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Sample records for cassette arrays identified

  1. Novel cassette array in a class 1 integron in clinical isolates of Acinetobacter baumannii from central Iran.

    Science.gov (United States)

    Japoni-Nejad, Alireza; Farshad, Shohreh; van Belkum, Alex; Ghaznavi-Rad, Ehsanollah

    2013-12-01

    Antibiotic resistance in Acinetobacter baumannii is a major problem in the hospital and outbreaks caused by this organism have been reported frequently. The present study aimed at determining the antibiotic susceptibility patterns, the prevalence of different classes of integrons and the characterization of integron class 1 gene cassettes in Iranian A. baumannii isolates. A total of 63 non-duplicate A. baumannii isolates were collected from clinical and environmental specimens in the Vali-Asr hospital in the central province of Iran (March to September, 2011). The antimicrobial susceptibility for 15 antibiotics which are used conventionally was determined by disk diffusion. The presence of different integron classes was investigated by PCR and the size of gene cassettes in class 1 integrons was then determined by PCR as well. Moreover, integron cassette arrays of isolates were delineated by RFLP and sequencing amplicons with different lengths. Of 63 isolates 62 (98.4%) carried a class 1 integron. The prevalence of IntI2 was 15.9% and the length of the amplicons ranged from 500 bp to 3 kb. Sequencing of integrons of class 1 revealed the presence of many resistance genes (aadA, aacA, aacC, dfrA, bla(GES) and bla(IMP)). We identified a completely new gene cassette which contained aacA7-qacF-aadA5-bla(IMP), this cassette has not been reported previously in A. baumannii. PMID:24161711

  2. Identification of a Novel Cassette Array in Integronbearing Helicobacter Pylori Strains Isolated from Iranian Patients.

    Science.gov (United States)

    Goudarzi, Mehdi; Seyedjavadi, Sima Sadat; Fazeli, Maryam; Roshani, Maryam; Azad, Mehdi; Heidary, Mohsen; Navidinia, Masoumeh; Goudarzi, Hossein

    2016-01-01

    Helicobacter pylori as the second most common cause of gastric cancer in the world infects approximately half of the developed countries population and 80% of the population living in developing countries. Integrons as genetic reservoirs play major roles in dissemination of antimicrobial resistance genes. To the best of our knowledge, this is the first study to report carriage of class 1 and 2 integrons and associated gene cassettes in H. pylori isolates from Iran. This crosssectional study was conducted in Tehran among 110 patients with H. pylori infection. Antimicrobial susceptibility testing (AST) for H. pylori strains were assessed by the micro broth dilution method. Class 1 and 2 integrons were detected using PCR. In order to determine gene cassettes, amplified fragments were subjected to DNA sequencing of both amplicon strands. The prevalence of resistance to clarithromycin, metronidazole, clarithromycin, tetracycline, amoxicillin, rifampin, and levofloxacin were 68.2% (n=75), 25.5% (n=28), 24.5% (n=27), 19.1% (n=21), 18.2% (n=20) and 16.4% (n=18), respectively. Frequency of multidrug resistance among H. pylori isolates was 12.7%. Class 2 integron was detected in 50 (45.5%) and class 1 integron in 10 (9.1%) H. pylori isolates. The most predominant gene cassette arrays in class 2 integron bearing H. pylori were included sateraaadA1, dfrA1sat2aadA1, blaoxa2 and, aadB whereas common gene cassette arrays in class 1 integron were aadBaadA1cmlA6, aacA4, blaoxa2, and catB3. The high frequency of class 2 integron and multidrug resistance in the present study should be considered as a warning for clinicians that continuous surveillance is necessary to prevent the further spread of resistant isolates. PMID:27509968

  3. Crystal Structure of an Integron Gene Cassette-Associated Protein from Vibrio cholerae Identifies a Cationic Drug-Binding Module

    Energy Technology Data Exchange (ETDEWEB)

    Deshpande, Chandrika N.; Harrop, Stephen J.; Boucher, Yan; Hassan, Karl A.; Di Leo, Rosa; Xu, Xiaohui; Cui, Hong; Savchenko, Alexei; Chang, Changsoo; Labbate, Maurizio; Paulsen, Ian T.; Stokes, H.W.; Curmi, Paul M.G.; Mabbutt, Bridget C. (MIT); (UT-Australia); (Macquarie); (Toronto); (New South)

    2012-02-15

    The direct isolation of integron gene cassettes from cultivated and environmental microbial sources allows an assessment of the impact of the integron/gene cassette system on the emergence of new phenotypes, such as drug resistance or virulence. A structural approach is being exploited to investigate the modularity and function of novel integron gene cassettes. We report the 1.8 {angstrom} crystal structure of Cass2, an integron-associated protein derived from an environmental V. cholerae. The structure defines a monomeric beta-barrel protein with a fold related to the effector-binding portion of AraC/XylS transcription activators. The closest homologs of Cass2 are multi-drug binding proteins, such as BmrR. Consistent with this, a binding pocket made up of hydrophobic residues and a single glutamate side chain is evident in Cass2, occupied in the crystal form by polyethylene glycol. Fluorescence assays demonstrate that Cass2 is capable of binding cationic drug compounds with submicromolar affinity. The Cass2 module possesses a protein interaction surface proximal to its drug-binding cavity with features homologous to those seen in multi-domain transcriptional regulators. Genetic analysis identifies Cass2 to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and closely-related species. We propose that the Cass2 family not only has capacity to form functional transcription regulator complexes, but represents possible evolutionary precursors to multi-domain regulators associated with cationic drug compounds.

  4. Crystal structure of an integron gene cassette-associated protein from Vibrio cholerae identifies a cationic drug-binding module.

    Directory of Open Access Journals (Sweden)

    Chandrika N Deshpande

    Full Text Available The direct isolation of integron gene cassettes from cultivated and environmental microbial sources allows an assessment of the impact of the integron/gene cassette system on the emergence of new phenotypes, such as drug resistance or virulence. A structural approach is being exploited to investigate the modularity and function of novel integron gene cassettes.We report the 1.8 Å crystal structure of Cass2, an integron-associated protein derived from an environmental V. cholerae. The structure defines a monomeric beta-barrel protein with a fold related to the effector-binding portion of AraC/XylS transcription activators. The closest homologs of Cass2 are multi-drug binding proteins, such as BmrR. Consistent with this, a binding pocket made up of hydrophobic residues and a single glutamate side chain is evident in Cass2, occupied in the crystal form by polyethylene glycol. Fluorescence assays demonstrate that Cass2 is capable of binding cationic drug compounds with submicromolar affinity. The Cass2 module possesses a protein interaction surface proximal to its drug-binding cavity with features homologous to those seen in multi-domain transcriptional regulators.Genetic analysis identifies Cass2 to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and closely-related species. We propose that the Cass2 family not only has capacity to form functional transcription regulator complexes, but represents possible evolutionary precursors to multi-domain regulators associated with cationic drug compounds.

  5. Use of Cassette Dosing in Sandwich-Cultured Rat and Human Hepatocytes to Identify Drugs that Inhibit Bile Acid Transport

    OpenAIRE

    Kristina K Wolf; Vora, Sapana; Webster, Lindsey O.; Generaux, Grant T.; Polli, Joseph W; Brouwer, Kim L.R.

    2009-01-01

    Hepatocellular accumulation of bile acids due to inhibition of the canalicular bile salt export pump (BSEP/ABCB11) is one proposed mechanism of drug-induced liver injury (DILI). Some hepatotoxic compounds also are potent inhibitors of bile acid uptake by Na+-dependent taurocholate cotransporting polypeptide (NTCP/SLC10A1). This study used a cassette dosing approach in rat and human sandwich-cultured hepatocytes (SCH) to determine whether known or suspected hepatotoxic drugs inhibit bile acid ...

  6. An array-based method to identify multivalent inhibitors.

    Science.gov (United States)

    Zhang, Yalong; Li, Qian; Rodriguez, Luis G; Gildersleeve, Jeffrey C

    2010-07-21

    Carbohydrate-protein interactions play a critical role in a variety of biological processes, and agonists/antagonists of these interactions are useful as biological probes and therapeutic agents. Most carbohydrate-binding proteins achieve tight binding through formation of a multivalent complex. Therefore, both ligand structure and presentation contribute to recognition. Since there are many potential combinations of structure, spacing, and orientation to consider and the optimal one cannot be predicted, high-throughput approaches for analyzing carbohydrate-protein interactions and designing inhibitors are appealing. In this report, we develop a strategy to vary neoglycoprotein density on a surface of a glycan array. This feature of presentation was combined with variations in glycan structure and glycan density to produce an array with approximately 600 combinations of glycan structure and presentation. The unique array platform allows one to distinguish between different types of multivalent complexes on the array surface. To illustrate the advantages of this format, it was used to rapidly identify multivalent probes for various lectins. The new array was first tested with several plant lectins, including concanavalin A (conA), Vicia villosa isolectin B4 (VVL-B(4)), and Ricinus communis agglutinin (RCA120). Next, it was used to rapidly identify potent multivalent inhibitors of Pseudomonas aeruginosa lectin I (PA-IL), a key protein involved in opportunistic infections of P. aeruginosa , and mouse macrophage galactose-type lectin (mMGL-2), a protein expressed on antigen presenting cells that may be useful as a vaccine targeting receptor. An advantage of the approach is that structural information about the lectin/receptor is not required to obtain a multivalent inhibitor/probe. PMID:20583754

  7. Antibody Arrays Identify Potential Diagnostic Markers of Hepatocellular Carcinoma

    Directory of Open Access Journals (Sweden)

    Brian J. Peter

    2008-01-01

    Full Text Available Hepatocellular carcinoma (HCC is the third leading cause of cancer deaths worldwide. Effective treatment of HCC patients is hampered by the lack of sensitive and specific diagnostic markers of HCC. Alpha-fetoprotein (AFP, the currently used HCC marker, misses 30%–50% of HCC patients, who therefore remain undiagnosed and untreated. In order to identify novel diagnostic markers that can be used individually or in combination with AFP, we used an antibody array platform to detect the levels of candidate proteins in the plasma of HCC patients (n = 48 and patients with chronic hepatitis B or C viral infections (n = 19 (both of which are the major risk factors of HCC. We identified 7 proteins that significantly differentiate HCC patients from hepatitis patients (p < 0.05 (AFP, CTNNB, CSF1, SELL, IGFBP6, IL6R, and VCAM1.Importantly, we also identified 8 proteins that significantly differentiate HCC patients with ‘normal’ levels of AFP (<20 ng/ml from hepatitis patients (p < 0.05 (IL1RN, IFNG, CDKN1A, RETN, CXCL14, CTNNB, FGF2, and SELL. These markers are potentially important complementary markers to AFP. Using an independent immunoassay method in an independent group of 23 HCC patients and 22 hepatitis patients, we validated that plasma levels of CTNNB were significantly higher in the HCC group (p = 0.020. In conclusion, we used an antibody array platform to identify potential circulating diagnostic markers of HCC, some of which may be valuable when used in combination with AFP. The clinical utility of these newly identified HCC diagnostic markers needs to be systematically evaluated.

  8. Blood pressure loci identified with a gene-centric array.

    Science.gov (United States)

    Johnson, Toby; Gaunt, Tom R; Newhouse, Stephen J; Padmanabhan, Sandosh; Tomaszewski, Maciej; Kumari, Meena; Morris, Richard W; Tzoulaki, Ioanna; O'Brien, Eoin T; Poulter, Neil R; Sever, Peter; Shields, Denis C; Thom, Simon; Wannamethee, Sasiwarang G; Whincup, Peter H; Brown, Morris J; Connell, John M; Dobson, Richard J; Howard, Philip J; Mein, Charles A; Onipinla, Abiodun; Shaw-Hawkins, Sue; Zhang, Yun; Davey Smith, George; Day, Ian N M; Lawlor, Debbie A; Goodall, Alison H; Fowkes, F Gerald; Abecasis, Gonçalo R; Elliott, Paul; Gateva, Vesela; Braund, Peter S; Burton, Paul R; Nelson, Christopher P; Tobin, Martin D; van der Harst, Pim; Glorioso, Nicola; Neuvrith, Hani; Salvi, Erika; Staessen, Jan A; Stucchi, Andrea; Devos, Nabila; Jeunemaitre, Xavier; Plouin, Pierre-François; Tichet, Jean; Juhanson, Peeter; Org, Elin; Putku, Margus; Sõber, Siim; Veldre, Gudrun; Viigimaa, Margus; Levinsson, Anna; Rosengren, Annika; Thelle, Dag S; Hastie, Claire E; Hedner, Thomas; Lee, Wai K; Melander, Olle; Wahlstrand, Björn; Hardy, Rebecca; Wong, Andrew; Cooper, Jackie A; Palmen, Jutta; Chen, Li; Stewart, Alexandre F R; Wells, George A; Westra, Harm-Jan; Wolfs, Marcel G M; Clarke, Robert; Franzosi, Maria Grazia; Goel, Anuj; Hamsten, Anders; Lathrop, Mark; Peden, John F; Seedorf, Udo; Watkins, Hugh; Ouwehand, Willem H; Sambrook, Jennifer; Stephens, Jonathan; Casas, Juan-Pablo; Drenos, Fotios; Holmes, Michael V; Kivimaki, Mika; Shah, Sonia; Shah, Tina; Talmud, Philippa J; Whittaker, John; Wallace, Chris; Delles, Christian; Laan, Maris; Kuh, Diana; Humphries, Steve E; Nyberg, Fredrik; Cusi, Daniele; Roberts, Robert; Newton-Cheh, Christopher; Franke, Lude; Stanton, Alice V; Dominiczak, Anna F; Farrall, Martin; Hingorani, Aroon D; Samani, Nilesh J; Caulfield, Mark J; Munroe, Patricia B

    2011-12-01

    Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a bespoke gene-centric array to genotype an independent discovery sample of 25,118 individuals that combined hypertensive case-control and general population samples. We followed up four SNPs associated with BP at our p < 8.56 × 10(-7) study-specific significance threshold and six suggestively associated SNPs in a further 59,349 individuals. We identified and replicated a SNP at LSP1/TNNT3, a SNP at MTHFR-NPPB independent (r(2) = 0.33) of previous reports, and replicated SNPs at AGT and ATP2B1 reported previously. An analysis of combined discovery and follow-up data identified SNPs significantly associated with BP at p < 8.56 × 10(-7) at four further loci (NPR3, HFE, NOS3, and SOX6). The high number of discoveries made with modest genotyping effort can be attributed to using a large-scale yet targeted genotyping array and to the development of a weighting scheme that maximized power when meta-analyzing results from samples ascertained with extreme phenotypes, in combination with results from nonascertained or population samples. Chromatin immunoprecipitation and transcript expression data highlight potential gene regulatory mechanisms at the MTHFR and NOS3 loci. These results provide candidates for further study to help dissect mechanisms affecting BP and highlight the utility of studying SNPs and samples that are independent of those studied previously even when the sample size is smaller than that in previous studies. PMID:22100073

  9. Radiographic film cassette

    International Nuclear Information System (INIS)

    This patent specification describes the design of a radiographic cassette which combines the advantages of a classical cassette and the polymeric bag, on the one hand having an overall rigidity, imparted by the bottom and the marginal part of the cover as they are locked together, and on the other hand the object to be radiographed can be located very close to a film/screen set in the cassette because only the thickness of a flexible foil has to intervene. The cassette has the means by which the air can be a spirated from the inside after closure, and may have an intensifying screen which contacts that side of the flexible foil which faces the interior of the cassette. A preferred field of application is for mammography techniques. (U.K.)

  10. Co-assortment in integron-associated gene cassette assemblages in environmental DNA samples

    Directory of Open Access Journals (Sweden)

    Michael Carolyn A

    2010-08-01

    Full Text Available Abstract Background It has been shown that integron-associated gene cassettes exist largely in tandem arrays of variable size, ranging from antibiotic resistance arrays of three to five cassettes up to arrays of more than 100 cassettes associated with the vibrios. Further, the ecology of the integron/gene cassette system has been investigated by showing that very many different cassettes are present in even small environmental samples. In this study, we seek to extend the ecological perspective on the integron/gene cassette system by investigating the way in which this diverse cassette metagenome is apportioned amongst prokaryote lineages in a natural environment. Results We used a combination of PCR-based techniques applied to environmental DNA samples and ecological analytical techniques to establish co-assortment within cassette populations, then establishing the relationship between this co-assortment and genomic structures. We then assessed the distribution of gene cassettes within the environment and found that the majority of gene cassettes existed in large co-assorting groups. Conclusions Our results suggested that the gene cassette diversity of a relatively pristine sampling environment was structured into co-assorting groups, predominantly containing large numbers of cassettes per group. These co-assorting groups consisted of different gene cassettes in stoichiometric relationship. Conservatively, we then attributed co-assorting cassettes to the gene cassette complements of single prokaryote lineages and by implication, to large integron-associated arrays. The prevalence of large arrays in the environment raises new questions about the assembly, maintenance and utility of large cassette arrays in prokaryote populations.

  11. [Carriage of class 1 and 2 integrons in Acinetobacter baumannii and Pseudomonas aeruginosa isolated from clinical specimens and a novel gene cassette array: blaOXA-11-cmlA7].

    Science.gov (United States)

    Mengeloğlu, Fırat Zafer; Copur Çiçek, Ayşegül; Koçoğlu, Esra; Sandallı, Cemal; Budak, Emine Esra; Ozgümüş, Osman Birol

    2014-01-01

    cassettes. IntI2 gene was not detected in any of the isolates. Resistance to piperacillin/tazobactam, ceftazidime, cefepime, ceftriaxone and ampicillin/sulbactam was detected as the common resistance pattern in all integron-positive A.baumannii strains, whereas resistance to ceftazidime, gentamicin and ciprofloxacin was the common pattern in all integron-positive P.aeruginosa strains. DNA sequence analysis of variable regions of integrons indicated that two separate gene cassette arrays (aacC1-aadA1 and aac(3)-1) were carried by A.baumannii strains, and two types of gene cassette arrays (blaOXA-30-aadA1 and blaOXA-11-cmlA7) were carried by P.aeruginosa strains. To our best knowledge, this is the first report of the gene sequence of blaOXA-11-cmlA7 defined in an integron gene cassette of P.aeruginosa. PMID:24506715

  12. Radiographic film cassette unloading apparatus

    International Nuclear Information System (INIS)

    Apparatus for unloading cassettes, containing exposed radiographic films, has means for unfastening the cassettes, an inclined pathway for gravity feeding and rotating feed members (rollers or belts) to propel the films into the processor. (UK)

  13. Detection of oral Helicobacter Pylori infection using saliva test cassette

    OpenAIRE

    Yu, Min; Zhang, Xue-Yan; Yu, Qing

    2015-01-01

    Objective: To investigate the incidence of oral infection with Helicobacter pylori (H. pylori) and identify related epidemiological factors among freshmen of four colleges in Yancheng. Methods: The data, scored positive or negative, were collected on 160 individuals who had been diagnosed by H. pylori Saliva Test Cassette (HPS) during October 2013 to October 2014. H. pylori Saliva Test Cassette (HPS) is to use colloidal gold technique to specifically identify urease in saliva. A standard ques...

  14. Alternative splicing in colon, bladder, and prostate cancer identified by exon-array analysis

    DEFF Research Database (Denmark)

    Thorsen, Kasper; Sørensen, Karina D.; Brems-Eskildsen, Anne Sofie;

    2008-01-01

    Alternative splicing enhances proteome diversity and modulates cancer-associated proteins. To identify tissue- and tumor-specific alternative splicing, we used the GeneChip Human Exon 1.0 ST Array to measure whole-genome exon expression in 102 normal and cancer tissue samples of different stages ...

  15. Prognostic CpG Methylation Biomarkers Identified by Methylation Array in Esophageal Squamous Cell Carcinoma Patients

    OpenAIRE

    Kuo, I-Ying; Chang, Jia-Ming; Jiang, Shih-Sheng; Chen, Chung-Hsin; Chang, I-Shou; Sheu, Bor-Shyang; Lu, Pei-Jung; Chang, Wei-Lun; Lai, Wu-Wei; Wang, Yi-Ching

    2014-01-01

    Background: Esophageal squamous cell carcinoma (ESCC) is an aggressive cancer with poor prognosis. We aimed to identify a panel of CpG methylation biomarkers for prognosis prediction of ESCC patients. Methods: Illumina's GoldenGate methylation array, supervised principal components, Kaplan-Meier survival analyses and Cox regression model were conducted on dissected tumor tissues from a training cohort of 40 ESCC patients to identify potential CpG methylation biomarkers. Pyrosequencing quantit...

  16. Apparatus for unloading radiographic cassettes in daylight

    International Nuclear Information System (INIS)

    Mechanism, for automatically opening and unloading cassettes of exposed radiographic films, is contructed to unfasten them in inverted position and open them by hinging the container part of the cassette upwardly relative to the lid. (UK)

  17. Disinfection efficacy of an ultraviolet light on film cassettes for preventive of the nosocomial infection

    International Nuclear Information System (INIS)

    The bacterial infection on film cassette contact surface was examined at the diagnostic radiology department of the S. hospital. The objective of this study was to assess the contamination level on film cassette contact surface as a predictor of patient prevention from nosocomial infection and for improvement of the hospital environment. The laboratory result was identified non-pathologic bacterial in the five different cassette size of the contact surface. Film cassettes were exposed to ultraviolet light for 1, 2 and 3 minutes. Ultraviolet light disinfection is proven suitable for bacterial. The study concludes that presence of a bacterial infection will prevent a using antiseptic technique on film cassette contact surface. In addition education of nosocomial infection for radiographers will be required. In conclusion, ultraviolet is considered effective to irradiate bacterial. Additionally, two minutes are required to sterilize film cassettes

  18. Magnetic cassette for radiographic film material

    International Nuclear Information System (INIS)

    A radiographic film cassette having a plurality of magnet components integral with the cassette holder for adhering the cassette to ferrous material in X-raying for defects in welds or fissures in shipyards, pipe lines, or the like. What is provided is a substantially flexible cassette envelope comprising first and second layers of radiographic intensifying screens with a sheet of radiographic film positioned therebetween. The cassette would be a cassette envelope constructed of waterproof fabric or other suitable material providing a light-free environment, and having the ability to flex around the curvature of the surface of a pipe or the like to be x-rayed. There is further provided a plurality of magnet components, preferably situated in each corner of the cassette envelope and flexibly attached thereto for overall adherence of the envelope to the surface of the pipe or the like to be x-rayed during the process

  19. seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data

    Science.gov (United States)

    Kolde, Raivo; Märtens, Kaspar; Lokk, Kaie; Laur, Sven; Vilo, Jaak

    2016-01-01

    Motivation: One of the main goals of large scale methylation studies is to detect differentially methylated loci. One way is to approach this problem sitewise, i.e. to find differentially methylated positions (DMPs). However, it has been shown that methylation is regulated in longer genomic regions. So it is more desirable to identify differentially methylated regions (DMRs) instead of DMPs. The new high coverage arrays, like Illuminas 450k platform, make it possible at a reasonable cost. Few tools exist for DMR identification from this type of data, but there is no standard approach. Results: We propose a novel method for DMR identification that detects the region boundaries according to the minimum description length (MDL) principle, essentially solving the problem of model selection. The significance of the regions is established using linear mixed models. Using both simulated and large publicly available methylation datasets, we compare seqlm performance to alternative approaches. We demonstrate that it is both more sensitive and specific than competing methods. This is achieved with minimal parameter tuning and, surprisingly, quickest running time of all the tried methods. Finally, we show that the regional differential methylation patterns identified on sparse array data are confirmed by higher resolution sequencing approaches. Availability and Implementation: The methods have been implemented in R package seqlm that is available through Github: https://github.com/raivokolde/seqlm Contact: rkolde@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27187204

  20. An investigation of infection control for x-ray cassettes in a diagnostic imaging department

    Energy Technology Data Exchange (ETDEWEB)

    Fox, Matthew [School of Allied Health Professions and Science, Faculty of Health, Wellbeing and Science, University Campus Suffolk, Rope Walk, Ipswich, Suffolk, IP4 1LT (United Kingdom); Harvey, Jane M. [School of Allied Health Professions and Science, Faculty of Health, Wellbeing and Science, University Campus Suffolk, Rope Walk, Ipswich, Suffolk, IP4 1LT (United Kingdom)], E-mail: j.harvey@ucs.ac.uk

    2008-11-15

    Introduction: This research was conducted to investigate if X-ray cassettes could be a possible source of pathogens capable of causing nosocomial infections, and if they could be a possible vector for cross infection within the hospital environment. Method: The research involved the swabbing of X-ray cassettes in a Diagnostic Imaging Department of a large hospital in the east of England. Two areas of the Diagnostic Imaging Department were included in the study. Research concentrated on X-ray cassettes used for mobile radiography, accident and emergency and inpatient use. Forty cassettes were swabbed in total specifically for general levels of bacterial contamination, also for the presence or absence of methicillin-resistant Staphylococcus aureus (MRSA). A mapping exercise was completed following the location of an X-ray cassette typically used in mobile radiography. The exercise noted the level of direct contact with patient's skin and other possible routes of infection. Results: The results demonstrated that there were large levels of growth of samples taken from cassettes and developed in the Microbiology Department. Coagulase-negative Staphylococcus, Micrococci, Diptheroids and species of Bacillus were all identified. The mapping exercise in which the journey of a 35/43 cm cassette used for mobile radiography was tracked found that contact with patient's skin and potential pathogens or routes of cross infection was a common occurrence whilst undertaking mobile radiography. Conclusion: The research has identified the presence of bacterial contamination on cassettes. The research established that X-ray cassettes/imaging plates are often exposed to pathogens and possible routes of cross infection; also that patient's skin often comes directly in contact with the X-ray cassette/imaging plate. The research also shows that as cassettes/imaging plates are a potential source of cross infection, the Diagnostic Imaging Department may be partly responsible

  1. An investigation of infection control for x-ray cassettes in a diagnostic imaging department

    International Nuclear Information System (INIS)

    Introduction: This research was conducted to investigate if X-ray cassettes could be a possible source of pathogens capable of causing nosocomial infections, and if they could be a possible vector for cross infection within the hospital environment. Method: The research involved the swabbing of X-ray cassettes in a Diagnostic Imaging Department of a large hospital in the east of England. Two areas of the Diagnostic Imaging Department were included in the study. Research concentrated on X-ray cassettes used for mobile radiography, accident and emergency and inpatient use. Forty cassettes were swabbed in total specifically for general levels of bacterial contamination, also for the presence or absence of methicillin-resistant Staphylococcus aureus (MRSA). A mapping exercise was completed following the location of an X-ray cassette typically used in mobile radiography. The exercise noted the level of direct contact with patient's skin and other possible routes of infection. Results: The results demonstrated that there were large levels of growth of samples taken from cassettes and developed in the Microbiology Department. Coagulase-negative Staphylococcus, Micrococci, Diptheroids and species of Bacillus were all identified. The mapping exercise in which the journey of a 35/43 cm cassette used for mobile radiography was tracked found that contact with patient's skin and potential pathogens or routes of cross infection was a common occurrence whilst undertaking mobile radiography. Conclusion: The research has identified the presence of bacterial contamination on cassettes. The research established that X-ray cassettes/imaging plates are often exposed to pathogens and possible routes of cross infection; also that patient's skin often comes directly in contact with the X-ray cassette/imaging plate. The research also shows that as cassettes/imaging plates are a potential source of cross infection, the Diagnostic Imaging Department may be partly responsible for adding to

  2. Identifying firing mammalian neurons in networks with high-resolution multi-transistor array (MTA)

    Science.gov (United States)

    Lambacher, A.; Vitzthum, V.; Zeitler, R.; Eickenscheidt, M.; Eversmann, B.; Thewes, R.; Fromherz, P.

