays because of their advantage of integration to other active devices and circuits, e.g. phase shifters, power amplifiers, low noise amplifiers, mixers etc. However, when designing such arrays, the interplay between array performance characteristics, such as gain, side lobe level, back lobe level, mutual coupling etc. must be understood and optimized under multiple design constraints, e.g. substrate material properties and thicknesses, element to element spacing, and feed lines and their orientation and arrangements with respect to the antenna elements. The focus of this thesis is to investigate, design, and develop an aperture coupled patch array with wide operating bandwidth (30%), high gain (17.5 dBi), low side lobe level (20 dB), and high Forward to Backward (F/B) ratio (21.8 dB). The target frequency range is 2.4 to 3 GHz given its wide application in WLAN, LTE (Long Term Evolution) and other communication systems. Notwithstanding that the design concept can very well be adapted at other frequencies. Specifically, a 16 element, 4 by 4 planar microstrip patch array is designed using HFSS and experimentally developed and tested. Starting from mutual coupling minimization a corporate feeding scheme is designed to achieve the needed performance. To reduce the SLL the corporate feeding network is redesigned to obtain a specific amplitude taper. Studies are conducted to determine the optimum location for a metallic reflector under the feed line to improve the F/B. An experimental prototype of the antenna was built and tested validating and demonstrating the performance levels expected from simulation predictions

  16. Identification and strain differentiation of 'Bacteroides fragilis group' species and Prevotella bivia by PCR fingerprinting.

    Science.gov (United States)

    Claros, M; Schönian, G; Gräser, Y; Montag, T; Rodloff, A C; Citron, D M; Goldstein, E J

    1995-08-01

    Using single consensus primers of genomic nucleotide sequences, PCR-generated fingerprints were used for identification and differentiation of the Bacteroides fragilis group (B. fragilis, B. thetaiotaomicron, B. ovatus, B. distasonis, B. vulgatus) and Prevotella bivia (B. bivius) by comparing the DNA profiles with those of reference strains from the American Type Culture Collection and German Culture Collection. When primed by a single primer phage M13 core sequence, intra-species specific differences and species-specific bands were detected. Using primers derived from the evolutionarily conserved tRNA gene sequence, species-specific patterns were produced. A computer program, GelManager, was used to analyze the profiles and generate dendrograms. The correlation coefficients determined from the DNA fingerprint profiles of the clinical isolates (using the M13 core primer) fell within a narrow range, reflecting a high level of homology within the species. Based on the dendrograms, strains of one species were clearly differentiated from strains of other species. For comparison, SDS-PAGE analysis of whole cell extracts was also performed to obtain protein band patterns of various strains. Because of the simplicity of the PCR fingerprinting method and the ease of performance of computerized evaluation of data, this technique is a useful method for both species and strain differentiation, as well as for characterization of Bacteroides species and Prevotella bivia.

  17. Comparison of Two Suspension Arrays for Simultaneous Detection of Five Biothreat Bacterial in Powder Samples

    Directory of Open Access Journals (Sweden)

    Yu Yang

    2012-01-01

    Full Text Available We have developed novel Bio-Plex assays for simultaneous detection of Bacillus anthracis, Yersinia pestis, Brucella spp., Francisella tularensis, and Burkholderia pseudomallei. Universal primers were used to amplify highly conserved region located within the 16S rRNA amplicon, followed by hybridized to pathogen-specific probes for identification of these five organisms. The other assay is based on multiplex PCR to simultaneously amplify five species-specific pathogen identification-targeted regions unique to individual pathogen. Both of the two arrays are validated to be flexible and sensitive for simultaneous detection of bioterrorism bacteria. However, universal primer PCR-based array could not identify Bacillus anthracis, Yersinia pestis, and Brucella spp. at the species level because of the high conservation of 16S rDNA of the same genus. The two suspension arrays can be utilized to detect Bacillus anthracis sterne spore and Yersinia pestis EV76 from mimic “write powder” samples, they also proved that the suspension array system will be valuable tools for diagnosis of bacterial biothreat agents in environmental samples.

  18. DNA electrophoresis through microlithographic arrays

    International Nuclear Information System (INIS)

    Sevick, E.M.; Williams, D.R.M.