    2011-01-01

    The electrical activity of a network of mammalian neurons is mapped with a Multi-Transistor Array (MTA) fabricated with extended CMOS technology. The spatial resolution is 7.4 μm on an area of 1 mm2 at a sampling frequency of 6 kHz for a complete readout of 16,384 sensor transistors. Action potentials give rise to extracellular voltages with amplitudes in a range of 500 μV. On the basis of the high resolution in space and time, correlation algorithms are used to identify single action potentials with amplitudes as low as about 200μV, and to assign the signals to the activity of individual neurons even in a dense network.

  3. Proof of concept of using chromogenic arrays as a tool to identify blue cheese varieties.

    Science.gov (United States)

    Zaragozá, Patricia; Ros-Lis, José V; Vivancos, José-Luis; Martínez-Máñez, Ramón

    2015-04-01

    A new chromogenic array for the identification and classification of blue cheeses has been developed. It is based on the response of a chromogenic array composed of five sensing materials prepared by the incorporation of pH indicators to MCM-41 and alumina. Four blue cheeses were tested: Roquefort, Blue Stilton, blue cheese with leaves and blue cheese spread. The colour modulations of the chromogenic array were processed by the principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA). The statistical PCA analysis showed different responses to each cheese. PLS-DA models were developed by incorporating the data measured at diverse times, and this approach allowed us to obtain a perfect classification of all five cheeses in 5.5h. The results suggest that chromogenic arrays and optoelectronic noses can be a suitable approach to develop simple systems to classify blue cheeses and of potential use for the detection of food fraud. PMID:25442626

  4. Mulibrey nanism: Two novel mutations in a child identified by Array CGH and DNA sequencing.

    Science.gov (United States)

    Mozzillo, Enza; Cozzolino, Carla; Genesio, Rita; Melis, Daniela; Frisso, Giulia; Orrico, Ada; Lombardo, Barbara; Fattorusso, Valentina; Discepolo, Valentina; Della Casa, Roberto; Simonelli, Francesca; Nitsch, Lucio; Salvatore, Francesco; Franzese, Adriana

    2016-08-01

    In childhood, several rare genetic diseases have overlapping symptoms and signs, including those regarding growth alterations, thus the differential diagnosis is sometimes difficult. The proband, aged 3 years, was suspected to have Silver-Russel syndrome because of intrauterine growth retardation, postnatal growth retardation, typical facial dysmorphic features, macrocephaly, body asymmetry, and bilateral fifth finger clinodactyly. Other features were left atrial and ventricular enlargement and patent foramen ovale. Total X-ray skeleton showed hypoplasia of the twelfth rib bilaterally and of the coccyx, slender long bones with thick cortex, and narrow medullary channels. The genetic investigation did not confirm Silver-Russel syndrome. At the age of 5 the patient developed an additional sign: hepatomegaly. Array CGH revealed a 147 kb deletion (involving TRIM 37 and SKA2 genes) on one allele of chromosome 17, inherited from his mother. These results suggested Mulibrey nanism. The clinical features were found to fit this hypothesis. Sequencing of the TRIM 37 gene showed a single base change at a splicing locus, inherited from his father that provoked a truncated protein. The combined use of Array CGH and DNA sequencing confirmed diagnosis of Mulibrey nanism. The large deletion involving the SKA2 gene, along with the increased frequency of malignant tumours in mulibrey patients, suggests closed monitoring for cancer of our patient and his mother. Array CGH should be performed as first tier test in all infants with multiple anomalies. The clinician should reconsider the clinical features when the genetics suggests this. © 2016 Wiley Periodicals, Inc. PMID:27256967

  5. Using a binaural biomimetic array to identify bottom objects ensonified by echolocating dolphins

    Science.gov (United States)

    Heiweg, D.A.; Moore, P.W.; Martin, S.W.; Dankiewicz, L.A.

    2006-01-01

    The development of a unique dolphin biomimetic sonar produced data that were used to study signal processing methods for object identification. Echoes from four metallic objects proud on the bottom, and a substrate-only condition, were generated by bottlenose dolphins trained to ensonify the targets in very shallow water. Using the two-element ('binaural') receive array, object echo spectra were collected and submitted for identification to four neural network architectures. Identification accuracy was evaluated over two receive array configurations, and five signal processing schemes. The four neural networks included backpropagation, learning vector quantization, genetic learning and probabilistic network architectures. The processing schemes included four methods that capitalized on the binaural data, plus a monaural benchmark process. All the schemes resulted in above-chance identification accuracy when applied to learning vector quantization and backpropagation. Beam-forming or concatenation of spectra from both receive elements outperformed the monaural benchmark, with higher sensitivity and lower bias. Ultimately, best object identification performance was achieved by the learning vector quantization network supplied with beam-formed data. The advantages of multi-element signal processing for object identification are clearly demonstrated in this development of a first-ever dolphin biomimetic sonar. ?? 2006 IOP Publishing Ltd.

  6. A small towed beamforming array to identify vocalizing resident killer whales ( Orcinus orca) concurrent with focal behavioral observations

    Science.gov (United States)

    Miller, Patrick J.; Tyack, Peter L.

    Investigations of communication systems benefit from concurrent observation of vocal and visible behaviors of individual animals. A device has been developed to identify individual vocalizing resident killer whales ( Orcinus orca) during focal behavioral observations. The device consists of a 2-m, 15-element hydrophone array, which is easily towed behind a small vessel, on-board multi-channel recorders, and real-time signal processing equipment. Acoustic data from the hydrophones are digitized and processed using broadband frequency-domain beamforming to yield frequency-azimuth (FRAZ) and "directo-gram" displays of arriving sounds. Based upon statistical analysis of independent portions of typical killer whale calls, the precision of the angle-of-arrival estimate ranges from ±0° to ±2.5° with a mean precision of ±1.5°. Echolocation clicks also are resolved precisely with a typical -6 dB mainlobe width of ±2.0°. Careful positioning of the array relative to the animals minimizes the effects of depth ambiguities and allows identification of individual sources in many circumstances. Several strategies for identifying vocalizing individuals are discussed and an example of a successful identification is described. Use of the array with resident killer whales did not interfere with vessel maneuverability, animal tracking, or behavioral sampling of focal individuals. This localization technique has promise for advancing the abilities of researchers to conduct unbiased behavioral and acoustic sampling of individual free-ranging cetaceans.

  7. Array Manipulation And Matrix-Tree Method To Identify High Concentration Regions HCRs

    Directory of Open Access Journals (Sweden)

    Rachana Arora

    2015-08-01

    Full Text Available Abstract-Sequence Alignment and Analysis is one of the most important applications of bioinformatics. It involves alignment a pair or more sequences with each other and identify a common pattern that would ultimately lead to conclusions of homology or dissimilarity. A number of algorithms that make use of dynamic programming to perform alignment between sequences are available. One of their main disadvantages is that they involve complicated computations and backtracking methods that are difficult to implement. This paper describes a much simpler method to identify common regions in 2 sequences and align them based on the density of common sequences identified.

  8. Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes

    DEFF Research Database (Denmark)

    Weile, Christian; Gardner, Paul P; Hedegaard, Mads M;

    2007-01-01

    BACKGROUND: Within the last decade a large number of noncoding RNA genes have been identified, but this may only be the tip of the iceberg. Using comparative genomics a large number of sequences that have signals concordant with conserved RNA secondary structures have been discovered in the human...

  9. Books (on Cassette) Are Better Than Ever.

    Science.gov (United States)

    Davis, Bryan

    1984-01-01

    Describes introduction of books on tape at Oskaloosa (Iowa) Public Library, highlighting determination of audience and use, display of recorded books, packaging of tapes, cataloging, and quality of tapes. A list of 19 production companies and six distributors noting address, telephone number, type of cassettes, and price range is included. (EJS)

  10. Performance of a PET detector module utilizing an array of silicon photodiodes to identify the crystal of interaction

    International Nuclear Information System (INIS)

    The authors initial performance results for a new multi-layer PET detector module consisting of an array of 3 mm square by 30 mm deep BGO crystals coupled on one end to a single photomultiplier tube and on the opposite end to an array of 3 mm square silicon photodiodes. The photomultiplier tube provides an accurate timing pulse and energy discrimination for all the crystals in the module, while the silicon photodiodes identify the crystal of interaction. When a single BGO crystal at +25 C is excited with 511 keV photons, the authors measure a photodiode signal centered at 700 electrons (e-) with noise of 375 e- fwhm. When a four crystal/photodiode module is excited with a collimated line source of 511 keV photons, the crystal of interaction is correctly identified 82% of the time. The misidentification rate can be greatly reduced and an 8 x 8 crystal/photodiode module constructed by using thicker depletion layer photodiodes or cooling to 0 C

  11. BAC CGH-array identified specific small-scale genomic imbalances in diploid DMBA-induced rat mammary tumors

    Directory of Open Access Journals (Sweden)

    Samuelson Emma

    2012-08-01

    Full Text Available Abstract Background Development of breast cancer is a multistage process influenced by hormonal and environmental factors as well as by genetic background. The search for genes underlying this malignancy has recently been highly productive, but the etiology behind this complex disease is still not understood. In studies using animal cancer models, heterogeneity of the genetic background and environmental factors is reduced and thus analysis and identification of genetic aberrations in tumors may become easier. To identify chromosomal regions potentially involved in the initiation and progression of mammary cancer, in the present work we subjected a subset of experimental mammary tumors to cytogenetic and molecular genetic analysis. Methods Mammary tumors were induced with DMBA (7,12-dimethylbenz[a]anthrazene in female rats from the susceptible SPRD-Cu3 strain and from crosses and backcrosses between this strain and the resistant WKY strain. We first produced a general overview of chromosomal aberrations in the tumors using conventional kartyotyping (G-banding and Comparative Genome Hybridization (CGH analyses. Particular chromosomal changes were then analyzed in more details using an in-house developed BAC (bacterial artificial chromosome CGH-array platform. Results Tumors appeared to be diploid by conventional karyotyping, however several sub-microscopic chromosome gains or losses in the tumor material were identified by BAC CGH-array analysis. An oncogenetic tree analysis based on the BAC CGH-array data suggested gain of rat chromosome (RNO band 12q11, loss of RNO5q32 or RNO6q21 as the earliest events in the development of these mammary tumors. Conclusions Some of the identified changes appear to be more specific for DMBA-induced mammary tumors and some are similar to those previously reported in ACI rat model for estradiol-induced mammary tumors. The later group of changes is more interesting, since they may represent anomalies that involve

  12. BAC CGH-array identified specific small-scale genomic imbalances in diploid DMBA-induced rat mammary tumors

    International Nuclear Information System (INIS)

    Development of breast cancer is a multistage process influenced by hormonal and environmental factors as well as by genetic background. The search for genes underlying this malignancy has recently been highly productive, but the etiology behind this complex disease is still not understood. In studies using animal cancer models, heterogeneity of the genetic background and environmental factors is reduced and thus analysis and identification of genetic aberrations in tumors may become easier. To identify chromosomal regions potentially involved in the initiation and progression of mammary cancer, in the present work we subjected a subset of experimental mammary tumors to cytogenetic and molecular genetic analysis. Mammary tumors were induced with DMBA (7,12-dimethylbenz[a]anthrazene) in female rats from the susceptible SPRD-Cu3 strain and from crosses and backcrosses between this strain and the resistant WKY strain. We first produced a general overview of chromosomal aberrations in the tumors using conventional kartyotyping (G-banding) and Comparative Genome Hybridization (CGH) analyses. Particular chromosomal changes were then analyzed in more details using an in-house developed BAC (bacterial artificial chromosome) CGH-array platform. Tumors appeared to be diploid by conventional karyotyping, however several sub-microscopic chromosome gains or losses in the tumor material were identified by BAC CGH-array analysis. An oncogenetic tree analysis based on the BAC CGH-array data suggested gain of rat chromosome (RNO) band 12q11, loss of RNO5q32 or RNO6q21 as the earliest events in the development of these mammary tumors. Some of the identified changes appear to be more specific for DMBA-induced mammary tumors and some are similar to those previously reported in ACI rat model for estradiol-induced mammary tumors. The later group of changes is more interesting, since they may represent anomalies that involve genes with a critical role in mammary tumor development. Genetic

  13. Candidate cancer-targeting agents identified by expression-profiling arrays

    Directory of Open Access Journals (Sweden)

    Termglinchan V

    2013-04-01

    Full Text Available Vittavat Termglinchan,1 Wachiraporn Wanichnopparat,1 Kulachanya Suwanwongse,1 Chunhakarn Teeyapant,1 Kanticha Chatpermporn,1 Kanchana Leerunyakul,1 Khwanruthai Chuadpia,1 Onpailin Sirimaneethum,1 Parinya Wijitworawong,1 Wattanakitch Mutirangura,1 Chatchawit Aporntewan,2 Chanida Vinayanuwattikun,3 Apiwat Mutirangura4 1Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; 2Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand; 3Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and The King Chulalongkorn Memorial Hospital, Bangkok, Thailand; 4Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand Background: One particularly promising component of personalized medicine in cancer treatment is targeted therapy, which aims to maximize therapeutic efficacy while minimizing toxicity. However, the number of approved targeted agents remains limited. Expression microarray data for different types of cancer are resources to identify genes that were upregulated. The genes are candidate targets for cancer-targeting agents for future anticancer research and targeted treatments. Methods and findings: The gene expression profiles of 48 types of cancer from 2,141 microarrays reported in the Gene Expression Omnibus were analyzed. These data were organized into 78 experimental groups, on which we performed comprehensive analyses using two-tailed Student's t-tests with significance set at P < 0.01 to identify genes that were upregulated compared with normal cells in each cancer type. The resulting list of significantly upregulated genes was cross-referenced with three categories of protein inhibitor targets, categorized by inhibitor type ('Targets of US Food and Drug Administration (FDA-approved anticancer drugs', 'Targets of FDA

  14. A Mismatch EndoNuclease Array-Based Methodology (MENA for Identifying Known SNPs or Novel Point Mutations

    Directory of Open Access Journals (Sweden)

    Josep M. Comeron

    2016-04-01

    Full Text Available Accurate and rapid identification or confirmation of single nucleotide polymorphisms (SNPs, point mutations and other human genomic variation facilitates understanding the genetic basis of disease. We have developed a new methodology (called MENA (Mismatch EndoNuclease Array pairing DNA mismatch endonuclease enzymology with tiling microarray hybridization in order to genotype both known point mutations (such as SNPs as well as identify previously undiscovered point mutations and small indels. We show that our assay can rapidly genotype known SNPs in a human genomic DNA sample with 99% accuracy, in addition to identifying novel point mutations and small indels with a false discovery rate as low as 10%. Our technology provides a platform for a variety of applications, including: (1 genotyping known SNPs as well as confirming newly discovered SNPs from whole genome sequencing analyses; (2 identifying novel point mutations and indels in any genomic region from any organism for which genome sequence information is available; and (3 screening panels of genes associated with particular diseases and disorders in patient samples to identify causative mutations. As a proof of principle for using MENA to discover novel mutations, we report identification of a novel allele of the beethoven (btv gene in Drosophila, which encodes a ciliary cytoplasmic dynein motor protein important for auditory mechanosensation.

  15. Diversity of gene cassettes and the abundance of the class 1 integron-integrase gene in sediment polluted by metals.

    Science.gov (United States)

    Oliveira-Pinto, Clarisse; Costa, Patrícia S; Reis, Mariana P; Chartone-Souza, Edmar; Nascimento, Andréa M A

    2016-05-01

    The integron-gene cassette system has typically been associated with antibiotic-resistant pathogens. However, the diversity of gene cassettes and the abundance of class 1 integrons outside of the clinical context are not fully explored. Primers targeting the conserved segments of attC recombination sites were used to amplify gene cassettes from the sediment of the Mina stream, which exhibited a higher degree of stress to metal pollution in the dry season than the rainy season. Of the 143 total analyzed sequences, 101 had no matches to proteins in the database, where cassette open reading frames could be identified by homology with database entries. There was a predominance of sequences encoding essential cellular functions. Each season that was sampled yielded a specific pool of gene cassettes. Real-time PCR revealed that 8.5 and 41.6 % of bacterial cells potentially harbored a class 1 integron in the rainy and dry seasons, respectively. In summary, our findings demonstrate that most of the gene cassettes have no ascribable function and, apparently, historically metal-contaminated sediment favors the maintenance of bacteria containing the intI1 gene. Thus, the diversity of gene cassettes is far from being fully explored deserving further attention. PMID:26961777

  16. Novel streptomycin and spectinomycin resistance gene as a gene cassette within a class 1 integron isolated from Escherichia coli

    DEFF Research Database (Denmark)

    Sandvang, D.

    1999-01-01

    The aadA genes, encoding resistance to streptomycin and spectinomycin, have been found as gene cassettes in different gram-negative and gram-positive bacterial species. The present study has revealed the sequence of a new gene, aadA5, integrated as a gene cassette together with the trimethoprim r...... resistance gene dfr7 in a class 1 integron. The integron was located on a plasmid and was identified in a pathogenic porcine Escherichia coli isolate....

  17. Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis

    Directory of Open Access Journals (Sweden)

    Laurila Kirsti

    2011-10-01

    Full Text Available Abstract Background Approximately half of all human genes use alternative transcription start sites (TSSs to control mRNA levels and broaden the transcriptional output in healthy tissues. Aberrant expression patterns promoting carcinogenesis, however, may arise from alternative promoter usage. Results By profiling 108 colorectal samples using exon arrays, we identified nine genes (TCF12, OSBPL1A, TRAK1, ANK3, CHEK1, UGP2, LMO7, ACSL5, and SCIN showing tumor-specific alternative TSS usage in both adenoma and cancer samples relative to normal mucosa. Analysis of independent exon array data sets corroborated these findings. Additionally, we confirmed the observed patterns for selected mRNAs using quantitative real-time reverse-transcription PCR. Interestingly, for some of the genes, the tumor-specific TSS usage was not restricted to colorectal cancer. A comprehensive survey of the nine genes in lung, bladder, liver, prostate, gastric, and brain cancer revealed significantly altered mRNA isoform ratios for CHEK1, OSBPL1A, and TCF12 in a subset of these cancer types. To identify the mechanism responsible for the shift in alternative TSS usage, we antagonized the Wnt-signaling pathway in DLD1 and Ls174T colorectal cancer cell lines, which remarkably led to a shift in the preferred TSS for both OSBPL1A and TRAK1. This indicated a regulatory role of the Wnt pathway in selecting TSS, possibly also involving TP53 and SOX9, as their transcription binding sites were enriched in the promoters of the tumor preferred isoforms together with their mRNA levels being increased in tumor samples. Finally, to evaluate the prognostic impact of the altered TSS usage, immunohistochemistry was used to show deregulation of the total protein levels of both TCF12 and OSBPL1A, corresponding to the mRNA levels observed. Furthermore, the level of nuclear TCF12 had a significant correlation to progression free survival in a cohort of 248 stage II colorectal cancer samples

  18. A Cassette Based System for Hydrogen Storage and Delivery

    Energy Technology Data Exchange (ETDEWEB)

    Britton Wayne E.

    2006-11-29

    A hydrogen storage system is described and evaluated. This is based upon a cassette, that is a container for managing hydrogen storage materials. The container is designed to be safe, modular, adaptable to different chemistries, inexpensive, and transportable. A second module receives the cassette and provides the necessary infrastructure to deliver hydrogen from the cassette according to enduser requirements. The modular concept has a number of advantages over approaches that are all in one stand alone systems. The advantages of a cassette based system are discussed, along with results from model and laboratory testing.

  19. Specific lectin biomarkers for isolation of human pluripotent stem cells identified through array-based glycomic analysis

    Institute of Scientific and Technical Information of China (English)

    Yu-Chieh Wang; Trevor R Leonardo; Ying Liu; Suzanne E Peterson; Louise C Laurent; Shinya Yamanaka; Jeanne F Loring; Masato Nakagawa; Ibon Garitaonandia; Ileana Slavin; Gulsah Altun; Robert M Lacharite; Kristopher L Nazor; Ha T Tran; Candace L Lynch

    2011-01-01

    Rapid and dependable methods for isolating human pluripotent stem cell (hPSC) populations are urgently needed for quality control in basic research and in cell-based therapy applications.Using lectin arrays,we analyzed glycoproteins extracted from 26 hPSC samples and 22 differentiated cell samples,and identified a small group of iectins with distinctive binding signatures that were sufficient to distinguish hPSCs from a variety of non-pluripotent cell types.These specific biomarkers were shared by all the 12 human embryonic stem cell and the 14 human induced pluripotent stem cell samples examined,regardless of the laboratory of origin,the culture conditions,the somatic cell type reprogrammed,or the reprogramming method used.We demonstrated a practical application of specific lectin binding by detecting hPSCs within a differentiated cell population with lectin-mediated staining followed by fluorescence microscopy and flow cytometry,and by enriching and purging viable hPSCs from mixed cell populations using lectin-mediated cell separation.Global gene expression analysis showed pluripotency-associated differential expression of specific fucosyltransferases and sialyltransferases,which may underlie these differences in protein glycosylation and lectin binding.Taken together,our results show that protein glycosylation differs considerably between pluripotent and non-pluripotent cells,and demonstrate that lectins may be used as biomarkers to monitor pluripotency in stem cell populations and for removal of viable hPSCs from mixed cell populations.

  20. A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene.

    Directory of Open Access Journals (Sweden)

    Maider Ibarrola-Villava

    Full Text Available As the incidence of Malignant Melanoma (MM reflects an interaction between skin colour and UV exposure, variations in genes implicated in pigmentation and tanning response to UV may be associated with susceptibility to MM. In this study, 363 SNPs in 65 gene regions belonging to the pigmentation pathway have been successfully genotyped using a SNP array. Five hundred and ninety MM cases and 507 controls were analyzed in a discovery phase I. Ten candidate SNPs based on a p-value threshold of 0.01 were identified. Two of them, rs35414 (SLC45A2 and rs2069398 (SILV/CKD2, were statistically significant after conservative Bonferroni correction. The best six SNPs were further tested in an independent Spanish series (624 MM cases and 789 controls. A novel SNP located on the SLC45A2 gene (rs35414 was found to be significantly associated with melanoma in both phase I and phase II (P<0.0001. None of the other five SNPs were replicated in this second phase of the study. However, three SNPs in TYR, SILV/CDK2 and ADAMTS20 genes (rs17793678, rs2069398 and rs1510521 respectively had an overall p-value<0.05 when considering the whole DNA collection (1214 MM cases and 1296 controls. Both the SLC45A2 and the SILV/CDK2 variants behave as protective alleles, while the TYR and ADAMTS20 variants seem to function as risk alleles. Cumulative effects were detected when these four variants were considered together. Furthermore, individuals carrying two or more mutations in MC1R, a well-known low penetrance melanoma-predisposing gene, had a decreased MM risk if concurrently bearing the SLC45A2 protective variant. To our knowledge, this is the largest study on Spanish sporadic MM cases to date.

  1. X-ray film cassette and method of making

    International Nuclear Information System (INIS)

    An x-ray film cassette which is capable of providing forces on the film that vary across the surface of the cassette is described. Methods of manufacture are discussed. The system is of particular use when large area films are used in conjunction with intensifying screens. (U.K.)

  2. 21 CFR 892.1850 - Radiographic film cassette.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Radiographic film cassette. 892.1850 Section 892.1850 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Diagnostic Devices § 892.1850 Radiographic film cassette....