    1996-01-01

    Electrophoresis is one of the most widely used techniques in biochemistry and genetics for size-separating charged molecular chains such as DNA or synthetic polyelectrolytes. The separation is achieved by driving the chains through a gel with an external electric field. As a result of the field and the obstacles that the medium provides, the chains have different mobilities and are physically separated after a given process time. The macroscopically observed mobility scales inversely with chain size: small molecules move through the medium quickly while larger molecules move more slowly. However, electrophoresis remains a tool that has yet to be optimised for most efficient size separation of polyelectrolytes, particularly large polyelectrolytes, e.g. DNA in excess of 30-50 kbp. Microlithographic arrays etched with an ordered pattern of obstacles provide an attractive alternative to gel media and provide wider avenues for size separation of polyelectrolytes and promote a better understanding of the separation process. Its advantages over gels are (1) the ordered array is durable and can be re-used, (2) the array morphology is ordered and can be standardized for specific separation, and (3) calibration with a marker polyelectrolyte is not required as the array is reproduced to high precision. Most importantly, the array geometry can be graduated along the chip so as to expand the size-dependent regime over larger chain lengths and postpone saturation. In order to predict the effect of obstacles upon the chain-length dependence in mobility and hence, size separation, we study the dynamics of single chains using theory and simulation. We present recent work describing: 1) the release kinetics of a single DNA molecule hooked around a point, frictionless obstacle and in both weak and strong field limits, 2) the mobility of a chain impinging upon point obstacles in an ordered array of obstacles, demonstrating the wide range of interactions possible between the chain and

  19. Microfabricated Multianalyte Sensor Arrays for Metabolic Monitoring

    National Research Council Canada - National Science Library

    Pishko, Michael V

    2006-01-01

    ...(ethylene glycol) diacrylate or PEG-DA on the array electrodes. The fabricated microarray sensors were individually addressable and with no cross-talk between adjacent array elements as assessed using cyclic voltammetry...

  20. Microfabricated Multianalyte Sensor Arrays for Metabolic Monitoring

    National Research Council Canada - National Science Library

    Pishko, Michael V

    2007-01-01

    ...(ethylene glycol) diacrylate or PEG-DA on the array electrodes. The fabricated microarray sensors were individually addressable and with no cross-talk between adjacent array elements as assessed using cyclic voltammetry...

  1. Leakage analysis of crossbar memristor arrays

    KAUST Repository

    Zidan, Mohammed A.; Salem, Ahmed Sultan; Fahmy, Hossam Aly Hassan; Salama, Khaled N.

    2014-01-01

    the readout operation. In this work we study the trade-off between the crossbar array density and the power consumption required for its readout. Our analysis is based on simulating full memristor arrays on a SPICE platform.

  2. Statistical monitoring of linear antenna arrays

    KAUST Repository

    Harrou, Fouzi; Sun, Ying

    2016-01-01

    The paper concerns the problem of monitoring linear antenna arrays using the generalized likelihood ratio (GLR) test. When an abnormal event (fault) affects an array of antenna elements, the radiation pattern changes and significant deviation from

  3. Photovoltaic array: Power conditioner interface characteristics

    Science.gov (United States)

    Gonzalez, C. C.; Hill, G. M.; Ross, R. G., Jr.

    1982-01-01

    The electrical output (power, current, and voltage) of flat plate solar arrays changes constantly, due primarily to changes in cell temperature and irradiance level. As a result, array loads such as dc-to-ac power conditioners must be capable of accommodating widely varying input levels while maintaining operation at or near the maximum power point of the array. The array operating characteristics and extreme output limits necessary for the systematic design of array load interfaces under a wide variety of climatic conditions are studied. A number of interface parameters are examined, including optimum operating voltage, voltage energy, maximum power and current limits, and maximum open circuit voltage. The effect of array degradation and I-V curve fill factor or the array power conditioner interface is also discussed. Results are presented as normalized ratios of power conditioner parameters to array parameters, making the results universally applicable to a wide variety of system sizes, sites, and operating modes.

  4. PCR-DGGE fingerprints of microbial succession during a manufacture of traditional water buffalo mozzarella cheese.

    Science.gov (United States)

    Ercolini, D; Mauriello, G; Blaiotta, G; Moschetti, G; Coppola, S

    2004-01-01

    To monitor the process and the starter effectiveness recording a series of fingerprints of the microbial diversity occurring at different steps of mozzarella cheese manufacture and to investigate the involvement of the natural starter to the achievement of the final product. Samples of raw milk, natural whey culture (NWC) used as starter, curd after ripening and final product were collected during a mozzarella cheese manufacture. Total microbial DNA was directly extracted from the dairy samples as well as bulk colonies collected from the plates of appropriate culture media generally used for viable counts of mesophilic and thermophilic lactic acid bacteria (LAB) and used in polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) experiments. The analysis of the DGGE profiles showed a strong influence of the microflora of the NWC on the whole process because after the starter addition, the profile of all the dairy samples was identical to the one shown by the NWC. Simple indexes were calculated for the DGGE profiles to have an objective estimation of biodiversity and of technological importance of specific groups of organisms. LAB grown on Man Rogosa Sharp (MRS) and Rogosa agar at 30 degrees C showed high viable counts and the highest diversity in species indicating their importance in the cheese making, which had not been considered so far. Moreover, the NWC profiles were shown to be the most similar to the curd profile suggesting to be effective in manufacture. The PCR-DGGE analysis showed that in premium quality manufacture the NWC used as starter had a strong influence on the microflora responsible for process development. The molecular approach appeared to be valid as a tool to control process development, starter effectiveness and product identity as well as to rank cheese quality.

  5. Microsatellite instability in pediatric high grade glioma is associated with genomic profile and differential target gene inactivation.

    Directory of Open Access Journals (Sweden)

    Marta Viana-Pereira

    Full Text Available High grade gliomas (HGG are one of the leading causes of cancer-related deaths in children, and there is increasing evidence that pediatric HGG may harbor distinct molecular characteristics compared to adult tumors. We have sought to clarify the role of microsatellite instability (MSI in pediatric versus adult HGG. MSI status was determined in 144 patients (71 pediatric and 73 adults using a well established panel of five quasimonomorphic mononucleotide repeat markers. Expression of MLH1, MSH2, MSH6 and PMS2 was determined by immunohistochemistry, MLH1 was assessed for mutations by direct sequencing and promoter methylation using MS-PCR. DNA copy number profiles were derived using array CGH, and mutations in eighteen MSI target genes studied by multiplex PCR and genotyping. MSI was found in 14/71 (19.7% pediatric cases, significantly more than observed in adults (5/73, 6.8%; p = 0.02, Chi-square test. MLH1 expression was downregulated in 10/13 cases, however no mutations or promoter methylation were found. MSH6 was absent in one pediatric MSI-High tumor, consistent with an inherited mismatch repair deficiency associated with germline MSH6 mutation. MSI was classed as Type A, and associated with a remarkably stable genomic profile. Of the eighteen classic MSI target genes, we identified mutations only in MSH6 and DNAPKcs and described a polymorphism in MRE11 without apparent functional consequences in DNA double strand break detection and repair. This study thus provides evidence for a potential novel molecular pathway in a proportion of gliomas associated with the presence of MSI.

  6. COMPARISON OF 16S rRNA-PCR-RFLP, LipL32-PCR AND OmpL1-PCR METHODS IN THE DIAGNOSIS OF LEPTOSPIROSIS

    Directory of Open Access Journals (Sweden)