  3. Use of a bovine genome array to identify new biological pathways for beef marbling in Hanwoo (Korean Cattle

    Directory of Open Access Journals (Sweden)

    Lim Da-jeong

    2010-11-01

    Full Text Available Abstract Background Marbling (intramuscular fat is a valuable trait that impacts on meat quality and an important factor determining price of beef in the Korean beef market. Animals that are destined for this high marbling market are fed a high concentrate ration for approximately 30 months in the Korean finishing farms. However, this feeding strategy leads to inefficiencies and excessive fat production. This study aimed to identify candidate genes and pathways associated with intramuscular fat deposition on highly divergent marbling phenotypes in adult Hanwoo cattle. Results Bovine genome array analysis was conducted to detect differentially expressed genes (DEGs in m. longissimus with divergent marbling phenotype (marbling score 2 to 7. Three data-processing methods (MAS5.0, GCRMA and RMA were used to test for differential expression (DE. Statistical analysis identified 21 significant transcripts from at least two data-processing methods (P . All 21 differentially expressed genes were validated by real-time PCR. Results showed a high concordance in the gene expression fold change between the microarrays and the real time PCR data. Gene Ontology (GO and pathway analysis demonstrated that some genes (ADAMTS4, CYP51A and SQLE over expressed in high marbled animals are involved in a protein catabolic process and a cholesterol biosynthesis process. In addition, pathway analysis also revealed that ADAMTS4 is activated by three regulators (IL-17A, TNFα and TGFβ1. QRT-PCR was used to investigate gene expression of these regulators in muscle with divergent intramuscular fat contents. The results demonstrate that ADAMTS4 and TGFβ1 are associated with increasing marbling fat. An ADAMTS4/TGFβ1 pathway seems to be associated with the phenotypic differences between high and low marbled groups. Conclusions Marbling differences are possibly a function of complex signaling pathway interactions between muscle and fat. These results suggest that ADAMTS4

  4. Quality assurance tests of the NRPB dental monitoring cassette

    International Nuclear Information System (INIS)

    This report describes the tests designed to assess the performance of the NRPB dental monitoring cassette; it complements NRPB-R164. Measurements have been made for both the original and new cassettes with film manufactured by Kodak Ltd and Agfa-Gevaert Ltd. The performance parameters investigated were the ability to measure the X-ray tube potential, the filtration of the X-ray beam, the exposure given to the cassette, and the diameter of the beam. The consistency between different cassette inserts was also assessed. The values given by the processing laboratory and the values from the irradiating laboratory are presented, and the results are then analysed statistically to determine the influence of the various parameters on the assessment of individual parameters. The performance of the cassette was found to be satisfactory. (author)

  5. Cellular pathways controlling integron cassette site folding.

    Science.gov (United States)

    Loot, Céline; Bikard, David; Rachlin, Anna; Mazel, Didier

    2010-08-01

    By mobilizing small DNA units, integrons have a major function in the dissemination of antibiotic resistance among bacteria. The acquisition of gene cassettes occurs by recombination between the attI and attC sites catalysed by the IntI1 integron integrase. These recombination reactions use an unconventional mechanism involving a folded single-stranded attC site. We show that cellular bacterial processes delivering ssDNA, such as conjugation and replication, favour proper folding of the attC site. By developing a very sensitive in vivo assay, we also provide evidence that attC sites can recombine as cruciform structures by extrusion from double-stranded DNA. Moreover, we show an influence of DNA superhelicity on attC site extrusion in vitro and in vivo. We show that the proper folding of the attC site depends on both the propensity to form non-recombinogenic structures and the length of their variable terminal structures. These results draw the network of cell processes that regulate integron recombination. PMID:20628355

  6. Using Array Methods to Identify and Process Weak Signals Generated by the Brightlight(Ⅰ)50t Explosion

    Institute of Scientific and Technical Information of China (English)

    Hao Chunyue; Zheng Zhong; Zhang Shuang

    2010-01-01

    Waveforms generated by the 50t explosion of project Brightlight(Ⅰ)were recorded by HILR array.Using array techniques,the author performed identification,f-k analysis,velocity spectrum analysis,etc.of the weak signals.The analysis results show that the signal-to-noise ratio after beamforming was obviously enhanced,and the signal could be clearly shown.The energy from this explosion was mainly concentrated in the 1~8Hz range from f-k analysis.The velocity spectrum gave clear positions of event phases,which could not be seen in the original weak signals.The maximum energy distribution obtained by the Beaman method is close to the theoretical value in the azimuth-slowness domain.

  7. Identifying the similarities and differences between single nucleotide polymorphism array (SNPa analysis and karyotyping in acute myeloid leukemia and myelodysplastic syndromes

    Directory of Open Access Journals (Sweden)

    Thiago Rodrigo de Noronha

    2015-02-01

    Full Text Available Objective: To standardize the single nucleotide polymorphism array (SNPa method in acute myeloid leukemia/myelodysplastic syndromes, and to identify the similarities and differ- ences between the results of this method and karyotyping. Methods: Twenty-two patients diagnosed with acute myeloid leukemia and three with myelodysplastic syndromes were studied. The G-banding karyotyping and single nucleotide polymorphism array analysis (CytoScan(r HD were performed using cells from bone marrow, DNA extracted from mononuclear cells from bone marrow and buccal cells (BC. Results: The mean age of the patients studied was 54 years old, and the median age was 55 years (range: 28-93. Twelve (48% were male and 13 (52% female. Ten patients showed abnormal karyotypes (40.0%, 11 normal (44.0% and four had no mitosis (16.0%. Regarding the results of bone marrow single nucleotide polymorphism array analysis: 17 were abnor- mal (68.0% and eight were normal (32.0%. Comparing the two methods, karyotyping identified a total of 17 alterations (8 deletions/losses, 7 trissomies/gains, and 2 translocations and single nucleotide polymorphism array analysis identified a total of 42 alterations (17 losses, 16 gains and 9 copy-neutral loss of heterozygosity. Conclusion: It is possible to standardize single nucleotide polymorphism array analysis in acute myeloid leukemia/myelodysplastic syndromes and compare the results with the abnormalities detected by karyotyping. Single nucleotide polymorphism array analysis increased the detection rate of abnormalities compared to karyotyping and also identified a new set of abnormalities that deserve further investigation in future studies.

  8. Exon array analysis of head and neck cancers identifies a hypoxia related splice variant of LAMA3 associated with a poor prognosis.

    OpenAIRE

    Moller-Levet, Carla S.; Guy N J Betts; Harris, Adrian L; Homer, Jarrod J.; West, Catharine M. L.; Miller, Crispin J.

    2009-01-01

    The identification of alternatively spliced transcript variants specific to particular biological processes in tumours should increase our understanding of cancer. Hypoxia is an important factor in cancer biology, and associated splice variants may present new markers to help with planning treatment. A method was developed to analyse alternative splicing in exon array data, using probeset multiplicity to identify genes with changes in expression across their loci, and a combination of the spl...

  9. A Novel Approach to Signal Detection of Sensor Array Units Using 5-3-1 Rule Based Matched Filter Algorithm with Intelligent Identifiers

    Directory of Open Access Journals (Sweden)

    Mahmoud Z. Iskandarani

    2010-01-01

    Full Text Available A novel approach to signal detection and identification was developed and tested. The new algorithm was based on provision of tagging a Matched Filter (MF with identifiers to recognize the source signal with and without noise, so that classification can be carried out. The algorithm was applied successfully to chemical Sensor Array Units (SAU. Problem statement: Signals obtained from chemical sensors were sometimes contaminated with noise. Detection of known signals from noisy surroundings was critical in the field of sensors and their applications. Approach: Six chemical sensor array units were tested at different gas concentrations. The testing was carried out under normal conditions and with the presence of noise. The developed algorithm was then applied to detect, identify and classify the results. Results: The 5-3-1 algorithm produced symmetrical arrays with the source signal identifiers at the corners. The symmetry allowed the use of one-third of the produced data for identification, saving processing time and memory storage. Conclusion: The obtained data also proved that gap separation between conducting electrodes to inversely affect device conductance, with different gap widths affected similarly with temperature change per constant deposited film thickness. Also, each device conductance increased in response to increase in applied gas concentration.

  10. Observing cassette culture: user interface implications for digital music libraries

    OpenAIRE

    Toal, Jason

    2007-01-01

    Many people keep their collections of music on cassette tape even if they rarely listen to them. Images of these collections can be found online on photo sharing websites. What can we learn from such collections and what might they tell us about designing interfaces for new digital music libraries? The author conducts an online ethnographic study of over two hundred cassette tape collections, and over sixty participants with the aim of guiding future design of music collections. The author pr...

  11. Transcription, Processing, and Function of CRISPR Cassettes in Escherichia coli

    OpenAIRE

    Pougach, Ksenia; Semenova, Ekaterina; Bogdanova, Ekaterina; Datsenko, Kirill A.; Djordjevic, Marko; Wanner, Barry L.; Severinov, Konstantin

    2010-01-01

    CRISPR/Cas, bacterial and archaeal systems of interference with foreign genetic elements such as viruses or plasmids, consist of DNA loci called CRISPR cassettes (a set of variable spacers regularly separated by palindromic repeats) and associated cas genes. When a CRISPR spacer sequence exactly matches a sequence in a viral genome, the cell can become resistant to the virus. The CRISPR/Cas systems function through small RNAs originating from longer CRISPR cassette transcripts. While laborato...

  12. The Use of High-Density SNP Array to Map Homozygosity in Consanguineous Families to Efficiently Identify Candidate Genes: Application to Woodhouse-Sakati Syndrome

    Directory of Open Access Journals (Sweden)

    Molly B. Sheridan

    2015-01-01

    Full Text Available Two consanguineous Qatari siblings presented for evaluation: a 17-4/12-year-old male with hypogonadotropic hypogonadism, alopecia, intellectual disability, and microcephaly and his 19-year-old sister with primary amenorrhea, alopecia, and normal cognition. Both required hormone treatment to produce secondary sex characteristics and pubertal development beyond Tanner 1. SNP array analysis of both probands was performed to detect shared regions of homozygosity which may harbor homozygous mutations in a gene causing their common features of abnormal pubertal development, alopecia, and variable cognitive delay. Our patients shared multiple homozygous genomic regions; ten shared regions were >1 Mb in length and constituted 0.99% of the genome. DCAF17, encoding a transmembrane nuclear protein of uncertain function, was the only gene identified in a homozygous region known to cause hypogonadotropic hypogonadism. DCAF17 mutations are associated with Woodhouse-Sakati syndrome, a rare disorder characterized by alopecia, hypogonadotropic hypogonadism, sensorineural hearing loss, diabetes mellitus, and extrapyramidal movements. Sequencing of the coding exons and flanking intronic regions of DCAF17 in the proband revealed homozygosity for a previously described founder mutation (c.436delC. Targeted DCAF17 sequencing of his affected sibling revealed the same homozygous mutation. This family illustrates the utility of SNP array testing in consanguineous families to efficiently and inexpensively identify regions of genomic homozygosity in which genetic candidates for recessive conditions can be identified.

  13. Fatigue analysis of steam generator cassette parts based on CAE

    International Nuclear Information System (INIS)

    Fatigue analysis has been performed for steam generator nozzle header and tube based on CAE. Three dimensional model was produced using the commercial CAD program, IDEAS and the geometry and boundary condition information have been transformed into input format of ABAQUS for thermal analysis, stress analysis, and fatigue analysis. Cassette nozzle, which has a complex geometry, has been analysed by using the three dimensional model. But steam generator tube has been analysed according to ASME procedure since it can be modelled as a two dimensional finite element model. S-N curve for the titanium alloy of the steam generator tube material was obtained from the material tests. From the analysis, it has been confirmed that these parts of the steam generator cassette satisfy the lifetime of the steam generator cassette. Three dimensional modelling strategy from the thermal analysis to fatigue analysis should be implemented into the design of reactor major components to enhance the efficiency of design procedure

  14. A High-Throughput Computational Framework for Identifying Significant Copy Number Aberrations from Array Comparative Genomic Hybridisation Data

    OpenAIRE

    Ian Roberts; Carter, Stephanie A; Scarpini, Cinzia G.; Konstantina Karagavriilidou; Barna, Jenny C. J.; Mark Calleja; Nicholas Coleman

    2012-01-01

    Reliable identification of copy number aberrations (CNA) from comparative genomic hybridization data would be improved by the availability of a generalised method for processing large datasets. To this end, we developed swatCGH, a data analysis framework and region detection heuristic for computational grids. swatCGH analyses sequentially displaced (sliding) windows of neighbouring probes and applies adaptive thresholds of varying stringency to identify the 10% of each chromosome that contain...

  15. Use of a bovine genome array to identify new biological pathways for beef marbling in Hanwoo (Korean Cattle)

    OpenAIRE

    Lim Da-jeong; Kim Nam-Kuk; Werf Julius; Gondro Cedric; Lee Seung-Hwan; Park Eung-Woo; Oh Sung-Jong; Gibson John P; Thompson John M

    2010-01-01

    Abstract Background Marbling (intramuscular fat) is a valuable trait that impacts on meat quality and an important factor determining price of beef in the Korean beef market. Animals that are destined for this high marbling market are fed a high concentrate ration for approximately 30 months in the Korean finishing farms. However, this feeding strategy leads to inefficiencies and excessive fat production. This study aimed to identify candidate genes and pathways associated with intramuscular ...

  16. Evaluation of the metabochip genotyping array in African Americans and implications for fine mapping of GWAS-identified loci: the PAGE study.

    Directory of Open Access Journals (Sweden)

    Steven Buyske

    Full Text Available The Metabochip is a custom genotyping array designed for replication and fine mapping of metabolic, cardiovascular, and anthropometric trait loci and includes low frequency variation content identified from the 1000 Genomes Project. It has 196,725 SNPs concentrated in 257 genomic regions. We evaluated the Metabochip in 5,863 African Americans; 89% of all SNPs passed rigorous quality control with a call rate of 99.9%. Two examples illustrate the value of fine mapping with the Metabochip in African-ancestry populations. At CELSR2/PSRC1/SORT1, we found the strongest associated SNP for LDL-C to be rs12740374 (p = 3.5 × 10(-11, a SNP indistinguishable from multiple SNPs in European ancestry samples due to high correlation. Its distinct signal supports functional studies elsewhere suggesting a causal role in LDL-C. At CETP we found rs17231520, with risk allele frequency 0.07 in African Americans, to be associated with HDL-C (p = 7.2 × 10(-36. This variant is very rare in Europeans and not tagged in common GWAS arrays, but was identified as associated with HDL-C in African Americans in a single-gene study. Our results, one narrowing the risk interval and the other revealing an associated variant not found in Europeans, demonstrate the advantages of high-density genotyping of common and rare variation for fine mapping of trait loci in African American samples.

  17. Peptide Array on Cellulose Support—A Screening Tool to Identify Peptides with Dipeptidyl-Peptidase IV Inhibitory Activity within the Sequence of α-Lactalbumin

    Directory of Open Access Journals (Sweden)

    Isabelle M. E. Lacroix

    2014-11-01

    Full Text Available The inhibition of the enzyme dipeptidyl-peptidase IV (DPP-IV is an effective pharmacotherapeutic approach for the management of type 2 diabetes. Recent findings have suggested that dietary proteins, including bovine α-lactalbumin, could be precursors of peptides able to inhibit DPP-IV. However, information on the location of active peptide sequences within the proteins is far from being comprehensive. Moreover, the traditional approach to identify bioactive peptides from foods can be tedious and long. Therefore, the objective of this study was to use peptide arrays to screen α-lactalbumin-derived peptides for their interaction with DPP-IV. Deca-peptides spanning the entire α-lactalbumin sequence, with a frame shift of 1 amino acid between successive sequences, were synthesized on cellulose membranes using “SPOT” technology, and their binding to and inhibition of DPP-IV was studied. Among the 114 α-lactalbumin-derived decamers investigated, the peptides 60WCKDDQNPHS69 (αKi = 76 µM, 105LAHKALCSEK114 (Ki = 217 µM and 110LCSEKLDQWL119 (Ki = 217 µM were among the strongest DPP-IV inhibitors. While the SPOT- and traditionally-synthesized peptides showed consistent trends in DPP-IV inhibitory activity, the cellulose-bound peptides’ binding behavior was not correlated to their ability to inhibit the enzyme. This research showed, for the first time, that peptide arrays are useful screening tools to identify DPP-IV inhibitory peptides from dietary proteins.

  18. A pharmacologically-based array to identify targets of cyclosporine A-induced toxicity in cultured renal proximal tubule cells

    International Nuclear Information System (INIS)

    Mechanisms of cyclosporine A (CsA)-induced nephrotoxicity were generally thought to be hemodynamic in origin; however, there is now accumulating evidence of a direct tubular effect. Although genomic and proteomic experiments by our group and others provided overall information on genes and proteins up- or down-regulated by CsA in proximal tubule cells (PTC), a comprehensive view of events occurring after CsA exposure remains to be described. For this purpose, we applied a pharmacologic approach based on the use of known activities of a large panel of potentially protective compounds and evaluated their efficacy in preventing CsA toxicity in cultured mouse PTC. Our results show that compounds that blocked protein synthesis and apoptosis, together with the CK2 inhibitor DMAT and the PI3K inhibitor apigenin, were the most efficient in preventing CsA toxicity. We also identified GSK3, MMPs and PKC pathways as potential targets to prevent CsA damage. Additionally, heparinase-I and MAPK inhibitors afforded partial but significant protection. Interestingly, antioxidants and calcium metabolism-related compounds were unable to ameliorate CsA-induced cytotoxicity. Subsequent experiments allowed us to clarify the hierarchical relationship of targeted pathways after CsA treatment, with ER stress identified as an early effector of CsA toxicity, which leads to ROS generation, phenotypical changes and cell death. In summary, this work presents a novel experimental approach to characterizing cellular responses to cytotoxics while pointing to new targets to prevent CsA-induced toxicity in proximal tubule cells. Highlights: ► We used a novel pharmacological approach to elucidate cyclosporine (CsA) toxicity. ► The ability of a broad range of compounds to prevent CsA toxicity was evaluated. ► CsA toxicity was monitored using LDH release assay and PARP cleavage. ► Protein synthesis, PI3K, GSK3, MMP, PKC and caspase inhibitors prevented CsA toxicity. ► We also identified ER

  19. A pharmacologically-based array to identify targets of cyclosporine A-induced toxicity in cultured renal proximal tubule cells

    Energy Technology Data Exchange (ETDEWEB)

    Sarró, Eduard, E-mail: eduard.sarro@vhir.org [Departament de Bioquímica i Biologia Molecular, Unitat de Bioquímica de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona) (Spain); Renal Physiopathology, CIBBIM-Nanomedicine, Vall d' Hebron Research Institute (VHIR), 08035 Barcelona (Spain); Jacobs-Cachá, Conxita, E-mail: conxita.jacobs@vhir.org [Renal Physiopathology, CIBBIM-Nanomedicine, Vall d' Hebron Research Institute (VHIR), 08035 Barcelona (Spain); Itarte, Emilio, E-mail: emili.itarte@uab.es [Departament de Bioquímica i Biologia Molecular, Unitat de Bioquímica de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona) (Spain); Meseguer, Anna, E-mail: ana.meseguer@vhir.org [Renal Physiopathology, CIBBIM-Nanomedicine, Vall d' Hebron Research Institute (VHIR), 08035 Barcelona (Spain); Departament de Bioquimica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona) (Spain)

    2012-01-15

    Mechanisms of cyclosporine A (CsA)-induced nephrotoxicity were generally thought to be hemodynamic in origin; however, there is now accumulating evidence of a direct tubular effect. Although genomic and proteomic experiments by our group and others provided overall information on genes and proteins up- or down-regulated by CsA in proximal tubule cells (PTC), a comprehensive view of events occurring after CsA exposure remains to be described. For this purpose, we applied a pharmacologic approach based on the use of known activities of a large panel of potentially protective compounds and evaluated their efficacy in preventing CsA toxicity in cultured mouse PTC. Our results show that compounds that blocked protein synthesis and apoptosis, together with the CK2 inhibitor DMAT and the PI3K inhibitor apigenin, were the most efficient in preventing CsA toxicity. We also identified GSK3, MMPs and PKC pathways as potential targets to prevent CsA damage. Additionally, heparinase-I and MAPK inhibitors afforded partial but significant protection. Interestingly, antioxidants and calcium metabolism-related compounds were unable to ameliorate CsA-induced cytotoxicity. Subsequent experiments allowed us to clarify the hierarchical relationship of targeted pathways after CsA treatment, with ER stress identified as an early effector of CsA toxicity, which leads to ROS generation, phenotypical changes and cell death. In summary, this work presents a novel experimental approach to characterizing cellular responses to cytotoxics while pointing to new targets to prevent CsA-induced toxicity in proximal tubule cells. Highlights: ► We used a novel pharmacological approach to elucidate cyclosporine (CsA) toxicity. ► The ability of a broad range of compounds to prevent CsA toxicity was evaluated. ► CsA toxicity was monitored using LDH release assay and PARP cleavage. ► Protein synthesis, PI3K, GSK3, MMP, PKC and caspase inhibitors prevented CsA toxicity. ► We also identified ER

  20. Identification of antibiotic resistance cassettes in class 1 integrons in Aeromonas spp. strains isolated from fresh fish (Cyprinus carpio L.).

    Science.gov (United States)

    Sarria-Guzmán, Yohanna; López-Ramírez, María Patricia; Chávez-Romero, Yosef; Ruiz-Romero, Erick; Dendooven, Luc; Bello-López, Juan Manuel

    2014-05-01

    Forty-six Aeromonas spp. strains were isolated from fresh fish and investigated for their antimicrobial susceptibility, detection of Class 1 integrons by PCR, and arrangement of gene cassettes. Selected isolates were further characterized by enterobacterial repetitive intergenic consensus-PCR. Twenty isolates were found to carry Class 1 integrons. Amplification of the variable regions of the integrons revealed diverse bands ranging in size from 150 to 1,958 pb. Sequence analysis of the variable regions revealed the presence of several gene cassettes, such as adenylyl transferases (aadA2 and aadA5), dihydrofolate reductases (dfrA17 and dfrA1), chloramphenicol acetyl transferase (catB3), β-lactamase (oxa2), lincosamide nucleotidil transferase (linF), aminoglycoside-modifying enzyme (apha15), and oxacillinase (bla OXA-10). Two open reading frames with an unknown function were identified as orfC and orfD. The aadA2 cassette was the most common integron found in this study. Interestingly, five integrons were detected in the plasmids that might be involved in the transfer of resistance genes to other bacteria. This is a first report of cassette encoding for lincosamides (linF) resistance in Aeromonas spp. Implications on the incidence of integrons in isolates of Aeromonas spp. from fresh fish for human consumption, and its possible consequences to human health are discussed. PMID:24370627

  1. Exon array analysis of head and neck cancers identifies a hypoxia related splice variant of LAMA3 associated with a poor prognosis.

    Science.gov (United States)

    Moller-Levet, Carla S; Betts, Guy N J; Harris, Adrian L; Homer, Jarrod J; West, Catharine M L; Miller, Crispin J

    2009-11-01

    The identification of alternatively spliced transcript variants specific to particular biological processes in tumours should increase our understanding of cancer. Hypoxia is an important factor in cancer biology, and associated splice variants may present new markers to help with planning treatment. A method was developed to analyse alternative splicing in exon array data, using probeset multiplicity to identify genes with changes in expression across their loci, and a combination of the splicing index and a new metric based on the variation of reliability weighted fold changes to detect changes in the splicing patterns. The approach was validated on a cancer/normal sample dataset in which alternative splicing events had been confirmed using RT-PCR. We then analysed ten head and neck squamous cell carcinomas using exon arrays and identified differentially expressed splice variants in five samples with high versus five with low levels of hypoxia-associated genes. The analysis identified a splice variant of LAMA3 (Laminin alpha 3), LAMA3-A, known to be involved in tumour cell invasion and progression. The full-length transcript of the gene (LAMA3-B) did not appear to be hypoxia-associated. The results were confirmed using qualitative RT-PCR. In a series of 59 prospectively collected head and neck tumours, expression of LAMA3-A had prognostic significance whereas LAMA3-B did not. This work illustrates the potential for alternatively spliced transcripts to act as biomarkers of disease prognosis with improved specificity for particular tissues or conditions over assays which do not discriminate between splice variants. PMID:19936049

  2. Exon array analysis of head and neck cancers identifies a hypoxia related splice variant of LAMA3 associated with a poor prognosis.

    Directory of Open Access Journals (Sweden)

    Carla S Moller-Levet

    2009-11-01

    Full Text Available The identification of alternatively spliced transcript variants specific to particular biological processes in tumours should increase our understanding of cancer. Hypoxia is an important factor in cancer biology, and associated splice variants may present new markers to help with planning treatment. A method was developed to analyse alternative splicing in exon array data, using probeset multiplicity to identify genes with changes in expression across their loci, and a combination of the splicing index and a new metric based on the variation of reliability weighted fold changes to detect changes in the splicing patterns. The approach was validated on a cancer/normal sample dataset in which alternative splicing events had been confirmed using RT-PCR. We then analysed ten head and neck squamous cell carcinomas using exon arrays and identified differentially expressed splice variants in five samples with high versus five with low levels of hypoxia-associated genes. The analysis identified a splice variant of LAMA3 (Laminin alpha 3, LAMA3-A, known to be involved in tumour cell invasion and progression. The full-length transcript of the gene (LAMA3-B did not appear to be hypoxia-associated. The results were confirmed using qualitative RT-PCR. In a series of 59 prospectively collected head and neck tumours, expression of LAMA3-A had prognostic significance whereas LAMA3-B did not. This work illustrates the potential for alternatively spliced transcripts to act as biomarkers of disease prognosis with improved specificity for particular tissues or conditions over assays which do not discriminate between splice variants.

  3. 21 CFR 892.1860 - Radiographic film/cassette changer.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Radiographic film/cassette changer. 892.1860 Section 892.1860 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Diagnostic Devices § 892.1860 Radiographic...