    Tülin GÜVEN GÖKMEN

    Full Text Available SUMMARY Leptospirosis is still one of the most important health problems in developing countries located in humid tropical and subtropical regions. Human infections are generally caused by exposure to water, soil or food contaminated with the urine of infected wild and domestic animals such as rodents and dogs. The clinical course of leptospirosis is variable and may be difficult to distinguish from many other infectious diseases. The dark-field microscopy (DFM, serology and nucleic acid amplification techniques are used to diagnose leptospirosis, however, a distinctive standard reference method is still lacking. Therefore, in this study, we aimed to determine the presence of Leptospira spp., to differentiate the pathogenic L. interrogans and the non-pathogenic L. biflexa, and also to determine the sensitivity and specificity values of molecular methods as an alternative to conventional ones. A total of 133 serum samples, from 47 humans and 86 cattle were evaluated by two conventional tests: the Microagglutination Test (MAT and the DFM, as well as three molecular methods, the 16S rRNA-PCR followed by Restriction Fragment Lenght Polymorphism (RFLP of the amplification products 16S rRNA-PCR-RFLP, LipL32-PCR and OmpL1-PCR. In this study, for L. interrogans, the specificity and sensitivity rates of the 16S rRNA-PCR and the LipL32-PCR were considered similar (100% versus 98.25% and 100% versus 98.68%, respectively. The OmpL1-PCR was able to classify L. interrogans into two intergroups, but this PCR was less sensitive (87.01% than the other two PCR methods. The 16S rRNA-PCR-RFLP could detect L. biflexa DNA, but LipL32-PCR and OmpL1-PCR could not. The 16S rRNA-PCR-RFLP provided an early and accurate diagnosis and was able to distinguish pathogenic and non-pathogenic Leptospira species, hence it may be used as an alternative method to the conventional gold standard techniques for the rapid disgnosis of leptospirosis.

  7. A practical platform for blood biomarker study by using global gene expression profiling of peripheral whole blood.

    Directory of Open Access Journals (Sweden)

    Ze Tian

    Full Text Available Although microarray technology has become the most common method for studying global gene expression, a plethora of technical factors across the experiment contribute to the variable of genome gene expression profiling using peripheral whole blood. A practical platform needs to be established in order to obtain reliable and reproducible data to meet clinical requirements for biomarker study.We applied peripheral whole blood samples with globin reduction and performed genome-wide transcriptome analysis using Illumina BeadChips. Real-time PCR was subsequently used to evaluate the quality of array data and elucidate the mode in which hemoglobin interferes in gene expression profiling. We demonstrated that, when applied in the context of standard microarray processing procedures, globin reduction results in a consistent and significant increase in the quality of beadarray data. When compared to their pre-globin reduction counterparts, post-globin reduction samples show improved detection statistics, lowered variance and increased sensitivity. More importantly, gender gene separation is remarkably clearer in post-globin reduction samples than in pre-globin reduction samples. Our study suggests that the poor data obtained from pre-globin reduction samples is the result of the high concentration of hemoglobin derived from red blood cells either interfering with target mRNA binding or giving the pseudo binding background signal.We therefore recommend the combination of performing globin mRNA reduction in peripheral whole blood samples and hybridizing on Illumina BeadChips as the practical approach for biomarker study.

  8. Multiplex enrichment quantitative PCR (ME-qPCR): a high-throughput, highly sensitive detection method for GMO identification.

    Science.gov (United States)

    Fu, Wei; Zhu, Pengyu; Wei, Shuang; Zhixin, Du; Wang, Chenguang; Wu, Xiyang; Li, Feiwu; Zhu, Shuifang

    2017-04-01

    Among all of the high-throughput detection methods, PCR-based methodologies are regarded as the most cost-efficient and feasible methodologies compared with the next-generation sequencing or ChIP-based methods. However, the PCR-based methods can only achieve multiplex detection up to 15-plex due to limitations imposed by the multiplex primer interactions. The detection throughput cannot meet the demands of high-throughput detection, such as SNP or gene expression analysis. Therefore, in our study, we have developed a new high-throughput PCR-based detection method, multiplex enrichment quantitative PCR (ME-qPCR), which is a combination of qPCR and nested PCR. The GMO content detection results in our study showed that ME-qPCR could achieve high-throughput detection up to 26-plex. Compared to the original qPCR, the Ct values of ME-qPCR were lower for the same group, which showed that ME-qPCR sensitivity is higher than the original qPCR. The absolute limit of detection for ME-qPCR could achieve levels as low as a single copy of the plant genome. Moreover, the specificity results showed that no cross-amplification occurred for irrelevant GMO events. After evaluation of all of the parameters, a practical evaluation was performed with different foods. The more stable amplification results, compared to qPCR, showed that ME-qPCR was suitable for GMO detection in foods. In conclusion, ME-qPCR achieved sensitive, high-throughput GMO detection in complex substrates, such as crops or food samples. In the future, ME-qPCR-based GMO content identification may positively impact SNP analysis or multiplex gene expression of food or agricultural samples. Graphical abstract For the first-step amplification, four primers (A, B, C, and D) have been added into the reaction volume. In this manner, four kinds of amplicons have been generated. All of these four amplicons could be regarded as the target of second-step PCR. For the second-step amplification, three parallels have been taken for

  9. Leakage analysis of crossbar memristor arrays

    KAUST Repository

    Zidan, Mohammed A.