  4. DIY series of genetic cassettes useful in construction of versatile vectors specific for Alphaproteobacteria.

    Science.gov (United States)

    Dziewit, Lukasz; Adamczuk, Marcin; Szuplewska, Magdalena; Bartosik, Dariusz

    2011-08-01

    We have developed a DIY (Do It Yourself) series of genetic cassettes, which facilitate construction of novel versatile vectors for Alphaproteobacteria. All the cassettes are based on defined genetic modules derived from three natural plasmids of Paracoccus aminophilus JCM 7686. We have constructed over 50 DIY cassettes, which differ in structure and specific features. All of them are functional in eight strains representing three orders of Alphaproteobacteria: Rhodobacterales, Rhizobiales and Caulobacterales. Besides various replication and stabilization systems, many of the cassettes also contain selective markers appropriate for Alphaproteobacteria (40 cassettes) and genetic modules responsible for mobilization for conjugal transfer (24 cassettes). All the DIY cassettes are bordered by different types of polylinkers, which facilitate vector construction. Using these DIY cassettes, we have created a set of compatible Escherichia coli-Alphaproteobacteria mobilizable shuttle vectors (high or low copy number in E. coli), which will greatly assist the genetic manipulation of Alphaproteobacteria. PMID:21569803

  5. 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)

    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

  6. 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

  7. Nucleolar targeting of proteins by the tandem array of basic amino acid stretches identified in the RNA polymerase I-associated factor PAF49

    International Nuclear Information System (INIS)

    There is accumulating evidence to indicate that the regulation of subnuclear compartmentalization plays important roles in cellular processes. The RNA polymerase I-associated factor PAF49 has been shown to accumulate in the nucleolus in growing cells, but disperse into the nucleoplasm in growth-arrested cells. Serial deletion analysis revealed that amino acids 199-338 were necessary for the nucleolar localization of PAF49. Combinatorial point mutation analysis indicated that the individual basic amino acid stretches (BS) within the central (BS1-4) and the C-terminal (BS5 and 6) regions may cooperatively confer the nucleolar localization of PAF49. Addition of the basic stretches in tandem to a heterologous protein, such as the interferon regulatory factor-3, translocated the tagged protein into the nucleolus, even in the presence of an intrinsic nuclear export sequence. Thus, tandem array of the basic amino acid stretches identified here functions as a dominant nucleolar targeting sequence

  8. Reverse phase protein array based tumor profiling identifies a biomarker signature for risk classification of hormone receptor-positive breast cancer

    Directory of Open Access Journals (Sweden)

    Johanna Sonntag

    2014-03-01

    Full Text Available A robust subclassification of luminal breast cancer, the most common molecular subtype of human breast cancer, is crucial for therapy decisions. While a part of patients is at higher risk of recurrence and requires chemo-endocrine treatment, the other part is at lower risk and also poorly responds to chemotherapeutic regimens. To approximate the risk of cancer recurrence, clinical guidelines recommend determining histologic grading and abundance of a cell proliferation marker in tumor specimens. However, this approach assigns an intermediate risk to a substantial number of patients and in addition suffers from a high interobserver variability. Therefore, the aim of our study was to identify a quantitative protein biomarker signature to facilitate risk classification. Reverse phase protein arrays (RPPA were used to obtain quantitative expression data for 128 breast cancer relevant proteins in a set of hormone receptor-positive tumors (n = 109. Proteomic data for the subset of histologic G1 (n = 14 and G3 (n = 22 samples were used for biomarker discovery serving as surrogates of low and high recurrence risk, respectively. A novel biomarker selection workflow based on combining three different classification methods identified caveolin-1, NDKA, RPS6, and Ki-67 as top candidates. NDKA, RPS6, and Ki-67 were expressed at elevated levels in high risk tumors whereas caveolin-1 was observed as downregulated. The identified biomarker signature was subsequently analyzed using an independent test set (AUC = 0.78. Further evaluation of the identified biomarker panel by Western blot and mRNA profiling confirmed the proteomic signature obtained by RPPA. In conclusion, the biomarker signature introduced supports RPPA as a tool for cancer biomarker discovery.

  9. Genome-wide identification and characterization of ATP-binding cassette transporters in the silkworm, Bombyx mori

    OpenAIRE

    Liu, Shumin; Zhou, Shun; Tian, Ling; Guo, Enen; Luan, Yunxia; Zhang, Jianzhen; Li, Sheng

    2011-01-01

    Background The ATP-binding cassette (ABC) transporter superfamily is the largest transporter gene family responsible for transporting specific molecules across lipid membranes in all living organisms. In insects, ABC transporters not only have important functions in molecule transport, but also play roles in insecticide resistance, metabolism and development. Results From the genome of the silkworm, Bombyx mori, we have identified 51 putative ABC genes which are classified into eight subfamil...

  10. Generation of Cell Lines to Complement Adenovirus Vectors using Recombination-Mediated Cassette Exchange

    Directory of Open Access Journals (Sweden)

    Farley Daniel C

    2010-12-01

    Full Text Available Abstract Background Adenovirus serotype 5 (Ad5 has many favourable characteristics for development as a gene therapy vector. However, the utility of current Ad5 vectors is limited by transient transgene expression, toxicity and immunogenicity. The most promising form of vector is the high capacity type, which is deleted for all viral genes. However, these vectors can only be produced to relatively low titres and with the aid of helper virus. Therefore a continuing challenge is the generation of more effective Ad5 vectors that can still be grown to high titres. Our approach is to generate complementing cell lines to support the growth of Ad5 vectors with novel late gene deficiencies. Results We have used LoxP/Cre recombination mediated cassette exchange (RMCE to generate cell lines expressing Ad5 proteins encoded by the L4 region of the genome, the products of which play a pivotal role in the expression of Ad5 structural proteins. A panel of LoxP parent 293 cell lines was generated, each containing a GFP expression cassette under the control of a tetracycline-regulated promoter inserted at a random genome location; the cassette also contained a LoxP site between the promoter and GFP sequence. Clones displayed a variety of patterns of regulation, stability and level of GFP expression. Clone A1 was identified as a suitable parent for creation of inducible cell lines because of the tight inducibility and stability of its GFP expression. Using LoxP-targeted, Cre recombinase-mediated insertion of an L4 cassette to displace GFP from the regulated promoter in this parent clone, cell line A1-L4 was generated. This cell line expressed L4 100K, 22K and 33K proteins at levels sufficient to complement L4-33K mutant and L4-deleted viruses. Conclusions RMCE provides a method for rapid generation of Ad5 complementing cell lines from a pre-selected parental cell line, chosen for its desirable transgene expression characteristics. Parent cell lines can be

  11. Fully Automated Data Collection Using PAM and the Development of PAM/SPACE Reversible Cassettes

    Science.gov (United States)

    Hiraki, Masahiko; Watanabe, Shokei; Chavas, Leonard M. G.; Yamada, Yusuke; Matsugaki, Naohiro; Igarashi, Noriyuki; Wakatsuki, Soichi; Fujihashi, Masahiro; Miki, Kunio; Baba, Seiki; Ueno, Go; Yamamoto, Masaki; Suzuki, Mamoru; Nakagawa, Atsushi; Watanabe, Nobuhisa; Tanaka, Isao

    2010-06-01

    To remotely control and automatically collect data in high-throughput X-ray data collection experiments, the Structural Biology Research Center at the Photon Factory (PF) developed and installed sample exchange robots PAM (PF Automated Mounting system) at PF macromolecular crystallography beamlines; BL-5A, BL-17A, AR-NW12A and AR-NE3A. We developed and installed software that manages the flow of the automated X-ray experiments; sample exchanges, loop-centering and X-ray diffraction data collection. The fully automated data collection function has been available since February 2009. To identify sample cassettes, PAM employs a two-dimensional bar code reader. New beamlines, BL-1A at the Photon Factory and BL32XU at SPring-8, are currently under construction as part of Targeted Proteins Research Program (TPRP) by the Ministry of Education, Culture, Sports, Science and Technology of Japan. However, different robots, PAM and SPACE (SPring-8 Precise Automatic Cryo-sample Exchanger), will be installed at BL-1A and BL32XU, respectively. For the convenience of the users of both facilities, pins and cassettes for PAM and SPACE are developed as part of the TPRP.

  12. 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.

  13. An array of Escherichia coli clones over-expressing essential proteins: A new strategy of identifying cellular targets of potent antibacterial compounds

    International Nuclear Information System (INIS)

    With the advancement of high throughput screening, it has become easier and faster to discover hit compounds that inhibit proliferation of bacterial cells. However, development in technologies used to identify cellular targets of potent antibacterial inhibitors has lagged behind. Here, we describe a novel strategy of target identification for antibacterial inhibitors using an array of Escherichia coli clones each over-expressing one essential protein. In a proof-of-concept study, eight essential genes were cloned into pLex5BA vector under the control of an inducible promoter. Over-expression of target proteins was confirmed. For two clones, one over-expressing FabI and the other over-expressing MurA enzymes, the host cells became 17- and 139-fold more resistant to the specific inhibitors triclosan and phosphomycin, respectively, while the susceptibility of other clones towards these inhibitors remained unchanged after induction of gene expression. Target identification via target protein over-expression was demonstrated using both mixed clone and individual clone assay formats

  14. Structural variations of staphylococcal cassette chromosome mec Type IVa in Staphylococcus aureus clonal complex 8 and unrelated lineages

    DEFF Research Database (Denmark)

    Damborg, Peter Panduro; Bartels, Mette Damkjær; Boye, Kit; Guardabassi, Luca; Westh, Henrik T.

    2011-01-01

    PCR mapping of staphylococcal cassette chromosome mec type IVa and adjacent mobile elements in 94 methicillin-resistant Staphylococcus aureus (MRSA) strains identified two primary structures (A and B) that could be further classified into two (A1 and A2) and five (B1 to B5) variants, primarily ba...

  15. Balloon-borne video cassette recorders for digital data storage

    International Nuclear Information System (INIS)

    A high-speed, high-capacity digital data storage system has been developed for a new balloon-borne gamma-ray telescope. The system incorporates sophisticated, yet easy to use and economical consumer products: the portable video cassette recorder (VCR) and a relatively newer item - the digital audio processor. The in-flight recording system employs eight VCRs and will provide a continuous data storage rate of 1.4 megabits/sec throughout a 40 hour balloon flight. Data storage capacity is 25 gigabytes and power consumption is only 10 watts

  16. Chromosome inversions, adaptive cassettes and the evolution of species' ranges.

    Science.gov (United States)

    Kirkpatrick, Mark; Barrett, Brian

    2015-05-01

    A chromosome inversion can spread when it captures locally adapted alleles or when it is introduced into a species by hybridization with adapted alleles that were previously absent. We present a model that shows how both processes can cause a species range to expand. Introgression of an inversion that carries novel, locally adapted alleles is a particularly powerful mechanism for range expansion. The model supports the earlier proposal that introgression of an inversion triggered a large range expansion of a malaria mosquito. These results suggest a role for inversions as cassettes of genes that can accelerate adaptation by crossing species boundaries, rather than protecting genomes from introgression. PMID:25583098

  17. Efficient Genome Editing in Caenorhabditis elegans with a Toolkit of Dual-Marker Selection Cassettes.

    Science.gov (United States)

    Norris, Adam D; Kim, Hyun-Min; Colaiácovo, Mónica P; Calarco, John A

    2015-10-01

    Use of the CRISPR/Cas9 RNA-guided endonuclease complex has recently enabled the generation of double-strand breaks virtually anywhere in the C. elegans genome. Here, we present an improved strategy that makes all steps in the genome editing process more efficient. We have created a toolkit of template-mediated repair cassettes that contain an antibiotic resistance gene to select for worms carrying the repair template and a fluorescent visual marker that facilitates identification of bona fide recombinant animals. Homozygous animals can be identified as early as 4-5 days post-injection, and minimal genotyping by PCR is required. We demonstrate that our toolkit of dual-marker vectors can generate targeted disruptions, deletions, and endogenous tagging with fluorescent proteins and epitopes. This strategy should be useful for a wide variety of additional applications and will provide researchers with increased flexibility when designing genome editing experiments. PMID:26232410

  18. Array CGH identifies distinct DNA copy number profiles of oncogenes and tumor suppressor genes in chromosomal- and microsatellite-unstable sporadic colorectal carcinomas.

    Science.gov (United States)

    Lassmann, Silke; Weis, Roland; Makowiec, Frank; Roth, Jasmine; Danciu, Mihai; Hopt, Ulrich; Werner, Martin

    2007-03-01

    DNA copy number changes represent molecular fingerprints of solid tumors and are as such relevant for better understanding of tumor development and progression. In this study, we applied genome-wide array comparative genomic hybridization (aCGH) to identify gene-specific DNA copy number changes in chromosomal (CIN)- and microsatellite (MIN)-unstable sporadic colorectal cancers (sCRC). Genomic DNA was extracted from microdissected, matching normal colorectal epithelium and invasive tumor cells of formalin-fixed and paraffin-embedded tissues of 22 cases with colorectal cancer (CIN = 11, MIN = 11). DNA copy number changes were determined by aCGH for 287 target sequences in tumor cell DNAs, using pooled normal DNAs as reference. aCGH data of tumor cell DNAs was confirmed by fluorescence in situ hybridization (FISH) for three genes on serial tissues as those used for aCGH. aCGH revealed DNA copy number changes previously described by metaphase CGH (gains 7, 8q, 13q, and 20q; losses 8p, 15q, 18q, and 17p). However, chromosomal regions 20q, 13q, 7, and 17p were preferentially altered in CIN-type tumors and included DNA amplifications of eight genes on chromosome 20q (TOP1, AIB1, MYBL2, CAS, PTPN1, STK15, ZNF217, and CYP24), two genes on chromosome 13q (BRCA2 and D13S25), and three genes on chromosome 7 (IL6, CYLN2, and MET) as well as DNA deletions of two genes on chromosome 17p (HIC1 and LLGL1). Finally, additional CIN-tumor-associated DNA amplifications were identified for EXT1 (8q24.11) and MYC (8q24.12) as well as DNA deletions for MAP2K5 (15q23) and LAMA3 (18q11.2). In contrast, distinct MIN-tumor-associated DNA amplifications were detected for E2F5 (8p22-q21.3), GARP (11q13.5-q14), ATM (11q22.3), KAL (Xp22.3), and XIST (Xq13.2) as well as DNA deletions for RAF1 (3p25), DCC (18q21.3), and KEN (21q tel). aCGH revealed distinct DNA copy number changes of oncogenes and tumor suppressor genes in CIN- and MIN-type sporadic colorectal carcinomas. The identified candidate

  19. Integrones y cassettes genéticos de resistencia a antimicrobianos en cepas de Shigella flexneri Integrons and antimicrobial resistance gene cassettes in Shigella flexneri strains

    OpenAIRE

    Jeannette Muñoz A; Helia Bello T; Mariana Domínguez Y; Sergio Mella M; Raúl Zemelman Z; Gerardo González R

    2003-01-01

    Background: The resistance of Shigella flexneri to antimicrobial agents can be associated to the presence of integrons that may contain and express antimicrobial resistance gene cassettes. Aim: To study antimicrobial resistance and the presence of integrons and antimicrobial gene cassettes in Shigella flexneri strains. Material and methods: In vitro susceptibility to 27 antimicrobials was studied in twenty four Shigella flexneri strains isolated from stools. The presence of integrons class 1,...

  20. On design and development of additional End-Effectors for the Cassette Multifunctional Mover

    International Nuclear Information System (INIS)

    The divertor area of ITER Vacuum Vessel (VV) consists of 54 modular cassettes which must be replaced three times during the estimated 20 years of operation of the ITER. Cassette Multifunctional Mover (CMM) and Cassette Toroidal Mover (CTM) are used in the cassette remote handling (RH). In this paper we discuss the design and development process for the RH equipment to be used in the ITER environment. Design concepts for the Standard Cassette End-Effector and Central Cassette End-Effector are described and the conceptual design phase methodology is presented. The main improvements of the new End-Effector concept designs are more robust and reliable assembly process with reduced CMM mover assembly accuracy requirement. New Central Cassette locking system was developed to address the high forces and contact pressures emerging during the Central Cassette installation. The chosen design concepts are verified with virtual reality simulations and are fulfilling the requirements defined in the concept design phase, including structural, assembly sequence, safety and reliability.

  1. Identification and Characterization of a Brucella abortus ATP-Binding Cassette Transporter Homolog to Rhizobium meliloti ExsA and Its Role in Virulence and Protection in Mice

    OpenAIRE

    G.M.S. Rosinha; Freitas, Daniela A.; Miyoshi, Anderson; Azevedo, Vasco; Campos, Eleonora; Cravero, Silvio L; Rossetti, Osvaldo; Splitter, Gary; S.C. Oliveira

    2002-01-01

    Brucella abortus is a facultative intracellular bacterial pathogen that causes abortion in domestic animals and undulant fever in humans. The mechanism of virulence of Brucella spp. is not fully understood yet. Furthermore, genes that allow Brucella to reach the intracellular niche and to interact with host cells need to be identified. Using the genomic survey sequence (GSS) approach, we identified the gene encoding an ATP-binding cassette (ABC) transporter of B. abortus strain S2308. The ded...

  2. Recombinogenic engineering of conjugative plasmids with fluorescent marker cassettes

    DEFF Research Database (Denmark)

    Reisner, A.; Molin, Søren; Zechner, E.L.

    2002-01-01

    An efficient approach for the insertion of fluorescent marker genes with sequence specificity into conjugative plasmids in Escherichia coli is described. For this purpose, homologous recombination of linear double-stranded targeting DNA was mediated by the bacteriophage lambda recombination...... functions using very short regions of homology. Initial manipulation of the IncFII target plasmids R1 and R1drd19 indicated that the linear targeting DNA should be devoid of all extraneous homologies to. the target molecule for optimal insertion specificity. Indeed, a simple recombination assay proved...... resistance genes and fluorescent markers. The choice of 5' non-homologous extensions in primer pairs used for amplifying the marker cassettes determines the site specificity of the targeting DNA. This methodology is applicable to the modification of all plasmids that replicate in E coli and is not restricted...

  3. Protein Arrays for Multidrug-resistance in Human Leukemia Cell Determination

    Directory of Open Access Journals (Sweden)

    Zuhong Lu

    2005-05-01

    Full Text Available A novel technique was developed, that was high throughput simultaneousscreening of multiple resistance protein expression based on a protein array system. Themethod combined the advantage of the specificity of enzyme-linked immunosorbentassays with the sensitivity and high throughput of microspot. In this system, the multipleresistance protein arrays were created by spotting the captured antibodies onto the glassslide. The arrays were then incubated with cell samples of leukemia patients. The boundproteins were recognized by biotin-conjugated antibodies and detected by CCD.Experiments demonstrated that three multiple resistance proteins, including Pgp, MRPand BCRP which are members of the ATP-binding-cassette (ABC superfamily ofmembrane transporters could be simultaneously detected using this new approach.Research work shows the result is coincident with flow cytometry (FCM (P>0.01. Itprovided a methodology to develop many high-density protein array systems to detect avariety of proteins. The protein arrays will provide a powerful tool to identify theleukemia cell protein expression and rapidly validate their MDR determination.

  4. Trans-spliced Cas9 allows cleavage of HBB and CCR5 genes in human cells using compact expression cassettes

    OpenAIRE

    Fine, Eli J; Appleton, Caleb M.; Douglas E. White; Brown, Matthew T.; Harshavardhan Deshmukh; Kemp, Melissa L.; Gang Bao

    2015-01-01

    CRISPR/Cas9 systems have been used in a wide variety of biological studies; however, the large size of CRISPR/Cas9 presents challenges in packaging it within adeno-associated viruses (AAVs) for clinical applications. We identified a two-cassette system expressing pieces of the S. pyogenes Cas9 (SpCas9) protein which splice together in cellula to form a functional protein capable of site-specific DNA cleavage. With specific CRISPR guide strands, we demonstrated the efficacy of this system in c...

  5. A two-cassette reporter system for assessing target gene translation and target gene product inclusion body formation

    DEFF Research Database (Denmark)

    2016-01-01

    The present invention relates to a dual cassette reporter system capable of assessing target gene translation and target gene product folding. The present invention further relates to vectors and host cells comprising the dual cassette reporter system. In addition the invention relates to the use...... of the dual cassette reporter system for assessing target gene translation and target gene product folding....

  6. A clinical trial of a rare earth screen/film system in a periapical cassette

    International Nuclear Information System (INIS)

    In a clinical trial, a slow rare earth screen/film system (Siemens Titan 2D/Kodak XG) was used to obtain intraoral radiographs at conventional monitoring stages in endodontic treatment. The screen film image proved to be an effective substitute for the direct-exposure Ultraspeed periapical film. The intraoral cassettes, designed and fabricated for the study, were an adaptation of the flexible, vacuum-sealed cassettes used in mammography. It is believed that when a practicable periapical cassette is manufactured, many additional indications for the system are probable. Major reductions in patient exposure of at least 85% to 90% per periapical film would be effected

  7. Radiation exposure reduction by use of Kevlar cassettes in the neonatal nursery

    International Nuclear Information System (INIS)

    A study was performed to determine whether the use of Kevlar cassettes in the neonatal intensive care nursery would reduce radiation exposure to patients. The radiation dose to the neonates was measured by using thermoluminescent dosimeters. In addition, the attenuation of the Kevlar cassettes and the sensitivity of the film-screen combination were compared with the previously used system. The greatest radiation reduction using a mobile X-ray unit was 27%; based on sensitivity measurements, the theoretical reduction averaged 38%. The reduction in radiation exposure resulted from reduced attenuation by the Kevlar cassette

  8. Genetic Variation of the Borrelia burgdorferi Gene vlsE Involves Cassette-Specific, Segmental Gene Conversion

    OpenAIRE

    Zhang, Jing-Ren; Norris, Steven J

    1998-01-01

    The Lyme disease spirochete Borrelia burgdorferi possesses 15 silent vls cassettes and a vls expression site (vlsE) encoding a surface-exposed lipoprotein. Segments of the silent vls cassettes have been shown to recombine with the vlsE cassette region in the mammalian host, resulting in combinatorial antigenic variation. Despite promiscuous recombination within the vlsE cassette region, the 5′ and 3′ coding sequences of vlsE that flank the cassette region are not subject to sequence variation...

  9. Disruption of lolCDE, Encoding an ATP-Binding Cassette Transporter, Is Lethal for Escherichia coli and Prevents Release of Lipoproteins from the Inner Membrane

    OpenAIRE

    Narita, Shin-ichiro; Tanaka, Kimie; Matsuyama, Shin-ichi; Tokuda, Hajime

    2002-01-01

    ATP-binding cassette transporter LolCDE was previously identified, by using reconstituted proteoliposomes, as an apparatus catalyzing the release of outer membrane-specific lipoproteins from the inner membrane of Escherichia coli. Mutations resulting in defective LolD were previously shown to be lethal for E. coli. The amino acid sequences of LolC and LolE are similar to each other, but the necessity of both proteins for lipoprotein release has not been proved. Moreover, previous reconstituti...

  10. Genome-wide identification and characterization of ATP-binding cassette transporters in the silkworm, Bombyx mori

    OpenAIRE

    Zhang Jianzhen; Luan Yunxia; Guo Enen; Tian Ling; Zhou Shun; Liu Shumin; Li Sheng

    2011-01-01

    Abstract Background The ATP-binding cassette (ABC) transporter superfamily is the largest transporter gene family responsible for transporting specific molecules across lipid membranes in all living organisms. In insects, ABC transporters not only have important functions in molecule transport, but also play roles in insecticide resistance, metabolism and development. Results From the genome of the silkworm, Bombyx mori, we have identified 51 putative ABC genes which are classified into eight...

  11. Domain Interactions in the Yeast ATP Binding Cassette Transporter Ycf1p: Intragenic Suppressor Analysis of Mutations in the Nucleotide Binding Domains

    OpenAIRE

    Falcón-Pérez, Juan M.; Martínez-Burgos, Mónica; Molano, Jesús; Mazón, María J.; Eraso, Pilar

    2001-01-01

    The yeast cadmium factor (Ycf1p) is a vacuolar ATP binding cassette (ABC) transporter required for heavy metal and drug detoxification. Cluster analysis shows that Ycf1p is strongly related to the human multidrug-associated protein (MRP1) and cystic fibrosis transmembrane conductance regulator and therefore may serve as an excellent model for the study of eukaryotic ABC transporter structure and function. Identifying intramolecular interactions in these transporters may help to elucidate ener...

  12. Human ATP-binding cassette (ABC transporter family

    Directory of Open Access Journals (Sweden)

    Vasiliou Vasilis

    2009-04-01

    Full Text Available Abstract There exist four fundamentally different classes of membrane-bound transport proteins: ion channels; transporters; aquaporins; and ATP-powered pumps. ATP-binding cassette (ABC transporters are an example of ATP-dependent pumps. ABC transporters are ubiquitous membrane-bound proteins, present in all prokaryotes, as well as plants, fungi, yeast and animals. These pumps can move substrates in (influx or out (efflux of cells. In mammals, ABC transporters are expressed predominantly in the liver, intestine, blood-brain barrier, blood-testis barrier, placenta and kidney. ABC proteins transport a number of endogenous substrates, including inorganic anions, metal ions, peptides, amino acids, sugars and a large number of hydrophobic compounds and metabolites across the plasma membrane, and also across intracellular membranes. The human genome contains 49 ABC genes, arranged in eight subfamilies and named via divergent evolution. That ABC genes are important is underscored by the fact that mutations in at least I I of these genes are already known to cause severe inherited diseases (eg cystic fibrosis and X-linked adrenoleukodystrophy [X-ALD]. ABC transporters also participate in the movement of most drugs and their metabolites across cell surface and cellular organelle membranes; thus, defects in these genes can be important in terms of cancer therapy, pharmacokinetics and innumerable pharmacogenetic disorders.

  13. In70 of plasmid pAX22, a bla(VIM-1)-containing integron carrying a new aminoglycoside phosphotransferase gene cassette.

    Science.gov (United States)

    Riccio, M L; Pallecchi, L; Fontana, R; Rossolini, G M

    2001-04-01

    An Achromobacter xylosoxydans strain showing broad-spectrum resistance to beta-lactams (including carbapenems) and aminoglycosides was isolated at the University Hospital of Verona (Verona, Italy). This strain was found to produce metallo-beta-lactamase activity and to harbor a 30-kb nonconjugative plasmid, named pAX22, carrying a bla(VIM-1) determinant inserted into a class 1 integron. Characterization of this integron, named In70, revealed an original array of four gene cassettes containing, respectively, the bla(VIM-1) gene and three different aminoglycoside resistance determinants, including an aacA4 allele, a new aph-like gene named aphA15, and an aadA1 allele. The aphA15 gene is the first example of an aph-like gene carried on a mobile gene cassette, and its product exhibits close similarity to the APH(3')-IIa aminoglycoside phosphotransferase encoded by Tn5 (36% amino acid identity) and to an APH(3')-IIb enzyme from Pseudomonas aeruginosa (38% amino acid identity). Expression of the cloned aphA15 gene in Escherichia coli reduced the susceptibility to kanamycin and neomycin as well as (slightly) to amikacin, netilmicin, and streptomycin. Characterization of the 5' and 3' conserved segments of In70 and of their flanking regions showed that In70 belongs to the group of class 1 integrons associated with defective transposon derivatives originating from Tn402-like elements. The structure of the 3' conserved segment indicates the closest ancestry with members of the In0-In2 lineage. In70, with its array of cassette-borne resistance genes, can mediate broad-spectrum resistance to most beta-lactams and aminoglycosides. PMID:11257042

  14. The cost-effectiveness of carbon-fibre cassettes in mobile chest radiography

    International Nuclear Information System (INIS)

    Employment of carbon fibre materials is an effective method of reducing radiation dose, yet the increased associated costs have led to a reluctance in implementation. This study investigates the level of dose reduction achievable, while maintaining image quality, in mobile chest radiography using carbon-fibre cassettes, compared with plastic cassettes, and balances this against increased expense of the cassettes. Dose measurements using thermoluminescent dosimeters were carried out on intensive therapy unit (ITU) patients undergoing an anteroposterior chest X-ray examination. Resultant image quality was assessed using objective Commission of European Communities (CEC) criteria. A retrospective audit recorded number of ITU patients currently having chest X-rays to determine total dose savings over the life of the cassettes. The results show significant reductions (p < 0.0001) of 32 % for entrance surface and effective dose with carbon-fibre cassettes. No deterioration in total image quality was noted. The added expense of ≤ 2260 per personSievert (calculated from the effective dose reduction) for employing carbon-fibre cassettes is minimal compared with the estimated cost of manSievert exposures reported by other workers. (orig.)