    2014-07-01

    Crossbar memristor arrays provide a promising high density alternative for the current memory and storage technologies. These arrays suffer from parasitic current components that significantly increase the power consumption, and could ruin the readout operation. In this work we study the trade-off between the crossbar array density and the power consumption required for its readout. Our analysis is based on simulating full memristor arrays on a SPICE platform.

  10. Method to fabricate hollow microneedle arrays

    Energy Technology Data Exchange (ETDEWEB)

    Kravitz, Stanley H [Placitas, NM; Ingersoll, David [Albuquerque, NM; Schmidt, Carrie [Los Lunas, NM; Flemming, Jeb [Albuquerque, NM

    2006-11-07

    An inexpensive and rapid method for fabricating arrays of hollow microneedles uses a photoetchable glass. Furthermore, the glass hollow microneedle array can be used to form a negative mold for replicating microneedles in biocompatible polymers or metals. These microneedle arrays can be used to extract fluids from plants or animals. Glucose transport through these hollow microneedles arrays has been found to be orders of magnitude more rapid than natural diffusion.

  11. An OSSE Study for Deep Argo Array using the GFDL Ensemble Coupled Data Assimilation System

    Science.gov (United States)

    Chang, You-Soon; Zhang, Shaoqing; Rosati, Anthony; Vecchi, Gabriel A.; Yang, Xiaosong

    2018-03-01

    An observing system simulation experiment (OSSE) using an ensemble coupled data assimilation system was designed to investigate the impact of deep ocean Argo profile assimilation in a biased numerical climate system. Based on the modern Argo observational array and an artificial extension to full depth, "observations" drawn from one coupled general circulation model (CM2.0) were assimilated into another model (CM2.1). Our results showed that coupled data assimilation with simultaneous atmospheric and oceanic constraints plays a significant role in preventing deep ocean drift. However, the extension of the Argo array to full depth did not significantly improve the quality of the oceanic climate estimation within the bias magnitude in the twin experiment. Even in the "identical" twin experiment for the deep Argo array from the same model (CM2.1) with the assimilation model, no significant changes were shown in the deep ocean, such as in the Atlantic meridional overturning circulation and the Antarctic bottom water cell. The small ensemble spread and corresponding weak constraints by the deep Argo profiles with medium spatial and temporal resolution may explain why the deep Argo profiles did not improve the deep ocean features in the assimilation system. Additional studies using different assimilation methods with improved spatial and temporal resolution of the deep Argo array are necessary in order to more thoroughly understand the impact of the deep Argo array on the assimilation system.

  12. Blood grouping based on PCR methods and agarose gel electrophoresis.

    Science.gov (United States)

    Sell, Ana Maria; Visentainer, Jeane Eliete Laguila

    2015-01-01

    The study of erythrocyte antigens continues to be an intense field of research, particularly after the development of molecular testing methods. More than 300 specificities have been described by the International Society for Blood Transfusion as belonging to 33 blood group systems. The polymerase chain reaction (PCR) is a central tool for red blood cells (RBC) genotyping. PCR and agarose gel electrophoresis are low cost, easy, and versatile in vitro methods for amplifying defined target DNA (RBC polymorphic region). Multiplex-PCR, AS-PCR (Specific Allele Polymerase Chain Reaction), and RFLP-PCR (Restriction Fragment Length Polymorphism-Polymerase Chain Reaction) techniques are usually to identify RBC polymorphisms. Furthermore, it is an easy methodology to implement. This chapter describes the PCR methodology and agarose gel electrophoresis to identify the polymorphisms of the Kell, Duffy, Kidd, and MNS blood group systems.