  15. Genome-Wide analysis of allelic imbalance in laser microdissected prostate cancer tissue using the Affymetrix 50K Mapping array identifies genomic patterns associated with metastasis and differentiation

    DEFF Research Database (Denmark)

    Tørring, Niels; Borre, Michael; Sørensen, Karina;

    2007-01-01

    to be developed for patient stratification based on risk of progression. We analysed laser-microdissected prostate tumour tissue from 43 patients with histologically verified PCa, using the new high-resolution Affymetrix Mapping 50K single-nucleotide polymorphism array. The results showed six major...... loss. However, tumour progression towards a metastatic stage, as well as poor differentiation, was identified by specific patterns of copy number gains of genomic regions located at chromosomes 8q, 1q, 3q and 7q. Androgen ablation therapy was further characterised by copy gain at chromosomes 2p and 10q...

  16. A novel flow cytometric HTS assay reveals functional modulators of ATP binding cassette transporter ABCB6.

    Directory of Open Access Journals (Sweden)

    Kishore Polireddy

    Full Text Available ABCB6 is a member of the adenosine triphosphate (ATP-binding cassette family of transporter proteins that is increasingly recognized as a relevant physiological and therapeutic target. Evaluation of modulators of ABCB6 activity would pave the way toward a more complete understanding of the significance of this transport process in tumor cell growth, proliferation and therapy-related drug resistance. In addition, this effort would improve our understanding of the function of ABCB6 in normal physiology with respect to heme biosynthesis, and cellular adaptation to metabolic demand and stress responses. To search for modulators of ABCB6, we developed a novel cell-based approach that, in combination with flow cytometric high-throughput screening (HTS, can be used to identify functional modulators of ABCB6. Accumulation of protoporphyrin, a fluorescent molecule, in wild-type ABCB6 expressing K562 cells, forms the basis of the HTS assay. Screening the Prestwick Chemical Library employing the HTS assay identified four compounds, benzethonium chloride, verteporfin, tomatine hydrochloride and piperlongumine, that reduced ABCB6 mediated cellular porphyrin levels. Validation of the identified compounds employing the hemin-agarose affinity chromatography and mitochondrial transport assays demonstrated that three out of the four compounds were capable of inhibiting ABCB6 mediated hemin transport into isolated mitochondria. However, only verteporfin and tomatine hydrochloride inhibited ABCB6's ability to compete with hemin as an ABCB6 substrate. This assay is therefore sensitive, robust, and suitable for automation in a high-throughput environment as demonstrated by our identification of selective functional modulators of ABCB6. Application of this assay to other libraries of synthetic compounds and natural products is expected to identify novel modulators of ABCB6 activity.

  17. 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.

  18. Functional analysis of the ATP-binding cassette (ABC transporter gene family of Tribolium castaneum

    Directory of Open Access Journals (Sweden)

    Broehan Gunnar

    2013-01-01

    Full Text Available Abstract Background The ATP-binding cassette (ABC transporters belong to a large superfamily of proteins that have important physiological functions in all living organisms. Most are integral membrane proteins that transport a broad spectrum of substrates across lipid membranes. In insects, ABC transporters are of special interest because of their role in insecticide resistance. Results We have identified 73 ABC transporter genes in the genome of T. castaneum, which group into eight subfamilies (ABCA-H. This coleopteran ABC family is significantly larger than those reported for insects in other taxonomic groups. Phylogenetic analysis revealed that this increase is due to gene expansion within a single clade of subfamily ABCC. We performed an RNA interference (RNAi screen to study the function of ABC transporters during development. In ten cases, injection of double-stranded RNA (dsRNA into larvae caused developmental phenotypes, which included growth arrest and localized melanization, eye pigmentation defects, abnormal cuticle formation, egg-laying and egg-hatching defects, and mortality due to abortive molting and desiccation. Some of the ABC transporters we studied in closer detail to examine their role in lipid, ecdysteroid and eye pigment transport. Conclusions The results from our study provide new insights into the physiological function of ABC transporters in T. castaneum, and may help to establish new target sites for insect control.

  19. Autonomous bioluminescent expression of the bacterial luciferase gene cassette (lux in a mammalian cell line.

    Directory of Open Access Journals (Sweden)

    Dan M Close

    Full Text Available The bacterial luciferase (lux gene cassette consists of five genes (luxCDABE whose protein products synergistically generate bioluminescent light signals exclusive of supplementary substrate additions or exogenous manipulations. Historically expressible only in prokaryotes, the lux operon was re-synthesized through a process of multi-bicistronic, codon-optimization to demonstrate for the first time self-directed bioluminescence emission in a mammalian HEK293 cell line in vitro and in vivo.Autonomous in vitro light production was shown to be 12-fold greater than the observable background associated with untransfected control cells. The availability of reduced riboflavin phosphate (FMNH(2 was identified as the limiting bioluminescence substrate in the mammalian cell environment even after the addition of a constitutively expressed flavin reductase gene (frp from Vibrio harveyi. FMNH(2 supplementation led to a 151-fold increase in bioluminescence in cells expressing mammalian codon-optimized luxCDE and frp genes. When injected subcutaneously into nude mice, in vivo optical imaging permitted near instantaneous light detection that persisted independently for the 60 min length of the assay with negligible background.The speed, longevity, and self-sufficiency of lux expression in the mammalian cellular environment provides a viable and powerful alternative for real-time target visualization not currently offered by existing bioluminescent and fluorescent imaging technologies.

  20. New aQTL SNPs for the CYP2D6 Identified by a Novel Mediation Analysis of Genome-Wide SNP Arrays, Gene Expression Arrays, and CYP2D6 Activity

    Directory of Open Access Journals (Sweden)

    Guanglong Jiang

    2013-01-01

    Full Text Available Background. The genome-wide association studies (GWAS have been successful during the last few years. A key challenge is that the interpretation of the results is not straightforward, especially for transacting SNPs. Integration of transcriptome data into GWAS may provide clues elucidating the mechanisms by which a genetic variant leads to a disease. Methods. Here, we developed a novel mediation analysis approach to identify new expression quantitative trait loci (eQTL driving CYP2D6 activity by combining genotype, gene expression, and enzyme activity data. Results. 389,573 and 1,214,416 SNP-transcript-CYP2D6 activity trios are found strongly associated (P<10-5, FDR=16.6% and 11.7% for two different genotype platforms, namely, Affymetrix and Illumina, respectively. The majority of eQTLs are trans-SNPs. A single polymorphism leads to widespread downstream changes in the expression of distant genes by affecting major regulators or transcription factors (TFs, which would be visible as an eQTL hotspot and can lead to large and consistent biological effects. Overlapped eQTL hotspots with the mediators lead to the discovery of 64 TFs. Conclusions. Our mediation analysis is a powerful approach in identifying the trans-QTL-phenotype associations. It improves our understanding of the functional genetic variations for the liver metabolism mechanisms.

  1. Array for detecting microbes

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, Gary L.; DeSantis, Todd D.

    2014-07-08

    The present embodiments relate to an array system for detecting and identifying biomolecules and organisms. More specifically, the present embodiments relate to an array system comprising a microarray configured to simultaneously detect a plurality of organisms in a sample at a high confidence level.

  2. Development of a full-size divertor cassette prototype for ITER

    International Nuclear Information System (INIS)

    Production of a full-size divertor cassette for the International Thermonuclear Experimental Reactor (ITER) involves eight major components. All of the components are mounted on the cassette body. Inner divertor channel components for both the vertical target and the gas box design are being provided by the Japan Home Team. Outer divertor channel components for the vertical target design are being provided by the European and United States Home Teams. Gas box liners are being provided by the Russian Home Team. The full-size components manufactured by the four parties will be shipped to the US Home Team for assembly into a full-size divertor cassette. The techniques for assembly and maintenance for the cassette will be demonstrated during this process. The assembled cassette will be tested for proper flow distribution and proof of the filling and draining procedures. The testing will include vacuum leak, cyclic heating to 150 deg. C, and verification of dimensional accuracy of the assembled components. The development of the divertor for ITER depends on successful R and D efforts on materials, joining and plasma-materials interactions. Results of the development program are presented. The scale-up of the process developed in the basic R and D tasks is accomplished by producing medium and full-scale mock-ups and testing them at high heat flux. The design of these mock-ups is discussed. (author). 18 refs, 3 figs

  3. Development of a full-size divertor cassette prototype for ITER

    International Nuclear Information System (INIS)

    Production of a full-size divertor cassette involves eight major components. All of the components are mounted on the cassette body. Inner divertor channel components for the vertical target design are being provided by the Japan Home Team. Outer divertor channel components for the vertical target design are being provided by the European and United States Home Teams. Gas box liners are being provided by the Russian Home Team. The full-size components manufactured by the four parties will be shipped to the US Home Team for assembly into a full size divertor cassette. The techniques for assembly and maintenance of the cassette will be demonstrated during this process. The assembled cassette will be tested for proper flow distribution and proof of the filling and draining procedures. The testing will include vacuum leak tightness at full temperature and pressure, cyclic heating to 150 degrees C, verification of dimensional accuracy of the assembled components, and application of thermal gradients to measure dimensional stability. The development of the divertor for the International Thermonuclear Experimental Reactor (ITER) depends on successful R ampersand D efforts on materials, joining, and plasma materials interactions. Results of the development program are presented. The scale-up of the processes developed in the basic research and development tasks is accomplished by producing and high-heat-flux testing medium and full-scale mock- ups. The design of the mock-ups is discussed

  4. ATP-binding cassette transporter A7 (ABCA7) loss of function alters Alzheimer amyloid processing.

    Science.gov (United States)

    Satoh, Kanayo; Abe-Dohmae, Sumiko; Yokoyama, Shinji; St George-Hyslop, Peter; Fraser, Paul E

    2015-10-01

    The ATP-binding cassette transporter A7 (ABCA7) has been identified as a susceptibility factor of late onset Alzheimer disease in genome-wide association studies. ABCA7 has been shown to mediate phagocytosis and affect membrane trafficking. The current study examined the impact of ABCA7 loss of function on amyloid precursor protein (APP) processing and generation of amyloid-β (Aβ). Suppression of endogenous ABCA7 in several different cell lines resulted in increased β-secretase cleavage and elevated Aβ. ABCA7 knock-out mice displayed an increased production of endogenous murine amyloid Aβ42 species. Crossing ABCA7-deficient animals to an APP transgenic model resulted in significant increases in the soluble Aβ as compared with mice expressing normal levels of ABCA7. Only modest changes in the amount of insoluble Aβ and amyloid plaque densities were observed once the amyloid pathology was well developed, whereas Aβ deposition was enhanced in younger animals. In vitro studies indicated a more rapid endocytosis of APP in ABCA7 knock-out cells that is mechanistically consistent with the increased Aβ production. These in vitro and in vivo findings indicate a direct role of ABCA7 in amyloid processing that may be associated with its primary biological function to regulate endocytic pathways. Several potential loss-of-function ABCA7 mutations and deletions linked to Alzheimer disease that in some instances have a greater impact than apoE allelic variants have recently been identified. A reduction in ABCA7 expression or loss of function would be predicted to increase amyloid production and that may be a contributing factor in the associated Alzheimer disease susceptibility. PMID:26260791

  5. Integrones y cassettes genéticos de resistencia: estructura y rol frente a los antibacterianos Integrons and resistance gene cassettes: structure and role against antimicrobials

    OpenAIRE

    Gerardo González R; Sergio Mella M; Raúl Zemelman Z; Helia Bello T; Mariana Domínguez Y

    2004-01-01

    Bacteria have developed sophisticated and successful genetic mechanisms to evade the action of antimicrobials. Bacterial multiresistance has caused serious problems in the treatment of nosocomial infections. Integrons and gene cassettes are considered the main genetic elements in the evolution of plasmids and transposons that actively participate in the mobilization of genes, codifying different bacterial resistance mechanisms. This article reviews the historical and structural aspects of int...

  6. Expression of heterologous genes from an IRES translational cassette in replication competent murine leukemia virus vectors

    DEFF Research Database (Denmark)

    Jespersen, Thomas; Duch, Mogens R.; Carrasco, M L;

    1999-01-01

    of neo or the enhanced green fluorescence protein gene (EGFP). Akv-MLV's with IRES-neo and IRES-EGFP cassettes replicated with titers of about 10(6) infectious units/ml while SL3-3-MLV with IRES-neo gave about 10(3)-fold lower titers. Interestingly, RNA analysis showed a drastic reduction in the amount...... of spliced env mRNA for the SL3-3 derived vector relative to the Akv derived vectors, seemingly contributing to its low replication capacity. The EGFP expressing Akv-MLV was genetically stable for multiple rounds of infection; marker-cassette deletion revertants appeared after several replication rounds...

  7. Diverse gene cassettes in class 1 integrons of facultative oligotrophic bacteria of River Mahananda,West Bengal, India.

    Directory of Open Access Journals (Sweden)

    Ranadhir Chakraborty

    Full Text Available BACKGROUND: In this study a large random collection (n=2188 of facultative oligotrophic bacteria, from 90 water samples gathered in three consecutive years (2007-2009 from three different sampling sites of River Mahananda in Siliguri, West Bengal, India, were investigated for the presence of class 1 integrons and sequences of the amplification products. METHODOLOGY/PRINCIPAL FINDINGS: Replica plating method was employed for determining the antibiotic resistance profile of the randomly assorted facultative oligotrophic isolates. Genomic DNA from each isolate was analyzed by PCR for the presence of class 1 integron. Amplicons were cloned and sequenced. Numerical taxonomy and 16S rRNA gene sequence analyses were done to ascertain putative genera of the class 1 integron bearing isolates. Out of 2188 isolates, 1667 (76.19% were antibiotic-resistant comprising of both single-antibiotic resistance (SAR and multiple-antibiotic resistant (MAR, and 521 (23.81% were sensitive to all twelve different antibiotics used in this study. Ninety out of 2188 isolates produced amplicon(s of varying sizes from 0.15 to 3.45 KB. Chi-square (χ(2 test revealed that the possession of class 1 integron in sensitive, SAR and MAR is not equally probable at the 1% level of significance. Diverse antibiotic-resistance gene cassettes, aadA1, aadA2, aadA4, aadA5, dfrA1, dfrA5, dfrA7, dfrA12, dfrA16, dfrA17, dfrA28, dfrA30, dfr-IIe, blaIMP-9, aacA4, Ac-6'-Ib, oxa1, oxa10 and arr2 were detected in 64 isolates. The novel cassettes encoding proteins unrelated to any known antibiotic resistance gene function were identified in 26 isolates. Antibiotic-sensitive isolates have a greater propensity to carry gene cassettes unrelated to known antibiotic-resistance genes. The integron-positive isolates under the class Betaproteobacteria comprised of only two genera, Comamonas and Acidovorax of family Comamonadaceae, while isolates under class Gammaproteobacteria fell under the families

  8. A Study on the Measurement of the Pollution Level of Bacteria and Disinfection of Table and IP Cassette

    International Nuclear Information System (INIS)

    For the number of microbes and the pollution level of bacteriology of IP Cassette and Table by laboratories, after identifying the bacteria before and after using alcohol and tissue including disinfectant and statistically testing, this research was intended to provide the basic data for the prevention and the right disinfection guideline for infection management of hospitals in diagnostic radiology. The subject of this research was the general room of diagnostic radiology of a university hospital in Daejeon City. The research was conducted from Apr 5 to Apr 12, 2007. The number of microbes and the pollution level of bacteriology of IP Cassette and Table by laboratories were tested before and after using alcohol and tissue for disinfection including disinfectant. In order to collect specimens exactly, they were collected with the nurse who specialized in infection management of the hospital, and statistical processing was done with SPSS V13.0. To compare the results before and after using alcohol and tissue, T-test was implemented, and post-hoc test was conducted. Bacteria were detected in 19 cases of 24 subjects(79.2%), however, they were not detected in 5 cases(20.8%). 7 kinds of bacteria were detected as isolated bacteria, of which Methicillin Resistant coagulase-negative Staphylococci(MRCNS) were detected in 15 cases(62.5%), which was most, Methicillin Resistant Staphylococcus Aureus(MRSA) in 6 cases(16.7%), Enterococcus Faecium(EFM) in 5 cases(20.8%), Acinetobacter baumannii(ABA) in 2 cases(8.3%), and Bacillus sp, Coagulase-negative Staphylococci(CNS), and Enterococcus sp(ENT) in 1 case, respectively(4.2%). In all bacteria except ABA, Gram positive bacillia were detected in 30 cases(97%), and Gram negative bacilli were detected only in 1 case(3%). As for the kinds of bacteria and the number of groups before and after using 70% Alcohol by Groups, when the bacteria were identified after disinfecting IP Cassette and Table with 70% Alcohol, all the bacteria became

  9. A Study on the Measurement of the Pollution Level of Bacteria and Disinfection of Table and IP Cassette

    Energy Technology Data Exchange (ETDEWEB)

    Bae, Seok Hwan; Lee, Moo Sik; Lim, Chang Seon; Kim, Gha Jung [Koyang University, Koyang (Korea, Republic of)

    2008-09-15

    For the number of microbes and the pollution level of bacteriology of IP Cassette and Table by laboratories, after identifying the bacteria before and after using alcohol and tissue including disinfectant and statistically testing, this research was intended to provide the basic data for the prevention and the right disinfection guideline for infection management of hospitals in diagnostic radiology. The subject of this research was the general room of diagnostic radiology of a university hospital in Daejeon City. The research was conducted from Apr 5 to Apr 12, 2007. The number of microbes and the pollution level of bacteriology of IP Cassette and Table by laboratories were tested before and after using alcohol and tissue for disinfection including disinfectant. In order to collect specimens exactly, they were collected with the nurse who specialized in infection management of the hospital, and statistical processing was done with SPSS V13.0. To compare the results before and after using alcohol and tissue, T-test was implemented, and post-hoc test was conducted. Bacteria were detected in 19 cases of 24 subjects(79.2%), however, they were not detected in 5 cases(20.8%). 7 kinds of bacteria were detected as isolated bacteria, of which Methicillin Resistant coagulase-negative Staphylococci(MRCNS) were detected in 15 cases(62.5%), which was most, Methicillin Resistant Staphylococcus Aureus(MRSA) in 6 cases(16.7%), Enterococcus Faecium(EFM) in 5 cases(20.8%), Acinetobacter baumannii(ABA) in 2 cases(8.3%), and Bacillus sp, Coagulase-negative Staphylococci(CNS), and Enterococcus sp(ENT) in 1 case, respectively(4.2%). In all bacteria except ABA, Gram positive bacillia were detected in 30 cases(97%), and Gram negative bacilli were detected only in 1 case(3%). As for the kinds of bacteria and the number of groups before and after using 70% Alcohol by Groups, when the bacteria were identified after disinfecting IP Cassette and Table with 70% Alcohol, all the bacteria became

  10. 21 CFR 892.1880 - Wall-mounted radiographic cassette holder.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Wall-mounted radiographic cassette holder. 892.1880 Section 892.1880 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Diagnostic Devices § 892.1880...

  11. Film cassette for quality assurance of dental X-ray tubes

    International Nuclear Information System (INIS)

    In this brief technical note, the authors describe a film cassette to enable routine quality assurance checks of equipment to be made by dental staff without the use of an ion chamber. The film is sent to the Physics Department of Guys Hospital, London, for processing and densitometric analysis. (UK)

  12. Construction of heterologous gene expression cassettes for the development of recombinant Clostridium beijerinckii.

    Science.gov (United States)

    Oh, Young Hoon; Eom, Gyeong Tae; Kang, Kyoung Hee; Joo, Jeong Chan; Jang, Young-Ah; Choi, Jae Woo; Song, Bong Keun; Lee, Seung Hwan; Park, Si Jae

    2016-04-01

    Gene-expression cassettes for the construction of recombinant Clostridium beijerinckii were developed as potential tools for metabolic engineering of C. beijerinckii. Gene expression cassettes containing ColE1 origin and pAMB origin along with the erythromycin resistance gene were constructed, in which promoters from Escherichia coli, Lactococcus lactis, Ralstonia eutropha, C. acetobutylicum, and C. beijerinckii are examined as potential promoters in C. beijerinckii. Zymogram analysis of the cell extracts and comparison of lipase activities of the recombinant C. beijerinckii strains expressing Pseudomonas fluorescens tliA gene suggested that the tliA gene was functionally expressed by all the examined promoters with different expression level. Also, recombinant C. beijerinckii expressing C. beijerinckii secondary alcohol dehydrogenase by the constructed expression cassettes successfully produced 2-propanol from glucose. The best promoter for TliA expression was the R. eutropha phaP promoter while that for 2-propanol production was the putative C. beijerinckii pta promoter. Gene expression cassettes developed in this study may be useful tools for the construction of recombinant C. beijerinckii strains as host strains for the valuable chemicals and fuels from renewable resources. PMID:26780375

  13. Atovaquone and quinine anti-malarials inhibit ATP binding cassette transporter activity

    OpenAIRE

    Rijpma, S.R.; Heuvel, J. J.; van de Velden, M.; Sauerwein, R. W.; Russel, F. G.; Koenderink, J.B.

    2014-01-01

    BACKGROUND: Therapeutic blood plasma concentrations of anti-malarial drugs are essential for successful treatment. Pharmacokinetics of pharmaceutical compounds are dependent of adsorption, distribution, metabolism, and excretion. ATP binding cassette (ABC) transport proteins are particularly involved in drug deposition, as they are located at membranes of many uptake and excretory organs and at protective barriers, where they export endogenous and xenobiotic compounds, including pharmaceutica...

  14. Stacking multiple transgenes at a selected genomic site via repeated recombinase-mediated DNA cassette exchanges.

    Science.gov (United States)

    Li, Zhongsen; Moon, Bryan P; Xing, Aiqiu; Liu, Zhan-Bin; McCardell, Richard P; Damude, Howard G; Falco, S Carl

    2010-10-01

    Recombinase-mediated DNA cassette exchange (RMCE) has been successfully used to insert transgenes at previously characterized genomic sites in plants. Following the same strategy, groups of transgenes can be stacked to the same site through multiple rounds of RMCE. A gene-silencing cassette, designed to simultaneously silence soybean (Glycine max) genes fatty acid ω-6 desaturase 2 (FAD2) and acyl-acyl carrier protein thioesterase 2 (FATB) to improve oleic acid content, was first inserted by RMCE at a precharacterized genomic site in soybean. Selected transgenic events were subsequently retransformed with the second DNA construct containing a Yarrowia lipolytica diacylglycerol acyltransferase gene (DGAT1) to increase oil content by the enhancement of triacylglycerol biosynthesis and three other genes, a Corynebacterium glutamicum dihydrodipicolinate synthetase gene (DHPS), a barley (Hordeum vulgare) high-lysine protein gene (BHL8), and a truncated soybean cysteine synthase gene (CGS), to improve the contents of the essential amino acids lysine and methionine. Molecular characterization confirmed that the second RMCE successfully stacked the four overexpression cassettes to the previously integrated FAD2-FATB gene-silencing cassette. Phenotypic analyses indicated that all the transgenes expressed expected phenotypes. PMID:20720171

  15. Multidrug transport by ATP binding cassette transporters : a proposed two-cylinder engine mechanism

    NARCIS (Netherlands)

    van Veen, HW; Higgins, CF; Konings, WN

    2001-01-01

    The elevated expression of ATP binding cassette (ABC) multidrug transporters in multidrug-resistant cells interferes with the drug-based control of cancers and infectious pathogenic microorganisms. Multidrug transporters interact directly with the drug substrates. This review summarizes current insi

  16. Identification of a novel streptococcal gene cassette mediating SOS mutagenesis in Streptococcus uberis

    NARCIS (Netherlands)

    Varhimo, Emilia; Savijoki, Kirsi; Jalava, Jari; Kuipers, Oscar P.; Varmanen, Pekka

    2007-01-01

    Streptococci have been considered to lack the classical SOS response, defined by increased mutation after UV exposure and regulation by LexA. Here we report the identification of a potential self-regulated SOS mutagenesis gene cassette in the Streptococcaceae family. Exposure to UV light was found t

  17. Temperature variations around medication cassette and carry bag in routine use of epoprostenol administration in healthy volunteers.

    Directory of Open Access Journals (Sweden)

    Yuichi Tamura

    Full Text Available BACKGROUND: According to several treatment guidelines, epoprostenol is an important treatment option for pulmonary arterial hypertension. However, the pharmacokinetic characteristics and poor stability of epoprostenol at room temperature make its administration challenging. We therefore studied temperature fluctuations between the drug administration cassette and atmosphere to promote the safe use of epoprostenol. METHODS AND FINDINGS: Five healthy volunteers carried a portable intravenous infusion pump attached to a medication cassette containing saline in a bag during their ordinary activities over 16 days during which the mean atmospheric temperature was 29.6 ± 1.5°C. The temperature around the medication cassette was not less than 25°C on any occasion, and the mean period over 24 h during which the temperature around the cassette exceeded 35°C and 40°C was 96.9 ± 156.4 min and 24.4 ± 77.3 min, respectively. Significant correlations were observed between the temperatures outside the bag and around the cassette, as well as between temperatures around the cassette and of the saline solution in the cassette (r = 0.9258 and 0.8276, respectively. There were no differences in the temperatures outside the bag or around the cassette with respect to the bag material. CONCLUSIONS: Temperatures around a medication cassette and outside the bag containing the medication increase with sunlight exposure. The temperature around cassettes used for administering epoprostenol must therefore be kept low for as long as possible during hot summer conditions to maintain the drug stability.