  13. Product differentiation during continuous-flow thermal gradient PCR.

    Science.gov (United States)

    Crews, Niel; Wittwer, Carl; Palais, Robert; Gale, Bruce

    2008-06-01

    A continuous-flow PCR microfluidic device was developed in which the target DNA product can be detected and identified during its amplification. This in situ characterization potentially eliminates the requirement for further post-PCR analysis. Multiple small targets have been amplified from human genomic DNA, having sizes of 108, 122, and 134 bp. With a DNA dye in the PCR mixture, the amplification and unique melting behavior of each sample is observed from a single fluorescent image. The melting behavior of the amplifying DNA, which depends on its molecular composition, occurs spatially in the thermal gradient PCR device, and can be observed with an optical resolution of 0.1 degrees C pixel(-1). Since many PCR cycles are within the field of view of the CCD camera, melting analysis can be performed at any cycle that contains a significant quantity of amplicon, thereby eliminating the cycle-selection challenges typically associated with continuous-flow PCR microfluidics.

  14. Selecting PCR for the Diagnosis of Intestinal Parasitosis

    DEFF Research Database (Denmark)

    Hartmeyer, G. N.; Hoegh, S. V.; Skov, M. N.

    2017-01-01

    Microscopy of stool samples is a labour-intensive and inaccurate technique for detection of intestinal parasites causing diarrhoea and replacement by PCR is attractive. Almost all cases of diarrhoea induced by parasites over a nine-year period in our laboratory were due to Giardia lamblia......, Cryptosporidium species, or Entamoeba histolytica detected by microscopy. We evaluated and selected in-house singleplex real-time PCR (RT-PCR) assays for these pathogens in 99 stool samples from patients suspected of having intestinal parasitosis tested by microscopy. The strategy included a genus-specific PCR...... assay for C. parvum and C. hominis, with subsequent identification by a PCR that distinguishes between the two species. G. lamblia was detected in five and C. parvum in one out of 68 microscopy-negative samples. The performance of the in-house RT-PCR assays was compared to three commercially available...

  15. Standardization of diagnostic PCR for the detection of foodborne pathogens

    DEFF Research Database (Denmark)

    Malorny, B.; Tassios, P.T.; Radstrom, P.

    2003-01-01

    In vitro amplification of nucleic acids using the polymerase chain reaction (PCR) has become, since its discovery in the 1980s, a powerful diagnostic tool for the analysis of microbial infections as well as for the analysis of microorganisms in food samples. However, despite its potential, PCR has...... neither gained wide acceptance in routine diagnostics nor been widely incorporated in standardized methods. Lack of validation and standard protocols, as well as variable quality of reagents and equipment, influence the efficient dissemination of PCR methodology from expert research laboratories to end......-user laboratories. Moreover, the food industry understandably requires and expects officially approved standards. Recognizing this, in 1999, the European Commission approved the research project, FOOD-PCR (http://www.PCR.dk), which aims to validate and standardize the use of diagnostic PCR for the detection...

  16. Antenna Arrays and Automotive Applications

    CERN Document Server

    Rabinovich, Victor

    2013-01-01

    This book throws a lifeline to designers wading through mounds of antenna array patents looking for the most suitable systems for their projects. Drastically reducing the research time required to locate solutions to the latest challenges in automotive communications, it sorts and systematizes material on cutting-edge antenna arrays that feature multi-element communication systems with enormous potential for the automotive industry. These new systems promise to make driving safer and more efficient, opening up myriad applications, including vehicle-to-vehicle traffic that prevents collisions, automatic toll collection, vehicle location and fine-tuning for cruise control systems. This book’s exhaustive coverage begins with currently deployed systems, frequency ranges and key parameters. It proceeds to examine system geometry, analog and digital beam steering technology (including "smart" beams formed in noisy environments), maximizing signal-to-noise ratios, miniaturization, and base station technology that ...

  17. Adaptive ground implemented phase array

    Science.gov (United States)

    Spearing, R. E.