  18. Utilizing ARC EMCS Seedling Cassettes as Highly Versatile Miniature Growth Chambers for Model Organism Experiments

    Science.gov (United States)

    Freeman, John L.; Steele, Marianne K.; Sun, Gwo-Shing; Heathcote, David; Reinsch, S.; DeSimone, Julia C.; Myers, Zachary A.

    2014-01-01

    The aim of our ground testing was to demonstrate the capability of safely putting specific model organisms into dehydrated stasis, and to later rehydrate and successfully grow them inside flight proven ARC EMCS seedling cassettes. The ARC EMCS seedling cassettes were originally developed to support seedling growth during space flight. The seeds are attached to a solid substrate, launched dry, and then rehydrated in a small volume of media on orbit to initiate the experiment. We hypothesized that the same seedling cassettes should be capable of acting as culture chambers for a wide range of organisms with minimal or no modification. The ability to safely preserve live organisms in a dehydrated state allows for on orbit experiments to be conducted at the best time for crew operations and more importantly provides a tightly controlled physiologically relevant growth experiment with specific environmental parameters. Thus, we performed a series of ground tests that involved growing the organisms, preparing them for dehydration on gridded Polyether Sulfone (PES) membranes, dry storage at ambient temperatures for varying periods of time, followed by rehydration. Inside the culture cassettes, the PES membranes were mounted above blotters containing dehydrated growth media. These were mounted on stainless steel bases and sealed with plastic covers that have permeable membrane covered ports for gas exchange. The results showed we were able to demonstrate acceptable normal growth of C.elegans (nematodes), E.coli (bacteria), S.cerevisiae (yeast), Polytrichum (moss) spores and protonemata, C.thalictroides (fern), D.discoideum (amoeba), and H.dujardini (tardigrades). All organisms showed acceptable growth and rehydration in both petri dishes and culture cassettes initially, and after various time lengths of dehydration. At the end of on orbit ISS European Modular Cultivation System experiments the cassettes could be frozen at ultra-low temperatures, refrigerated, or chemically

  19. Evaluating the accuracy of technicians and pharmacists in checking unit dose medication cassettes.

    Science.gov (United States)

    Ambrose, Peter J; Saya, Frank G; Lovett, Larry T; Tan, Sandy; Adams, Dale W; Shane, Rita

    2002-06-15

    The accuracy rates of board-registered pharmacy technicians and pharmacists in checking unit dose medication cassettes in the inpatient setting at two separate institutions were examined. Cedars-Sinai Medical Center and Long Beach Memorial Medical Center, both in Los Angeles county, petitioned the California State Board of Pharmacy to approve a waiver of the California Code of Regulations to conduct an experimental program to compare the accuracy of unit dose medication cassettes checked by pharmacists with that of cassettes checked by trained, certified pharmacy technicians. The study consisted of three parts: assessing pharmacist baseline checking accuracy (Phase I), developing a technician-training program and certifying technicians who completed the didactic and practical training (Phase II), and evaluating the accuracy of certified technicians checking unit dose medication cassettes as a daily function (Phase III). Twenty-nine pharmacists and 41 technicians (3 of whom were pharmacy interns) participated in the study. Of the technicians, all 41 successfully completed the didactic and practical training, 39 successfully completed the audits and became certified checkers, and 2 (including 1 of the interns) did not complete the certification audits because they were reassigned to another work area or had resigned. In Phase II, the observed accuracy rate and its lower confidence limit exceeded the predetermined minimum requirement of 99.8% for a certified checker. The mean accuracy rates for technicians were identical at the two institutions (p = 1.0). The difference in mean accuracy rates between pharmacists (99.52%; 95% confidence interval [CI] 99.44-99.58%) and technicians, (99.89%; 95% CI 99.87-99.90%) was significant (p medication cassettes filled by other technicians. PMID:12073859

  20. Ground Testing of the EMCS Seed Cassette for Biocompatibility with the Cellular Slime Mold, Dictyostelium Discoideum

    Science.gov (United States)

    Hanely, Julia C.; Reinsch, Sigrid; Myers, Zachary A.; Freeman, John; Steele, Marianne K.; Sun, Gwo-Shing; Heathcote, David G.

    2014-01-01

    The European Modular Cultivation System, EMCS, was developed by ESA for plant experiments. To expand the use of flight verified hardware for various model organisms, we performed ground experiments to determine whether ARC EMCS Seed Cassettes could be adapted for use with cellular slime mold for future space flight experiments. Dictyostelium is a cellular slime mold that can exist both as a single-celled independent organism and as a part of a multicellular colony which functions as a unit (pseudoplasmodium). Under certain stress conditions, individual amoebae will aggregate to form multicellular structures. Developmental pathways are very similar to those found in Eukaryotic organisms, making this a uniquely interesting organism for use in genetic studies. Dictyostelium has been used as a genetic model organism for prior space flight experiments. Due to the formation of spores that are resistant to unfavorable conditions such as desiccation, Dictyostelium is also a good candidate for use in the EMCS Seed Cassettes. The growth substratum in the cassettes is a gridded polyether sulfone (PES) membrane. A blotter beneath the PES membranes contains dried growth medium. The goals of this study were to (1) verify that Dictyostelium are capable of normal growth and development on PES membranes, (2) develop a method for dehydration of Dictyostelium spores with successful recovery and development after rehydration, and (3) successful mock rehydration experiments in cassettes. Our results show normal developmental progression in two strains of Dictyostelium discoideum on PES membranes with a bacterial food source. We have successfully performed a mock rehydration of spores with developmental progression from aggregation to slug formation, and production of morphologically normal spores within 9 days of rehydration. Our results indicate that experiments on the ISS using the slime mold, Dictyostelium discoideum could potentially be performed in the flight verified hardware of

  1. Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse

    Directory of Open Access Journals (Sweden)

    Zhang Xuegong

    2008-04-01

    Full Text Available Abstract Background Alternative splicing expands transcriptome diversity and plays an important role in regulation of gene expression. Previous studies focus on the regulation of a single cassette exon, but recent experiments indicate that multiple cassette exons within a gene may interact with each other. This interaction can increase the potential to generate various transcripts and adds an extra layer of complexity to gene regulation. Several cases of exon interaction have been discovered. However, the extent to which the cassette exons coordinate with each other remains unknown. Results Based on EST data, we employed a metric of correlation coefficients to describe the interaction between two adjacent cassette exons and then categorized these exon pairs into three different groups by their interaction (correlation patterns. Sequence analysis demonstrates that strongly-correlated groups are more conserved and contain a higher proportion of pairs with reading frame preservation in a combinatorial manner. Multiple genome comparison further indicates that different groups of correlated pairs have different evolutionary courses: (1 The vast majority of positively-correlated pairs are old, (2 most of the weakly-correlated pairs are relatively young, and (3 negatively-correlated pairs are a mixture of old and young events. Conclusion We performed a large-scale analysis of interactions between adjacent cassette exons. Compared with weakly-correlated pairs, the strongly-correlated pairs, including both the positively and negatively correlated ones, show more evidence that they are under delicate splicing control and tend to be functionally important. Additionally, the positively-correlated pairs bear strong resemblance to constitutive exons, which suggests that they may evolve from ancient constitutive exons, while negatively and weakly correlated pairs are more likely to contain newly emerging exons.

  2. Microphone arrays fundamentals

    OpenAIRE

    Embrechts, Jean-Jacques

    2011-01-01

    Microphone arrays are essentially directional sensors. They are therefore mainly used for locating, identifying, isolating, measuring and recording individual sound sources. The main principles governing the directivity of microphone arrays are reviewed: phase differences between signals create constructive and destructive interferences, depending on the direction of the sound source. Moreover, signal processing is applied to provide “beamforming”, i.e. beam shaping and steering. Contrary to ...

  3. A trial manufacture of cassette tape to standard MT data processing system controlled by microcomputer

    International Nuclear Information System (INIS)

    The data processing system controlled by a microcomputer has been developed for the purpose of data handling of cassette magnetic tape used as a recorder of pulse hight analyzer in market. This system has the following features; (1) This data acquisition system consists of a portable pulse hight analyzer and an audio-cassette magnetic tape recorder, which is low in price, light in weight and portable. (2) As the data processing part is composed by a microcomputer, one can easily deal with a different type of data code by a slight modification of a process program. (3) The processed output can be taken out to a standard 9 track 1600 BPI PE mode magnetic tape by a magnetic tape handler, and be available for a generally used bach-process computer. This report describes the hardware configuration and the process program in detail. Moreover, the operational manual, a sample operation and program lists are described in the appendix. (author)

  4. Serum albumin promotes ATP-binding cassette transporter-dependent sterol uptake in yeast

    DEFF Research Database (Denmark)

    Marek, Magdalena; Silvestro, Daniele; Fredslund, Maria D.;

    2014-01-01

    Sterol uptake in fungi is a multistep process that involves interaction between external sterols and the cell wall, incorporation of sterol molecules into the plasma membrane, and subsequent integration into intracellular membranes for turnover. ATP-binding cassette (ABC) transporters have been i...... donor in ATP-binding cassette-transporter-dependent sterol uptake, a process potentially important for growth of Candida glabrata inside infected humans....... implicated in sterol uptake, but key features of their activity remain to be elucidated. Here, we apply fluorescent cholesterol (NBD-cholesterol) to monitor sterol uptake under anaerobic and aerobic conditions in two fungal species, Candida glabrata (Cg) and Saccharomyces cerevisiae (Sc). We found that in....... cerevisiae requires the presence of serum or albumin for efficient cholesterol uptake. These results suggest that albumin can serve as sterol donor in ABC transporter-dependent sterol uptake, a process potentially important for growth of C. glabrata inside infected humans. Serum albumin can serve as sterol...

  5. Integration of multiple expression cassettes into mammalian genomes in a single step

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Andrijana Kriz, Katharina Schmid, Kurt Ballmer & Philipp Berger ### Abstract The modification of mammalian cells by the expression of multiple genes is a crucial technology in modern biological research. MultiLabel allows the modular assembly of independent expression units in a single plasmid which can be used for transient and stable modification of cells. In contrast to other methods, the assembly of the expression cassettes does not require restriction enzymes since i...

  6. ATP binding cassette transporter gene expression in rat liver progenitor cells

    OpenAIRE

    2003-01-01

    Background and aim: Liver regeneration after severe liver damage depends in part on proliferation and differentiation of hepatic progenitor cells (HPCs). Under these conditions they must be able to withstand the toxic milieu of the damaged liver. ATP binding cassette (ABC) transporters are cytoprotective efflux pumps that may contribute to the preservation of these cells. The aim of this study was to determine the ABC transporter phenotype of HPCs.

  7. Blood-Brain Barrier Active Efflux Transporters: ATP-Binding Cassette Gene Family

    OpenAIRE

    Löscher, Wolfgang; Potschka, Heidrun

    2005-01-01

    Summary: The blood-brain barrier (BBB) contributes to brain homeostasis by protecting the brain from potentially harmful endogenous and exogenous substances. BBB active drug efflux transporters of the ATP-binding cassette (ABC) gene family are increasingly recognized as important determinants of drug distribution to, and elimination from, the CNS. The ABC efflux transporter P-glycoprotein (Pgp) has been demonstrated as a key element of the BBB that can actively transport a huge variety of lip...

  8. Nitric oxide differentially regulates renal ATP-binding cassette transporters during endotoxemia

    OpenAIRE

    Heemskerk, Suzanne; van Koppen, Arianne; van den Broek, Luc; Poelen, Geert J. M.; Wouterse, Alfons C; Dijkman, Henry B. P. M.; Russel, Frans G. M.; Masereeuw, Rosalinde

    2007-01-01

    Nitric oxide (NO) is an important regulator of renal transport processes. In the present study, we investigated the role of NO, produced by inducible NO synthase (iNOS), in the regulation of renal ATP-binding cassette (ABC) transporters in vivo during endotoxemia. Wistar–Hannover rats were injected with lipopolysaccharide (LPS+) alone or in combination with the iNOS inhibitor, aminoguanidine. Controls received detoxified LPS (LPS−). After LPS+, proximal tubular damage and a reduction in renal...

  9. ATP-binding cassette transporter controls leaf surface secretion of anticancer drug components in Catharanthus roseus

    OpenAIRE

    Yu, Fang; De Luca, Vincenzo

    2013-01-01

    The presence of biologically active monoterpenoid indole alkaloids (MIAs) on the leaf surfaces of medicinally important Catharanthus roseus has led to questions about the secretion processes involved and their prevalence within MIA-producing species of plants. This report shows that a transporter closely related to those involved in cuticle assembly in plants and belonging to the pleiotropic drug resistance family of ATP-binding cassette transporters is specialized for transport of the MIA ca...

  10. Conceptual Design Studies of the KSTAR Bay-Nm Cassette and Thomson Scattering Optics

    International Nuclear Information System (INIS)

    A Multi-Channel Thomson Scattering System viewing the edge and core of the KSTAR plasma will be installed at the mid-plane port Bay-N. An engineering design study was undertaken at PPPL in collaboration with the Korea Basic Science Institute (KBSI) to determine the optimal optics and cassette design. Design criteria included environmental, mechanical and optical factors. All of the optical design options have common design features; the Thomson Scattering laser, an in-vacuum shutter, a quartz heat shield and primary vacuum window, a set of optical elements and a fiber optic bundle. Neutron radiation damage was a major factor in the choice of competing lens-based and mirror-based optical designs. Both the mirror based design and the lens design are constrained by physical limits of the Bay-N cassette and interference with the Bay-N micro-wave launcher. The cassette will contain the optics and a rail system for maintenance of the optics

  11. Conceptual Design Studies of the KSTAR Bay-Nm Cassette and Thomson Scattering Optics

    Energy Technology Data Exchange (ETDEWEB)

    Feder, R.; Ellis, R.; Johnson, D.; Park, H.; Lee, H. G.

    2005-09-26

    A Multi-Channel Thomson Scattering System viewing the edge and core of the KSTAR plasma will be installed at the mid-plane port Bay-N. An engineering design study was undertaken at PPPL in collaboration with the Korea Basic Science Institute (KBSI) to determine the optimal optics and cassette design. Design criteria included environmental, mechanical and optical factors. All of the optical design options have common design features; the Thomson Scattering laser, an in-vacuum shutter, a quartz heat shield and primary vacuum window, a set of optical elements and a fiber optic bundle. Neutron radiation damage was a major factor in the choice of competing lens-based and mirror-based optical designs. Both the mirror based design and the lens design are constrained by physical limits of the Bay-N cassette and interference with the Bay-N micro-wave launcher. The cassette will contain the optics and a rail system for maintenance of the optics.

  12. Conservation of gene cassettes among diverse viruses of the human gut.

    Directory of Open Access Journals (Sweden)

    Samuel Minot

    Full Text Available Viruses are a crucial component of the human microbiome, but large population sizes, high sequence diversity, and high frequencies of novel genes have hindered genomic analysis by high-throughput sequencing. Here we investigate approaches to metagenomic assembly to probe genome structure in a sample of 5.6 Gb of gut viral DNA sequence from six individuals. Tests showed that a new pipeline based on DeBruijn graph assembly yielded longer contigs that were able to recruit more reads than the equivalent non-optimized, single-pass approach. To characterize gene content, the database of viral RefSeq proteins was compared to the assembled viral contigs, generating a bipartite graph with functional cassettes linking together viral contigs, which revealed a high degree of connectivity between diverse genomes involving multiple genes of the same functional class. In a second step, open reading frames were grouped by their co-occurrence on contigs in a database-independent manner, revealing conserved cassettes of co-oriented ORFs. These methods reveal that free-living bacteriophages, while usually dissimilar at the nucleotide level, often have significant similarity at the level of encoded amino acid motifs, gene order, and gene orientation. These findings thus connect contemporary metagenomic analysis with classical studies of bacteriophage genomic cassettes. Software is available at https://sourceforge.net/projects/optitdba/.

  13. Antimicrobial resistance, class 1 and 2 integrons and gene cassettes in avian Escherichia coli

    Directory of Open Access Journals (Sweden)

    Patrizia Robino

    2010-01-01

    Full Text Available Seventy-four Escherichia coli isolates were collected from domestic, synanthropic free living birds as well as wild and exotic birds, all living in captivity. Antimicrobial susceptibility was tested against a panel of 9 antibiotics, and presence of integrons (Class 1 and Class 2 and gene cassettes was analysed by PCR and sequencing, respectively. Twenty-eight isolates proved positive for Class 1 integrons and 19 for Class 2. Gene cassette arrangements were determined in 23 integron-positive isolates, which harboured one (aadA1 two (dfrA1-aadA1 or three (dfrA7-dfrA1-aadA1, dfrA1-sat1-aadA1 cassettes in their variable region. E. coli multiresistance to antimicrobials was observed in all groups examined, in particular domestic and synanthropic birds showed resistance to at least 4 antibiotics. A large number of isolates from domestic and synantropic birds proved to be Class 1 integron- positive, but unexpectedly, we observed many Class 2 integrons, usually considered less frequent.

  14. Transient expression of minimum linear gene cassettes in onion epidermal cells via direct transformation.

    Science.gov (United States)

    Cheng, Yun-Qing; Yang, Jun; Xu, Feng-Ping; An, Li-Jia; Liu, Jian-Feng; Chen, Zhi-Wen

    2009-12-01

    A new method without any special devices for direct transformation of linear gene cassettes was developed. Its feasibility was verified through 5'-fluorescent dye (fluorescein isothiocyanate, FITC)-labeled fluorescent tracing and transient expression of a gus reporter gene. Minimal linear gene cassettes, containing necessary regulation elements and a gus reporter gene, was prepared by polymerase chain reaction and dissolved in transformation buffer solution to 100 ng/mL. The basic transformation solution used was Murashige and Skoog basal salt mixture (MS) liquid medium. Hypertonic pretreatment of explants and transformation cofactors, including Ca(2+), surfactant assistants, Agrobacterium LBA4404 cell culture on transformation efficiency were evaluated. Prior to the incubation of the explants and target linear cassette in each designed transformation solution for 3 h, the onion low epidermal explants were pre-cultured in darkness at 27 degrees C for 48 h and then transferred to MS solid media for 72 h. FITC-labeled linear DNA was used to trace the delivery of DNA entry into the cell and the nuclei. By GUS staining and flow-cytometry-mediated fluorescent detection, a significant increase of the ratios of fluorescent nuclei as well as expression of the gus reporter gene was observed by each designed transformation solution. This potent and feasible method showed prospective applications in plant transgenic research. PMID:19255730

  15. Coping with depression: a pilot study to assess the efficacy of a self-help audio cassette.

    OpenAIRE

    Blenkiron, P

    2001-01-01

    BACKGROUND: The self-help audio cassette 'Coping with Depression' was produced and widely distributed as part of the national Defeat Depression Campaign. A central aim was to improve public understanding and encourage the use of cognitive-behavioural techniques. AIM: To formally assess the ability of the audio cassette to change attitudes to depression in primary care and the degree to which patients are motivated to practice its recommended coping strategies. DESIGN OF STUDY: Comparison of L...

  16. 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.

  17. Array tomography: imaging stained arrays.

    Science.gov (United States)

    Micheva, Kristina D; O'Rourke, Nancy; Busse, Brad; Smith, Stephen J

    2010-11-01

    Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. In this protocol, tissue arrays are imaged using conventional wide-field fluorescence microscopy. Images can be captured manually or, with the appropriate software and hardware, the process can be automated. PMID:21041399

  18. Array tomography: production of arrays.

    Science.gov (United States)

    Micheva, Kristina D; O'Rourke, Nancy; Busse, Brad; Smith, Stephen J

    2010-11-01

    Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time consuming and require some practice to perfect. This protocol describes the sectioning of embedded tissues and the mounting of the serial arrays. The procedures require some familiarity with the techniques used for ultramicrotome sectioning for electron microscopy. PMID:21041397

  19. Structure, function, and evolution of bacterial ATP-binding cassette systems

    Energy Technology Data Exchange (ETDEWEB)

    Davidson, A.L.; Dassa, E.; Orelle, C.; Chen, J. (Purdue)

    2010-07-27

    The ATP-binding cassette (ABC) systems constitute one of the largest superfamilies of paralogous sequences. All ABC systems share a highly conserved ATP-hydrolyzing domain or protein (the ABC; also referred to as a nucleotide-binding domain [NBD]) that is unequivocally characterized by three short sequence motifs (Fig. 1): these are the Walker A and Walker B motifs, indicative of the presence of a nucleotide-binding site, and the signature motif, unique to ABC proteins, located upstream of the Walker B motif (426). Other motifs diagnostic of ABC proteins are also indicated in Fig. 1. The biological significance of these motifs is discussed in Structure, Function, and Dynamics of the ABC. ABC systems are widespread among living organisms and have been detected in all genera of the three kingdoms of life, with remarkable conservation in the primary sequence of the cassette and in the organization of the constitutive domains or subunits (203, 420). ABC systems couple the energy of ATP hydrolysis to an impressively large variety of essential biological phenomena, comprising not only transmembrane (TM) transport, for which they are best known, but also several non-transport-related processes, such as translation elongation (62) and DNA repair (174). Although ABC systems deserve much attention because they are involved in severe human inherited diseases (107), they were first discovered and characterized in detail in prokaryotes, as early as the 1970s (13, 148, 238, 468). The most extensively analyzed systems were the high-affinity histidine and maltose uptake systems of Salmonella enterica serovar Typhimurium and Escherichia coli. Over 2 decades ago, after the completion of the nucleotide sequences encoding these transporters in the respective laboratories of Giovanna Ames and Maurice Hofnung, Hiroshi Nikaido and colleagues noticed that the two systems displayed a global similarity in the nature of their components and, moreover, that the primary sequences of MalK and

  20. Genome-wide analysis of the ATP-binding cassette (ABC) transporter gene family in the silkworm, Bombyx mori.

    Science.gov (United States)

    Xie, Xiaodong; Cheng, Tingcai; Wang, Genhong; Duan, Jun; Niu, Weihuan; Xia, Qingyou

    2012-07-01

    The ATP-binding cassette (ABC) superfamily is a larger protein family with diverse physiological functions in all kingdoms of life. We identified 53 ABC transporters in the silkworm genome, and classified them into eight subfamilies (A-H). Comparative genome analysis revealed that the silkworm has an expanded ABCC subfamily with more members than Drosophila melanogaster, Caenorhabditis elegans, or Homo sapiens. Phylogenetic analysis showed that the ABCE and ABCF genes were highly conserved in the silkworm, indicating possible involvement in fundamental biological processes. Five multidrug resistance-related genes in the ABCB subfamily and two multidrug resistance-associated-related genes in the ABCC subfamily indicated involvement in biochemical defense. Genetic variation analysis revealed four ABC genes that might be evolving under positive selection. Moreover, the silkworm ABCC4 gene might be important for silkworm domestication. Microarray analysis showed that the silkworm ABC genes had distinct expression patterns in different tissues on day 3 of the fifth instar. These results might provide new insights for further functional studies on the ABC genes in the silkworm genome. PMID:22311044

  1. The ATP-binding Cassette Transporter OsABCG15 is Required for Anther Development and Pollen Fertility in Rice

    Institute of Scientific and Technical Information of China (English)

    Bai-Xiao Niu; Fu-Rong He; Ming He; Ding Ren; Le-Tian Chen; Yao-Guang Liu

    2013-01-01

    Plant male reproductive development is a complex biological process,but the underlying mechanism is not well understood.Here,we characterized a rice (Oryza sativa L.) male sterile mutant.Based on mapbased cloning and sequence analysis,we identified a 1,459-bp deletion in an adenosine triphosphate (ATP)-binding cassette (ABC) transporter gene,OsABCG15,causing abnormal anthers and male sterility.Therefore,we named this mutant osabcg15.Expression analysis showed that OsABCG15 is expressed specifically in developmental anthers from stage 8 (meiosis Ⅱ stage) to stage 10 (late microspore stage).Two genes CYP704B2 and WDA1,involved in the biosynthesis of very-long-chain fatty acids for the establishment of the anther cuticle and pollen exine,were downregulated in osabcg15 mutant,suggesting that OsABCG15 may play a key function in the processes related to sporopollenin biosynthesis or sporopollenin transfer from tapetal cells to anther locules.Consistently,histological analysis showed that osabcg15 mutants developed obvious abnormality in postmeiotic tapetum degeneration,leading to rapid degredation of young microspores.The results suggest that OsABCG15 plays a critical role in exine formation and pollen development,similar to the homologous gene of AtABCG26 in Arabidopsis.This work is helpful to understand the regulatory network in rice anther development.

  2. HG-829 is a potent noncompetitive inhibitor of the ATP-binding cassette multidrug resistance transporter ABCB1.

    Science.gov (United States)

    Caceres, Gisela; Robey, Robert W; Sokol, Lubomir; McGraw, Kathy L; Clark, Justine; Lawrence, Nicholas J; Sebti, Said M; Wiese, Michael; List, Alan F

    2012-08-15

    Transmembrane drug export mediated by the ATP-binding cassette (ABC) transporter P-glycoprotein contributes to clinical resistance to antineoplastics. In this study, we identified the substituted quinoline HG-829 as a novel, noncompetitive, and potent P-glycoprotein inhibitor that overcomes in vitro and in vivo drug resistance. We found that nontoxic concentrations of HG-829 restored sensitivity to P-glycoprotein oncolytic substrates. In ABCB1-overexpressing cell lines, HG-829 significantly enhanced cytotoxicity to daunorubicin, paclitaxel, vinblastine, vincristine, and etoposide. Coadministration of HG-829 fully restored in vivo antitumor activity of daunorubicin in mice without added toxicity. Functional assays showed that HG-829 is not a Pgp substrate or competitive inhibitor of Pgp-mediated drug efflux but rather acts as a noncompetitive modulator of P-glycoprotein transport function. Taken together, our findings indicate that HG-829 is a potent, long-acting, and noncompetitive modulator of P-glycoprotein export function that may offer therapeutic promise for multidrug-resistant malignancies. PMID:22761337

  3. Expression of the domain cassette 8 Plasmodium falciparum erythrocyte membrane protein 1 is associated with cerebral malaria in Benin.

    Directory of Open Access Journals (Sweden)

    Gwladys I Bertin

    Full Text Available BACKGROUND: Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP-1 is a highly polymorphic adherence receptor expressed on the surface of infected erythrocytes. Based on sequence homology PfEMP-1 variants have been grouped into three major groups A-C, the highly conserved VAR2CSA variants, and semi-conserved types defined by tandem runs of specific domains ("domain cassettes" (DC. The PfEMP-1 type expressed determines the adherence phenotype, and is associated with clinical outcome of infection. METHODS: Parasite isolates from Beninese children or women presenting with, respectively, CM or PAM were collected along with samples from patients with uncomplicated malaria (UM. We assessed the transcript level of var genes by RT-qPCR and the expression of PfEMP-1 proteins by LC-MS/MS. RESULTS: Var genes encoding DC8 and Group A PfEMP-1 were transcribed more often and at higher levels in cerebral malaria vs. uncomplicated malaria patients. LC-MS/MS identified peptides from group A, DC8 PfEMP-1 more frequently in cerebral malaria than in uncomplicated malaria and pregnancy-associated malaria samples. CONCLUSION: This is the first study to show association between PfEMP-1 subtype and disease outcome by direct analysis of parasites proteome. The results corroborate that group A and specifically the PfEMP-1 types DC8 are universally associated with cerebral malaria. This is a crucial observation for promoting studies on malaria pathogenesis.

  4. Hygromycin B and apramycin antibiotic resistance cassettes for use in Campylobacter jejuni.

    Directory of Open Access Journals (Sweden)

    Andrew Cameron

    Full Text Available Campylobacter jejuni genetic manipulation is restricted by the limited number of antibiotic resistance cassettes available for use in this diarrheal pathogen. In this study, two antibiotic resistance cassettes were developed, encoding for hygromycin B and apramycin resistance, for use in mutagenesis or for selection of gene expression and complementation constructs in C. jejuni. First, the marker genes were successfully modified to allow for insertional mutagenesis or deletion of a gene-of-interest, and were bracketed with restriction sites for the facilitation of site-specific cloning. These hygromycin B and apramycin markers are encoded by plasmids pAC1H and pAC1A, respectively. We also modified an insertional gene-delivery vector to create pRRH and pRRA, containing the hygromycin B and apramycin resistance genes, and 3 unique restriction sites for the directional introduction of genes into the conserved multi-copy rRNA gene clusters of the C. jejuni chromosome. We determined the effective antibiotic concentrations required for selection, and established that no harmful effects or fitness costs were associated with carrying hygromycin B or apramycin resistance under standard C. jejuni laboratory conditions. Using these markers, the arylsulfatase reporter gene astA was deleted, and the ability to genetically complement the astA deletion using pRRH and pRRA for astA gene insertion was demonstrated. Furthermore, the relative levels of expression from the endogenous astA promoter were compared to that of polycistronic mRNA expression from the constitutive promoter upstream of the resistance gene. The development of additional antibiotic resistance cassettes for use in Campylobacter will enable multiple gene deletion and expression combinations as well as more in-depth study of multi-gene systems important for the survival and pathogenesis of this important bacterium.

  5. Evaluation of retroviral vector design in defined chromosomal loci by Flp-mediated cassette replacement.

    Science.gov (United States)

    Verhoeyen, E; Hauser, H; Wirth, D

    2001-05-20

    Successful retroviral vector construction is still empirical. Test systems for vector efficiency are based on statistical comparison of numerous infectants with single proviral integrates, since their expression depends on the chromosomal surroundings. More reliable data would be obtained if different vector constructs were studied in an identical chromosomal context. Here, we demonstrate the use of a new method, in which chromosomal sites are provirally tagged in such a way that they can be targeted with other expression cassettes. The original tagging integrate is replaced in one step by the targeting element. This permits a reliable comparison of different retroviral vector configurations, eliminating the influence of neighboring chromosomal elements. We compared different retroviral vector types for coexpression of two genes: a vector containing an internal promoter and a vector with an internal ribosome entry site (IRES) element. In contrast to bicistronic retroviral vectors, dual-promoter proviruses exhibited rapid inactivation of the long terminal repeat (LTR)-driven gene expression. Targeted exchange of the dual-promoter provirus with a bicistronic retroviral cassette resulted in gain of expression stability. The reverse experiment confirmed this promoter interaction phenomenon since initial expression stability from a single-promoter bicistronic provirus was lost by targeted exchange with a dual-promoter cassette. In addition, targeting exchange of the dual-promoter provirus, replacing the LTR with an artificial (Tet) promoter restored expression stability. These observations, valid for various integration sites, prove the strong interaction between the LTR and the internal promoter. Our results have implications for retroviral vector design and suggest that retroviral coexpression of two genes is more predictable in the bicistronic configuration. PMID:11387058

  6. Repression of a mating type cassette in the fission yeast by four DNA elements

    DEFF Research Database (Denmark)

    Ekwall, K; Nielsen, O; Ruusala, T;

    1991-01-01

    difference between the active and the silent stage of the P determinant is controlled by four repressive elements that are located at the silent locus. There are two elements to the left and two to the right of the mating type cassette. Both elements to the left and either one of the two elements to the...... right are required for an effective blockage of transcription. When they are combined, the four elements define a highly efficient silencer functionally similar to the HMRE and HMLE and HMLI silencers in Saccharomyces cerevisiae. In addition, the DNA surrounding the silent P locus confers symmetric...

  7. New ATP-binding cassette A3 mutation causing surfactant metabolism dysfunction pulmonary type 3.

    Science.gov (United States)

    Piersigilli, Fiammetta; Peca, Donatella; Campi, Francesca; Corsello, Mirta; Landolfo, Francesca; Boldrini, Renata; Danhaive, Olivier; Dotta, Andrea

    2015-10-01

    Respiratory distress syndrome (RDS) may occur in term and near-term infants because of mutations in surfactant-related genes. ATP-binding cassette A3 (ABCA3), a phospholipid carrier specifically expressed in the alveolar epithelium, is the most frequently involved protein. We report the case of a couple of late-preterm fraternal twin infants of opposite sex carrying the same compound heterozygous ABCA3 mutations, one of which has never been previously reported, with different disease severity, suggesting variable penetrance or sex-related differences. ABCA3 deficiency should be considered in term or near-term babies who develop unexplained RDS. PMID:26508177

  8. Advances in the relationship between integron-gene cassette system and drug-resistance of bacteria%整合子-基因盒体系与细菌耐药关系及研究进展

    Institute of Scientific and Technical Information of China (English)

    张弘; 高伟利; 张双宅; 刘维华

    2013-01-01

    The bacteria resistance has posed a serious threat to the public health problem at present. Integron -gene cassette system played an important role in bacteria capturing and disseminating antibiotic resistance gene. Integron identified and captured free resistance gene box under the action of integrase. The spread of transposons and zygosity plasmid caused diffusion of drug - resistant genes and multiple resistance effects in different bacteria. This article reviewed the construction, class, distribution, source of integron and gene cassettes and spread mechanism of integron - gene cassette system.%目前,细菌耐药性已经对公共卫生问题构成严重威胁,整合子-基因盒体系是介导细菌获得耐药性与耐药基因播散的重要分子机制.整合子在整合酶作用下识别并俘获游离耐药基因盒,随着转座子或接合性质粒播散,造成细菌间耐药基因的扩散和多重耐药性的产生.本文就整合子-基因盒体系的结构、分类、分布、起源及播散机制等几方面研究近况开展讨论.

  9. Detection of staphylococcal cassette chromosome mec type XI carrying highly divergent mecA, mecI, mecR1, blaZ, and ccr genes in human clinical isolates of clonal complex 130 methicillin-resistant Staphylococcus aureus.

    LENUS (Irish Health Repository)

    Shore, Anna C

    2011-08-01

    Methicillin resistance in staphylococci is mediated by penicillin binding protein 2a (PBP 2a), encoded by mecA on mobile staphylococcal cassette chromosome mec (SCCmec) elements. In this study, two clonal complex 130 (CC130) methicillin-resistant Staphylococcus aureus (MRSA) isolates from patients in Irish hospitals were identified that were phenotypically PBP 2a positive but lacked mecA by conventional PCR and by DNA microarray screening. The isolates were identified as methicillin-susceptible S. aureus using the GeneXpert real-time PCR assay. Whole-genome sequencing of one isolate (M10\\/0061) revealed a 30-kb SCCmec element encoding a class E mec complex with highly divergent blaZ-mecA-mecR1-mecI, a type 8 cassette chromosome recombinase (ccr) complex consisting of ccrA1-ccrB3, an arsenic resistance operon, and flanking direct repeats (DRs). The SCCmec element was almost identical to that of SCCmec type XI (SCCmec XI) identified by the Sanger Institute in sequence type 425 bovine MRSA strain LGA251 listed on the website of the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements. The open reading frames (ORFs) identified within SCCmec XI of M10\\/0061 exhibited 21 to 93% amino acid identity to ORFs in GenBank. A third DR was identified ca. 3 kb downstream of SCCmec XI, indicating the presence of a possible SCC remnant. SCCmec XI was also identified in the second CC130 MRSA isolate by PCR and sequencing. The CC130 MRSA isolates may be of animal origin as previously reported CC130 S. aureus strains were predominantly from bovine sources. The highly divergent nature of SCCmec XI relative to other SCCmec elements indicates that it may have originated in another taxon.

  10. Plug-and-Play Genetic Access to Drosophila Cell Types using Exchangeable Exon Cassettes

    Directory of Open Access Journals (Sweden)

    Fengqiu Diao

    2015-03-01

    Full Text Available Genetically encoded effectors are important tools for probing cellular function in living animals, but improved methods for directing their expression to specific cell types are required. Here, we introduce a simple, versatile method for achieving cell-type-specific expression of transgenes that leverages the untapped potential of “coding introns” (i.e., introns between coding exons. Our method couples the expression of a transgene to that of a native gene expressed in the cells of interest using intronically inserted “plug-and-play” cassettes (called “Trojan exons” that carry a splice acceptor site followed by the coding sequences of T2A peptide and an effector transgene. We demonstrate the efficacy of this approach in Drosophila using lines containing suitable MiMIC (Minos-mediated integration cassette transposons and a palette of Trojan exons capable of expressing a range of commonly used transcription factors. We also introduce an exchangeable, MiMIC-like Trojan exon construct that can be targeted to coding introns using the Crispr/Cas system.

  11. Sub classification and targeted characterization of prophage-encoded two-component cell lysis cassette

    Indian Academy of Sciences (India)

    K V Srividhya; S Krishnaswamy

    2007-08-01

    Bacteriophage induced lysis of host bacterial cell is mediated by a two component cell lysis cassette comprised of holin and lysozyme. Prophages are integrated forms of bacteriophages in bacterial genomes providing a repertoire for bacterial evolution. Analysis using the prophage database (http://bicmku.in:8082) constructed by us showed 47 prophages were associated with putative two component cell lysis genes. These proteins cluster into four different subgroups. In this process, a putative holin (essd) and endolysin (ybcS), encoded by the defective lambdoid prophage DLP12 was found to be similar to two component cell lysis genes in functional bacteriophages like p21 and P1. The holin essd was found to have a characteristic dual start motif with two transmembrane regions and C-terminal charged residues as in class II holins. Expression of a fusion construct of essd in Escherichia coli showed slow growth. However, under appropriate conditions, this protein could be over expressed and purified for structure function studies. The second component of the cell lysis cassette, ybcS, was found to have an N-terminal SAR (Signal Arrest Release) transmembrane domain. The construct of ybcS has been over expressed in E. coli and the purified protein was functional, exhibiting lytic activity against E. coli and Salmonella typhi cell wall substrate. Such targeted sequence-structure-function characterization of proteins encoded by cryptic prophages will help understand the contribution of prophage proteins to bacterial evolution.

  12. Divertor cassette locking system remote handling trials with WHMAN at DTP2

    Energy Technology Data Exchange (ETDEWEB)

    Lyytikäinen, Ville; Kinnunen, Pasi; Koivumäki, Janne; Mattila, Jouni [Tampere University of Technology, Korkeakoulunkatu 6, 33720 Tampere (Finland); Siuko, Mikko [VTT Technical Research Centre of Finland, P.O. Box 1300, FI-33101 Tampere (Finland); Esque, Salvador [F4E, Fusion for Energy, Torres Diagonal Litoral B3, Josep Pla2, 08019, Barcelona (Spain); Palmer, Jim, E-mail: ville.lyytikainen@tut.fi [ITER Organization, Route de Vinon sur Verdon, 13115 Saint Paul Lez Durance (France)

    2013-10-15

    Highlights: ► RH requirements were developed from operator feedback, potential problem analysis and task description. ► Tools were designed according to these RH specific requirements. ► Two RH capable were developed and their functionality was verified at DPT2. -- Abstract: A key ITER maintenance activity is the exchange of the divertor cassettes. The current major step in this programme involves the full scale physical test facility, namely divertor test platform 2 (DTP2), in Tampere, Finland. The objective of the DTP2 is the design and proof of concept studies of various remote handling (RH) device prototypes and their RH control systems, but is also important to define principles for standardizing control systems and methods around the ITER maintenance equipment. The development process of divertor cassette locking system (CLS) RH Tool prototypes is presented in this paper. The validation of the developed CLS Tool prototypes is accomplished in RH trials at DTP2. For this RH Trial, a CLS task description (TD) and tool prototypes were developed, manufactured and, finally, tested under remote operations. These tools, designed to be operated by water hydraulic manipulator (WHMAN), are water hydraulic jack (WHJ), pin tool (PT) and wrench tool (WT)

  13. THE REAL ISSUE WITH WALL DEPOSITS IN CLOSED FILTER CASSETTES - WHAT'S THE SAMPLE?

    Energy Technology Data Exchange (ETDEWEB)

    Brisson, M.

    2009-09-12

    The measurement of aerosol dusts has long been utilized to assess the exposure of workers to metals. Tools used to sample and measure aerosol dusts have gone through many transitions over the past century. In particular, there have been several different techniques used to sample for beryllium, not all of which might be expected to produce the same result. Today, beryllium samples are generally collected using filters housed in holders of several different designs, some of which are expected to produce a sample that mimics the human capacity for dust inhalation. The presence of dust on the interior walls of cassettes used to hold filters during metals sampling has been discussed in the literature for a number of metals, including beryllium, with widely varying data. It appears that even in the best designs, particulates can enter the sampling cassette and deposit on the interior walls rather than on the sampling medium. The causes are not well understood but are believed to include particle bounce, electrostatic forces, particle size, particle density, and airflow turbulence. Historically, the filter catch has been considered to be the sample, but the presence of wall deposits, and the potential that the filter catch is not representative of the exposure to the worker, puts that historical position into question. This leads to a fundamental question: What is the sample? This article reviews the background behind the issue, poses the above-mentioned question, and discusses options and a possible path forward for addressing that question.

  14. Formation of a Chloride-conducting State in the Maltose ATP-binding Cassette (ABC) Transporter.

    Science.gov (United States)

    Carlson, Michael L; Bao, Huan; Duong, Franck

    2016-06-01

    ATP-binding cassette transporters use an alternating access mechanism to move substrates across cellular membranes. This mode of transport ensures the selective passage of molecules while preserving membrane impermeability. The crystal structures of MalFGK2, inward- and outward-facing, show that the transporter is sealed against ions and small molecules. It has yet to be determined whether membrane impermeability is maintained when MalFGK2 cycles between these two conformations. Through the use of a mutant that resides in intermediate conformations close to the transition state, we demonstrate that not only is chloride conductance occurring, but also to a degree large enough to compromise cell viability. Introduction of mutations in the periplasmic gate lead to the formation of a channel that is quasi-permanently open. MalFGK2 must therefore stay away from these ion-conducting conformations to preserve the membrane barrier; otherwise, a few mutations that increase access to the ion-conducting states are enough to convert an ATP-binding cassette transporter into a channel. PMID:27059961

  15. Large Format Uncooled Focal Plane Array Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Black Forest Engineering has identified innovative modifications in uncooled focal plane array (UFPA) architecture and processing that allows development of large...

  16. Evaluation of D-1 tape and cassette characteristics: Moisture content of Sony and Ampex D-1 tapes when delivered

    Science.gov (United States)

    Ashton, Gary

    Commercial D-1 cassette tapes and their associated recorders were designed to operate in broadcast studios and record in accordance with the International Radio Consultative Committee (CCIR) 607 digital video standards. The D-1 recorder resulted in the Society of Motion Picture and Television Engineers (SMPTE) standards 224 to 228 and is the first digital video recorder to be standardized for the broadcast industry. The D-1 cassette and associated media are currently marketed for broadcast use. The recorder was redesigned for data applications and is in the early stages of being evaluated. The digital data formats used are specified in MIL-STD-2179 and the American National Standards Institute (ANSI) X3.175-190 standard. In early 1990, the National Media Laboratory (NML) was asked to study the effects of time, temperature, and relative humidity on commercial D-1 cassettes. The environmental range to be studied was the one selected for the Advanced Tactical Air Reconnaissance System (ATARS) program. Several discussions between NML personnel, ATARS representatives, recorder contractors, and other interested parties were held to decide upon the experimental plan to be implemented. Review meetings were held periodically during the course of the experiment. The experiments were designed to determine the dimensional stability of the media and cassette since this is one of the major limiting factors of helical recorders when the media or recorders are subjected to non-broadcasting environments. Measurements were also made to characterize each sample of cassettes to give preliminary information on which purchase specifications could be developed. The actual tests performed on the cassettes and media before and after aging fall into the general categories listed.

  17. ATP-Binding Cassette (ABC) Transporters of the Human Respiratory Tract Pathogen, Moraxella catarrhalis: Role in Virulence.

    Science.gov (United States)

    Murphy, Timothy F; Brauer, Aimee L; Johnson, Antoinette; Kirkham, Charmaine

    2016-01-01

    Moraxella catarrhalis is a human respiratory tract pathogen that causes otitis media (middle ear infections) in children and respiratory tract infections in adults with chronic obstructive pulmonary disease. In view of the huge global burden of disease caused by M. catarrhalis, the development of vaccines to prevent these infections and better approaches to treatment have become priorities. In previous work, we used a genome mining approach that identified three substrate binding proteins (SBPs) of ATP-binding cassette (ABC) transporters as promising candidate vaccine antigens. In the present study, we performed a comprehensive assessment of 19 SBPs of 15 ABC transporter systems in the M. catarrhalis genome by engineering knockout mutants and studying their role in assays that assess mechanisms of infection. The capacity of M. catarrhalis to survive and grow in the nutrient-limited and hostile environment of the human respiratory tract, including intracellular growth, account in part for its virulence. The results show that ABC transporters that mediate uptake of peptides, amino acids, cations and anions play important roles in pathogenesis by enabling M. catarrhalis to 1) grow in nutrient-limited conditions, 2) invade and survive in human respiratory epithelial cells and 3) persist in the lungs in a murine pulmonary clearance model. The knockout mutants of SBPs and ABC transporters showed different patterns of activity in the assay systems, supporting the conclusion that different SBPs and ABC transporters function at different stages in the pathogenesis of infection. These results indicate that ABC transporters are nutritional virulence factors, functioning to enable the survival of M catarrhalis in the diverse microenvironments of the respiratory tract. Based on the role of ABC transporters as virulence factors of M. catarrhalis, these molecules represent potential drug targets to eradicate the organism from the human respiratory tract. PMID:27391026

  18. Molecular cloning and functional characterization of an ATP-binding cassette transporter OtrC from Streptomyces rimosus

    Directory of Open Access Journals (Sweden)

    Yu Lan

    2012-08-01

    Full Text Available Abstract Background The otrC gene of Streptomyces rimosus was previously annotated as an oxytetracycline (OTC resistance protein. However, the amino acid sequence analysis of OtrC shows that it is a putative ATP-binding cassette (ABC transporter with multidrug resistance function. To our knowledge, none of the ABC transporters in S. rimosus have yet been characterized. In this study, we aimed to characterize the multidrug exporter function of OtrC and evaluate its relevancy to OTC production. Results In order to investigate OtrC’s function, otrC is cloned and expressed in E. coli The exporter function of OtrC was identified by ATPase activity determination and ethidium bromide efflux assays. Also, the susceptibilities of OtrC-overexpressing cells to several structurally unrelated drugs were compared with those of OtrC-non-expressing cells by minimal inhibitory concentration (MIC assays, indicating that OtrC functions as a drug exporter with a broad range of drug specificities. The OTC production was enhanced by 1.6-fold in M4018 (P = 0.000877 and 1.4-fold in SR16 (P = 0.00973 duplication mutants, while it decreased to 80% in disruption mutants (P = 0.0182 and 0.0124 in M4018 and SR16, respectively. Conclusions The results suggest that OtrC is an ABC transporter with multidrug resistance function, and plays an important role in self-protection by drug efflux mechanisms. This is the first report of such a protein in S. rimosus, and otrC could be a valuable target for genetic manipulation to improve the production of industrial antibiotics.

  19. TSH increases synthesis of hepatic ATP-binding cassette subfamily A member 1 in hypercholesterolemia.

    Science.gov (United States)

    Zhang, Tiantian; Zhou, Lingyan; Li, Cong Cong; Shi, Hong; Zhou, Xinli

    2016-07-22

    Epidemiological evidence suggests that thyrotropin (TSH) levels are closely correlated with the severity of hypercholesterolemia. Reverse cholesterol transfer (RCT) plays an important role in regulating bloodcholesterol. However, the molecular mechanism of hypercholesterolemia in subclinical hypothyroidism (SCH) has not been fully clarified. The SCH mouse model, which is characterized by elevated serum TSH but not thyroid hormone levels, demonstrated a significant increase in plasma cholesterol compared with controls. Interestingly, Tshr KO mice, with normal thyroid hormone levels after thyroid hormone supplementation, showed lower plasma cholesterol levels compared with their wild-type littermates. ATP binding cassette subfamily A member 1(ABCA1) is a member of the ABC superfamily, which induces transfer of intracellular cholesterol to extracellular apolipoprotein. TSH upregulated hepatic ABCA1 to promote the efflux of intercellular cumulative cholesterol, resulting in increased plasma cholesterol. These data might partially explain the pathogenesis of hypercholesterolemia in SCH. PMID:27179782

  20. Protection against chemotherapy-induced alopecia: targeting ATP-binding cassette transporters in the hair follicle?

    Science.gov (United States)

    Haslam, Iain S; Pitre, Aaron; Schuetz, John D; Paus, Ralf

    2013-11-01

    Currently, efficacious treatments for chemotherapy-induced alopecia (hair loss) are lacking, and incidences of permanent hair loss following high-dose chemotherapy are on the increase. In this article, we describe mechanisms by which the pharmacological defense status of the hair follicle might be enhanced, thereby reducing the accumulation of cytotoxic cancer drugs and preventing or reducing hair loss and damage. We believe this could be achieved via the selective increase in ATP-binding cassette (ABC) transporter expression within the hair follicle epithelium, following application of topical agonists for regulatory nuclear receptors. Clinical application would require the development of hair follicle-targeted formulations, potentially utilizing nanoparticle technology. This novel approach has the potential to yield entirely new therapeutic options for the treatment and management of chemotherapy-induced alopecia, providing significant psychological and physical benefit to cancer patients. PMID:24100054

  1. Golden Gate Assembly of CRISPR gRNA expression array for simultaneously targeting multiple genes

    DEFF Research Database (Denmark)

    Vad-Nielsen, Johan; Lin, Lin; Bolund, Lars;

    2016-01-01

    The engineered CRISPR/Cas9 technology has developed as the most efficient and broadly used genome editing tool. However, simultaneously targeting multiple genes (or genomic loci) in the same individual cells using CRISPR/Cas9 remain one technical challenge. In this article, we have developed a...... Golden Gate Assembly method for the generation of CRISPR gRNA expression arrays, thus enabling simultaneous gene targeting. Using this method, the generation of CRISPR gRNA expression array can be accomplished in 2 weeks, and contains up to 30 gRNA expression cassettes. We demonstrated in the study that...

  2. The lysis cassette of DLP12 defective prophage is regulated by RpoE.

    Science.gov (United States)

    Rueggeberg, Karl-Gustav; Toba, Faustino A; Bird, Jeremy G; Franck, Nathan; Thompson, Mitchell G; Hay, Anthony G

    2015-08-01

    Expression of the lysis cassette (essD, ybcT, rzpD/rzoD) from the defective lambdoid prophage at the 12th minute of Escherichia coli's genome (DLP12) is required in some strains for proper curli expression and biofilm formation. Regulating production of the lytic enzymes encoded by these genes is critical for maintaining cell wall integrity. In lambdoid phages, late-gene regulation is mediated by the vegetative sigma factor RpoD and the lambda antiterminator Qλ. We previously demonstrated that DLP12 contains a Q-like protein (QDLP12) that positively regulates transcription of the lysis cassette, but the sigma factor responsible for this transcription initiation remained to be elucidated. In silico analysis of essDp revealed the presence of a putative - 35 and - 10 sigma site recognized by the extracytoplasmic stress response sigma factor, RpoE. In this work, we report that RpoE overexpression promoted transcription from essDp in vivo, and in vitro using purified RNAP. We demonstrate that the - 35 region is important for RpoE binding in vitro and that this region is also important for QDLP12-mediated transcription of essDp in vivo. A bacterial two-hybrid assay indicated that QDLP12 and RpoE physically interact in vivo, consistent with what is seen for Qλ and RpoD. We propose that RpoE regulates transcription of the DLP12 lysis genes through interaction with QDLP12 and that proper expression is dependent on an intact - 35 sigma region in essDp. This work provides evidence that the unique Q-dependent regulatory mechanism of lambdoid phages has been co-opted by E. coli harbouring defective DLP12 and has been integrated into the tightly controlled RpoE regulon. PMID:25998262

  3. On the integrity of a commercial cassette ultrafiltration membrane:implications for marine colloidal biogeochemistry

    Institute of Scientific and Technical Information of China (English)

    LIN Liangshi; CAI Yihua; SUN Xiuwu; CHEN Min

    2014-01-01

    The performance and integrity of a cassette cross-flow ultrafilter (Pellicon 2, Millipore) are examined with a suite of macromolecules of different molecular masses. The retention coefficient during the cross-flow ultrafiltration experiments increases with increasing molecular mass and reaches 90%with 10 kDa dextran in both milli-Q water and ultrafiltered seawater media. Based on a 90%retention coefficient, the molecular mass cut-off for the ultrafiltration membrane is defined at 10 kDa, which is ten times (1 kDa) that rated by the manufacturer. To further validate the accuracy of the laboratory calibration, the samples from the lower Zhujiang River and the Jiulong River Estuary are ultrafiltered with the cassette ultrafiltration membrane and the colloidal organic carbon abundances in these samples are quantified with the ultrafiltration per-meation model based on time series permeation subsamples. The colloidal organic carbon abundances are 5.8%-21.1%in the Jiulong River Estuary and 5.6%-11.0%in the lower Zhujiang River. These are consistent with the reported values for both estuaries as well as with the colloidal organic carbon abundances in ma-rine environments over the coastal and open oceans with 10 kDa cut-off membranes. Therefore, these field data support the laboratory calibration result and indicate the validity of the experimental and quantifica-tion procedure adopted. The discrepancy between the nominal molecular mass cut-off and the actual pore size of the ultrafiltration membrane should be of great concern for research in colloidal and nanoparticle biogeochemistry. Careful examination of the membrane integrity should be taken during ultrafiltration ex-periments in order to avoid misleading molecular mass cut-off information.