    1973-01-01

    The simulation of an adaptive ground implemented phased array of five antenna elements is reported for a very high frequency system design that is tolerant to the radio frequency interference environment encountered by a tracking data relay satellite. Signals originating from satellites are received by the VHF ring array and both horizontal and vertical polarizations from each of the five elements are multiplexed and transmitted down to ground station. A panel on the transmitting end of the simulation chamber contains up to 10 S-band RFI sources along with the desired signal to simulate the dynamic relationship between user and TDRS. The 10 input channels are summed, and desired and interference signals are separated and corrected until the resultant sum signal-to-interference ratio is maximized. Testing performed with this simulation equipment demonstrates good correlation between predicted and actual results.

  18. Invasive tightly coupled processor arrays

    CERN Document Server

    LARI, VAHID

    2016-01-01

    This book introduces new massively parallel computer (MPSoC) architectures called invasive tightly coupled processor arrays. It proposes strategies, architecture designs, and programming interfaces for invasive TCPAs that allow invading and subsequently executing loop programs with strict requirements or guarantees of non-functional execution qualities such as performance, power consumption, and reliability. For the first time, such a configurable processor array architecture consisting of locally interconnected VLIW processing elements can be claimed by programs, either in full or in part, using the principle of invasive computing. Invasive TCPAs provide unprecedented energy efficiency for the parallel execution of nested loop programs by avoiding any global memory access such as GPUs and may even support loops with complex dependencies such as loop-carried dependencies that are not amenable to parallel execution on GPUs. For this purpose, the book proposes different invasion strategies for claiming a desire...

  19. High voltage load resistor array

    Science.gov (United States)

    Lehmann, Monty Ray [Smithfield, VA

    2005-01-18

    A high voltage resistor comprising an array of a plurality of parallel electrically connected resistor elements each containing a resistive solution, attached at each end thereof to an end plate, and about the circumference of each of the end plates, a corona reduction ring. Each of the resistor elements comprises an insulating tube having an electrode inserted into each end thereof and held in position by one or more hose clamps about the outer periphery of the insulating tube. According to a preferred embodiment, the electrode is fabricated from stainless steel and has a mushroom shape at one end, that inserted into the tube, and a flat end for engagement with the end plates that provides connection of the resistor array and with a load.

  20. Profound Effect of Profiling Platform and Normalization Strategy on Detection of Differentially Expressed MicroRNAs – A Comparative Study

    Science.gov (United States)

    Meyer, Swanhild U.; Kaiser, Sebastian; Wagner, Carola; Thirion, Christian; Pfaffl, Michael W.

    2012-01-01

    Background Adequate normalization minimizes the effects of systematic technical variations and is a prerequisite for getting meaningful biological changes. However, there is inconsistency about miRNA normalization performances and recommendations. Thus, we investigated the impact of seven different normalization methods (reference gene index, global geometric mean, quantile, invariant selection, loess, loessM, and generalized procrustes analysis) on intra- and inter-platform performance of two distinct and commonly used miRNA profiling platforms. Methodology/Principal Findings We included data from miRNA profiling analyses derived from a hybridization-based platform (Agilent Technologies) and an RT-qPCR platform (Applied Biosystems). Furthermore, we validated a subset of miRNAs by individual RT-qPCR assays. Our analyses incorporated data from the effect of differentiation and tumor necrosis factor alpha treatment on primary human skeletal muscle cells and a murine skeletal muscle cell line. Distinct normalization methods differed in their impact on (i) standard deviations, (ii) the area under the receiver operating characteristic (ROC) curve, (iii) the similarity of differential expression. Loess, loessM, and quantile analysis were most effective in minimizing standard deviations on the Agilent and TLDA platform. Moreover, loess, loessM, invariant selection and generalized procrustes analysis increased the area under the ROC curve, a measure for the statistical performance of a test. The Jaccard index revealed that inter-platform concordance of differential expression tended to be increased by loess, loessM, quantile, and GPA normalization of AGL and TLDA data as well as RGI normalization of TLDA data. Conclusions/Significance We recommend the application of loess, or loessM, and GPA normalization for miRNA Agilent arrays and qPCR cards as these normalization approaches showed to (i) effectively reduce standard deviations, (ii) increase sensitivity and accuracy of