  4. The characteristics of Fugi IP Cassette Type PII and application for radiation oncology quality assurance tests and portal imaging

    International Nuclear Information System (INIS)

    Full text: The advancement of digital imaging has prompted more medical institutions to go filmless. The computed radiography (CR) system is becoming an important tool not only in diagnostic imaging, but also in radiation oncology. A new CR system that was specially designed for the use in radiation oncology. Fuji IP cassette type PII has been introduced to the market in the middle of year 2006. This project aimed to study some basic physical characteristics of this new type of cassette and explore its application for performing quality assurance (QA) tests and portal imaging in radiotherapy. All the images were read by FCR 5000 Plus reader. The image was found to reach its saturation value of 1023 (due to the image was stored in 10 bits data) by depending on the sensitivity value being adjusted. The uniformity test gave the result of 0.12%. The cassette was used to perform the QA tests which were previously performed using film. All the results met the specification as stated in AAPM Task Group 40. The comparison for the portal images of Portal Vision contrast-detail phantom showed that the spatial resolution of the images obtained by CR system (Fujifilm Co.. Ltd.. Tokyo. Japan) were better than the EPID (Varian Medical Systems. Inc.. Palo Alto. USA) and film system (Eastman Kodak Co.. New York. USA). The IP cassette type PII was found to be suitable as an alternative QA test tool and portal imaging in radiotherapy.

  5. Endotoxin deposits on the inner surfaces of closed-face cassettes during bioaerosol sampling: a field investigation at composting facilities.

    Science.gov (United States)

    Duquenne, Philippe; Simon, Xavier; Demange, Valérie; Harper, Martin; Wild, Pascal

    2015-05-01

    A set of 270 bioaerosol samples was taken from 15 composting facilities using polystyrene closed-face filter cassettes (CFCs). The objective was to measure the quantity of endotoxin deposits on the inner surfaces of the cassettes (sometimes referred to as 'wall deposits'). The results show that endotoxins are deposited on the inner surfaces of the CFCs through sampling and/or handling of samples. The quantity of endotoxins measured on inner surfaces range between 0.05 (the limit of detection of the method) and 3100 endotoxin units per cassette. The deposits can represent a large and variable percentage of the endotoxins sampled. More than a third of the samples presented a percentage of inner surface deposits >40% of the total quantity of endotoxins collected (filter + inner surfaces). Omitting these inner surface deposits in the analytical process lead to measurement errors relative to sampling all particles entering the CFC sampler, corresponding to a developing consensus on matching the inhalable particulate sampling convention. The result would be underestimated exposures and could affect the decision as to whether or not a result is acceptable in comparison to airborne concentration limits defined in terms of the inhalability convention. The results of this study suggest including the endotoxins deposited on the inner surfaces of CFCs during analysis. Further researches are necessary to investigate endotoxin deposits on the inner cassette surfaces in other working sectors. PMID:25535181

  6. New film-cassette system to obtain wider field of craniocaudal view compared with conventional technique in screening mammography

    International Nuclear Information System (INIS)

    To evaluate the efficacy of a newly designed cassette and film system used to obtain a craniocaudal (CC) image during mammographic examination. We designed a film-cassette system for use in obtaining a CC image. The merit of this system is that the contact plane between the film and film cassette and the thoracic wall of the examinee changed from linear to concave, thus including more tissue on the image. Twenty women examined by screening mammography underwent conventional and new CC plane examinations. The distance from the nipple to the posterior margin of the included breast tissue, as seen on CC mammograms, was measured using the two techniques, and the difference between the respective results was analyzed by paired t-test. The distance from the nipple to the posterior margin was 12.9±1.7cm and 14.5±1.4cm at the lateral portion of the conventional and new CC image, respectively. This distance was thus significantly greater on the new than on the conventional image (p<0.001), but there was no significant difference between their medial portions. The newly designed cassette and film system used to obtain a craniocaudal image during mammography includes more breast tissue than the conventional system and may be helpful for the mammographic screening and diagnosis of peripheral breast lesions

  7. Temperature Variations around Medication Cassette and Carry Bag in Routine Use of Epoprostenol Administration in Healthy Volunteers

    OpenAIRE

    Yuichi Tamura; Yasuo Nakajima; Yasushi Ozeki; Tomohiko Ono; Makoto Takei; Tsunehisa Yamamoto; Keiichi Fukuda

    2012-01-01

    BACKGROUND: According to several treatment guidelines, epoprostenol is an important treatment option for pulmonary arterial hypertension. However, the pharmacokinetic characteristics and poor stability of epoprostenol at room temperature make its administration challenging. We therefore studied temperature fluctuations between the drug administration cassette and atmosphere to promote the safe use of epoprostenol. METHODS AND FINDINGS: Five healthy volunteers carried a portable intravenous in...

  8. Integron gene cassettes and degradation of compounds associated with industrial waste: the case of the Sydney tar ponds.

    Directory of Open Access Journals (Sweden)

    Jeremy E Koenig

    Full Text Available Integrons are genetic platforms that accelerate lateral gene transfer (LGT among bacteria. They were first detected on plasmids bearing single and multiple drug resistance determinants in human pathogens, and it is abundantly clear that integrons have played a major role in the evolution of this public health menace. Similar genetic elements can be found in nonpathogenic environmental bacteria and in metagenomic environmental DNA samples, and it is reasonable to suppose that integrons have facilitated microbial adaptation through LGT in niches outside infectious disease wards. Here we show that a heavily impacted estuary, exposed for almost a century to products of coal and steel industries, has developed a rich and unique cassette metagenome, containing genes likely to aid in the catabolism of compounds associated with industrial waste found there. In addition, we report that the most abundant cassette recovered in this study is one that encodes a putative LysR protein. This autoregulatory transcriptional regulator is known to activate transcription of linked target genes or unlinked regulons encoding diverse functions including chlorocatechol and dichlorophenol catabolism. Finally, only class 1 integrase genes were amplified in this study despite using different primer sets, and it may be that the cassettes present in the Tar Ponds will prove to be associated with class 1 integrase genes. Nevertheless, our cassette library provides a snapshot of a complex evolutionary process involving integron-meditated LGT likely to be important in natural bioremediation.

  9. ROLE OF ATP BINDING CASSETTE SUB-FAMILY MEMBER 2 (ABCG2) IN MOUSE EMBRYONIC STEM CELL DEVELOPMENT.

    Science.gov (United States)

    ATP binding cassette sub-family member 2 (ABCG2), is a member of the ABC transporter superfamily and a principal xenobiotic transporter. ABCG2 is also highly expressed in certain stem cell populations where it is thought to be related to stem cell plasticity, although the role o...

  10. The saci_2123 gene of the hyperthermoacidophile Sulfolobus acidocaldarius encodes an ATP-binding cassette multidrug transporter

    NARCIS (Netherlands)

    Yang, Nuan; Driessen, Arnold J. M.

    2015-01-01

    Multidrug resistance (MDR) transporters are capable of secreting structurally and functionally unrelated toxic compounds from the cell. Among this group are ATP-binding cassette (ABC) transporters. These membrane proteins are typically arranged as either hetero- or homo-dimers of ABC half-transporte

  11. A new set of rDNA-NTS-based multiple integrative cassettes for the development of antibiotic-marker-free recombinant yeasts.

    Science.gov (United States)

    Moon, Hye Yun; Lee, Dong Wook; Sim, Gyu Hun; Kim, Hong-Jin; Hwang, Jee Youn; Kwon, Mun-Gyeong; Kang, Bo-Kyu; Kim, Jong Man; Kang, Hyun Ah

    2016-09-10

    The traditional yeast Saccharomyces cerevisiae has been widely used as a host system to produce recombinant proteins and metabolites of great commercial value. To engineer recombinant yeast that stably maintains expression cassettes without an antibiotic resistance gene, we developed new multiple integration cassettes by exploiting the non-transcribed spacer (NTS) of ribosomal DNA (rDNA) in combination with defective selection markers. The 5' and 3'-fragments of rDNA-NTS2 were used as flanking sequences for the expression cassettes carrying a set of URA3, LEU2, HIS3, and TRP1 selection markers with truncated promoters of different lengths. The integration numbers of NTS-based expression cassettes, ranging from one to ∼30 copies, showed a proportional increase with the extent of decreased expression of the auxotrophic markers. The NTS-based cassettes were used to construct yeast strains expressing the capsid protein of red-spotted grouper necrosis virus (RG-NNVCP) in a copy number-dependent manner. Oral administration of the recombinant yeast, harboring ∼30 copies of the integrated RG-NNVCP cassettes, provoked efficient immune responses in mice. In contrast, for the NTS cassettes expressing a truncated 3-hydroxyl-3-methylglutaryl-CoA reductase, the integrant carrying only 4 copies was screened as the highest producer of squalene, showing a 150-fold increase compared to that of the wild-type strain. The multiple integrated cassettes were stably retained under prolonged nonselective conditions. Altogether, our results strongly support that rDNA-NTS integrative cassettes are useful tools to construct recombinant yeasts carrying optimal copies of a desired expression cassette without an antibiotic marker gene, which are suitable as oral vaccines or feed additives for animal and human consumption. PMID:27411901

  12. Pharmacophore Modeling of Nilotinib as an Inhibitor of ATP-Binding Cassette Drug Transporters and BCR-ABL Kinase Using a Three-Dimensional Quantitative Structure–Activity Relationship Approach

    OpenAIRE

    Shukla, Suneet; Kouanda, Abdul; Silverton, Latoya; Talele, Tanaji T.; Suresh V Ambudkar

    2014-01-01

    Nilotinib (Tasigna) is a tyrosine kinase inhibitor approved by the FDA to treat chronic phase chronic myeloid leukemia patients. It is also a transport substrate of the ATP-binding cassette (ABC) drug efflux transporters ABCB1 (P-glycoprotein, P-gp) and ABCG2 (BCRP), which may have an effect on the pharmacokinetics and toxicity of this drug. The goal of this study was to identify pharmacophoric features of nilotinib in order to potentially develop specific inhibitors of BCR-ABL kinase with mi...

  13. Sensor arrays for detecting microorganisms

    Science.gov (United States)

    Lewis, Nathan S. (Inventor); Freund, Michael S. (Inventor)

    2000-01-01

    A sensor array for detecting a microorganism comprising first and second sensors electrically connected to an electrical measuring apparatus, wherein the sensors comprise a region of nonconducting organic material and a region of conducting material compositionally that is different than the nonconducting organic material and an electrical path through the regions of nonconducting organic material and the conducting material. A system for identifying microorganisms using the sensor array, a computer and a pattern recognition algorithm, such as a neural net are also disclosed.

  14. Novel pseudo-staphylococcal cassette chromosome mec element (ψSCCmec57395) in methicillin-resistant Staphylococcus pseudintermedius CC45.

    Science.gov (United States)

    Perreten, Vincent; Chanchaithong, Pattrarat; Prapasarakul, Nuvee; Rossano, Alexandra; Blum, Shlomo E; Elad, Daniel; Schwendener, Sybille

    2013-11-01

    Genetic characterization of methicillin-resistant Staphylococcus pseudintermedius (MRSP) from Thailand and Israel revealed the presence of a predominant atypical clonal lineage which was not typeable by SmaI-PFGE and SCCmec typing. All the atypical isolates (n = 34) belonged to CC45 (30 ST45 and 2 ST179 isolates, 1 ST57 isolate, and 1 ST85 isolate). The isolates originated from healthy and diseased dogs and cats, as well as from the environment of one clinic. Cfr9I-pulsed-field gel electrophoresis (Cfr9I-PFGE) and dru typing permitted the further distinction of CC45 isolates from the two different countries. Microarray analysis identified genes that confer resistance to β-lactams (mecA; blaZ), aminoglycosides [aac(6')-Ie-aph(2')-Ia; aph(3')-III; ant(6)-Ia], macrolides and lincosamides [erm(B)], tetracyclines [tet(M)], trimethoprim [dfr(G)], streptothricin (sat4), and chloramphenicol (catpC221). Fluoroquinolone resistance was attributed to specific amino acid substitutions, i.e., Ser84Leu in GyrA and Ser80Ile and Asp84Asn in GrlA. A novel pseudo-staphylococcal cassette chromosome (ΨSCCmec57395) element was identified in MRSP strain 57395 (sequence type ST45) by whole-genome sequencing. The 12,282-bp ΨSCCmec57395 element contained a class C1 mec gene complex but no ccr genes. In addition to the methicillin resistance gene mecA, ΨSCCmec57395 also carried determinants of resistance to heavy metals, such as arsenic, cadmium, and copper. Bsu36I restriction analysis of the ΨSCCmec57395 element amplified by long-range PCR revealed the presence of ΨSCCmec57395 in the 33 additional isolates of MRSP CC45. The ΨSCCmec57395 element represents a new class of SCCmec and has been identified in MRSP of CC45, which is a predominant clonal lineage in Israel and Thailand. PMID:23979735

  15. 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.

  16. Cooperative transcriptional activation of ATP-binding cassette sterol transporters ABCG5 and ABCG8 genes by nuclear receptors including Liver-X-Receptor

    Directory of Open Access Journals (Sweden)

    Su Sun Back

    2013-06-01

    Full Text Available The ATP-binding cassette transporters ABCG5 and ABCG8 formheterodimers that limit absorption of dietary sterols in theintestine and promote cholesterol elimination from the bodythrough hepatobiliary secretion. To identify cis-regulatoryelements of the two genes, we have cloned and analyzedtwenty-three evolutionary conserved region (ECR fragmentsusing the CMV-luciferase reporter system in HepG2 cells. TwoECRs were found to be responsive to the Liver-X-Receptor (LXR.Through elaborate deletion studies, regions containing putativeLXREs were identified and the binding of LXRα wasdemonstrated by EMSA and ChIP assay. When the LXREs wereinserted upstream of the intergenic promoter, synergisticactivation by LXRα/RXRα in combination with GATA4, HNF4α,and LRH-1, which had been shown to bind to the intergenicregion, was observed. In conclusion, we have identified twoLXREs in ABCG5/ABCG8 genes for the first time and proposethat these LXREs, especially in the ECR20, play major roles inregulating these genes. [BMB Reports 2013; 46(6: 322-327

  17. Use of DNA arrays to identify a mutation in the negative regulator, csrR, responsible for the high virulence of a naturally occurring type M3 group A streptococcus clinical isolate.

    Science.gov (United States)

    Miyoshi-Akiyama, Tohru; Ikebe, Tadayoshi; Watanabe, Haruo; Uchiyama, Takehiko; Kirikae, Teruo; Kawamura, Yoshiaki

    2006-06-15

    We previously reported that type M3 group A streptococcus (GAS) showed a wide range of 50% lethal dose values in mice. Analysis using DNA arrays indicated that the most virulent strain, M3-f, expressed significantly higher levels of the products of several virulence genes than did the other M3 isolates. Sequencing of the csrS, csrR, luxS, and rgg genes in the isolates showed that the M-3f csrR gene contained a specific point mutation. Disruption of wild-type (wt) csrR in an M3 strain increased its virulence and the expression of hyaluronic acid, whereas complementation with wt but not type M3-f csrR attenuated these changes. Expression experiments showed that type M3-f CsrR counteracted the effects of wt CsrR. Although wt CsrR bound to the hasA promoter region, type M3-f CsrR did not. Thus, the high virulence of the type M3-f strain is associated with the decreased binding of type M3-f CsrR to its target sequences. PMID:16703511

  18. Plug-and-Play Genetic Access to Drosophila Cell Types Using Exchangeable Exon Cassettes

    Science.gov (United States)

    Diao, Fengqiu; Ironfield, Holly; Luan, Haojiang; Diao, Feici; Shropshire, William C.; Ewer, John; Marr, Elizabeth; Potter, Christopher J.; Landgraf, Matthias; White, Benjamin H.

    2015-01-01

    Summary Genetically encoded effectors are important tools for probing cellular function in living animals, but improved methods for directing their expression to specific cell types are required. Here we introduce a simple, versatile method for achieving cell type-specific expression of transgenes that leverages the untapped potential of “coding introns” (i.e. introns between coding exons). Our method couples the expression of a transgene to that of a native gene expressed in the cells of interest using intronically inserted “plug-and-play” cassettes (called “Trojan exons”) that carry a splice acceptor site followed by the coding sequences of T2A peptide and an effector transgene. We demonstrate the efficacy of this approach in Drosophila using lines containing suitable MiMIC transposons and a palette of Trojan exons capable of expressing a range of commonly used transcription factors. We also introduce an exchangeable, MiMIC-like Trojan exon construct that can be targeted to coding introns using the Crispr/Cas system. PMID:25732830

  19. The effects on hearing from portable cassette players: A follow-up study

    Science.gov (United States)

    Hellström, P. A.

    1991-12-01

    The high-frequency hearing loss (3-8 kHz) in 230 male and 238 female subjects (age 16) was compared concerning their habits of listening to portable cassette players (PCPs). In the group that listened to PCPs daily, we found fewer subjects with high-frequency hearing loss compared to the group that never listened to PCPs. In a temporary threshold shift (TTS) study, three groups of subjects with different listening habits to music were exposed to {1}/{3} octave band noise (2 kHz). These groups participated in a TTS study on another occasion, on which they listened to music from PCPs at a high but comfortable level for 1 hour. Together with the music exposure, the sound pressure level ( SPL) was measured in the external auditory canal with a probe-provided mini-microphone (MMP). There was no significant difference in TTS between groups from the noise exposure. There were significant differences in listening levels and in the resulting TTS between groups. The noise exposure resulted in significantly higher TTS than the music exposure at comparable exposure levels.

  20. Multidrug ATP-binding cassette transporters are essential for hepatic development of Plasmodium sporozoites.

    Science.gov (United States)

    Rijpma, Sanna R; van der Velden, Maarten; González-Pons, Maria; Annoura, Takeshi; van Schaijk, Ben C L; van Gemert, Geert-Jan; van den Heuvel, Jeroen J M W; Ramesar, Jai; Chevalley-Maurel, Severine; Ploemen, Ivo H; Khan, Shahid M; Franetich, Jean-Francois; Mazier, Dominique; de Wilt, Johannes H W; Serrano, Adelfa E; Russel, Frans G M; Janse, Chris J; Sauerwein, Robert W; Koenderink, Jan B; Franke-Fayard, Blandine M

    2016-03-01

    Multidrug resistance-associated proteins (MRPs) belong to the C-family of ATP-binding cassette (ABC) transport proteins and are known to transport a variety of physiologically important compounds and to be involved in the extrusion of pharmaceuticals. Rodent malaria parasites encode a single ABC transporter subfamily C protein, whereas human parasites encode two: MRP1 and MRP2. Although associated with drug resistance, their biological function and substrates remain unknown. To elucidate the role of MRP throughout the parasite life cycle, Plasmodium berghei and Plasmodium falciparum mutants lacking MRP expression were generated. P. berghei mutants lacking expression of the single MRP as well as P. falciparum mutants lacking MRP1, MRP2 or both proteins have similar blood stage growth kinetics and drug-sensitivity profiles as wild type parasites. We show that MRP1-deficient parasites readily invade primary human hepatocytes and develop into mature liver stages. In contrast, both P. falciparum MRP2-deficient parasites and P. berghei mutants lacking MRP protein expression abort in mid to late liver stage development, failing to produce mature liver stages. The combined P. berghei and P. falciparum data are the first demonstration of a critical role of an ABC transporter during Plasmodium liver stage development. PMID:26332724

  1. Molecular Characterization of LjABCG1, an ATP-Binding Cassette Protein in Lotus japonicus.

    Directory of Open Access Journals (Sweden)

    Akifumi Sugiyama

    Full Text Available LjABCG1, a full-size ABCG subfamily of ATP-binding cassette proteins of a model legume, Lotus japonicus, was reported as a gene highly expressed during the early stages of nodulation, but have not been characterized in detail. In this study we showed that the induction of LjABCG1 expression was remarkable by methyl jasmonate treatment, and reporter gene experiments indicated that LjABCG1 was strongly expressed in the nodule parenchyma and cell layers adjacent to the root vascular tissue toward the nodule. LjABCG1 was suggested to be localized at the plasma membrane based on the fractionation of microsomal membranes as well as separation via aqueous two-phase partitioning. The physiological functions of LjABCG1 in symbiosis and pathogenesis were analyzed in homologous and heterologous systems. LjABCG1 knock-down L. japonicus plants did not show clear phenotypic differences in nodule formation, and not in defense against Pseudomonas syringae, either. In contrast, when LjABCG1 was expressed in the Arabidopsis pdr8-1 mutant, the penetration frequency of Phytophthora infestans, a potato late blight pathogen, was significantly reduced in LjABCG1/pdr8-1 than in pdr8-1 plants. This finding indicated that LjABCG1, at least partially, complemented the phenotype of pdr8 in Arabidopsis, suggesting the multiple roles of this protein in plant-microbe interactions.

  2. ATP-binding cassette transporters as pitfalls in selection of transgenic cells.

    Science.gov (United States)

    Theile, Dirk; Staffen, Bianca; Weiss, Johanna

    2010-04-15

    Puromycin, hygromycin, and geneticin (G418) are antibiotics frequently used to select genetically engineered eukaryotic cells after transfection or transduction. Because intrinsic or acquired high expression of ATP-binding cassette (ABC) transporters, such as P-glycoprotein (Pgp/ABCB1) and multidrug resistance-associated proteins (MRP/ABCC1), can hamper efficient selection, it is important to know whether these antibiotics are substrates and/or inducers of efflux transporters. Therefore, we investigated the influence of these antibiotics on drug transporter expression by quantitative real-time polymerase chain reaction in the induction model cell line LS180. Moreover, we assessed whether ABC transporters influence the growth inhibitory effects of these antibiotics by proliferation assays using Madin-Darby canine kidney II (MDCKII) cells overexpressing the particular transporter. The results obtained indicate that puromycin and G418 are substrates of several ABC transporters, mainly Pgp/ABCB1. In contrast, hygromycin seems to be no good substrate for any of the ABC transporters investigated. Puromycin induced ABCC1/MRP1, whereas G418 suppressed ABCB1/Pgp, at the messenger RNA (mRNA) level. In contrast, hygromycin had no effect on ABC transporter mRNA expressions. In conclusion, this study emphasizes the significance of ABC transporters for the efficacy of selection processes. Consciousness of the results is supposed to guide the molecular biologist to the right choice of adequate experimental conditions for successful selection of genetically engineered eukaryotic cells. PMID:20018165

  3. Product Variability of the ‘Cineole Cassette'Monoterpene Synthases of Related Nicotiana Species

    Institute of Scientific and Technical Information of China (English)

    Anke F(a)hnrich; Katrin Krause; Birgit Piechulla

    2011-01-01

    Nicotiana species of the section Alatae characteristically emit the floral scent compounds of the ‘cineole cassere' comprising 1,8-cineole,limonene,myrcene,α-pinene,β-pinene,sabinene,and α-terpineol.We successfully isolated genes of Nicotiana alata and Nicotiana langsdorfii that encoded enzymes,which produced the characteristic monoterpenes of this ‘cineole cassette' with α-terpineol being most abundant in the volatile spectra.The amino acid sequences of both terpineol synthases were 99% identical.The enzymes cluster in a monophyletic branch together with the closely related cineole synthase of Nicotiana suaveolens and monoterpene synthase 1 of Solanum lycopersicum.The cyclization reactions (α-terpineol to 1,8-cineole) of the terpineol synthases of N.alata and N.langsdorfii were less efficient compared to the ‘cineole cassette′ monoterpene synthases of Arabidopsis thaliana,N.suaveolens,Salvia fruticosa,Salvia officinalis,and Citrus unshiu.The terpineol synthases of N.alata and N.langsdorfii were localized in pistils and in the adaxial and abaxial epidermis of the petals.The enzyme activities reached their maxima at the second day after anthesis when flowers were fully opened and the enzyme activity in N.alata was highest at the transition from day to night (diurnal rhythm).

  4. Human T24 Ha-ras cassette suitable for expression in eukaryotic cells

    Energy Technology Data Exchange (ETDEWEB)

    Bailleul, B.; Lang, J.; Wilkie, N.; Balmain, A.

    1988-01-11

    The T24 Ha-ras-1 oncogene is known to transform a wide range of eukaryotic cell types both in vivo and in vitro. Interpretation of the role played by ras genes in transformed cells would clearly by aided by employing a biological system capable of regulating ras p21 production. This can be achieved by substitution of the transcriptional control signals of Ha-ras with heterologous eukaryotic promoters. In this way, ras p21 may be expressed at high or low levels or inducibly expressed, depending on the promoter used. To facilitate construction of ras fusion genes, the authors have produced a T24 Ha-ras a cassette containing multiple cloning sites 5' to the Ha-ras coding exons. The polyadenylic site and the VTR region have been retained while the splice acceptor site upstream the ATG initiator codon has been deleted. The pR8-T24 construct should be useful for a variety of research applications, allowing insertion of any desired promoter into the 5' polylinker. In addition, potential regulatory elements could be inserted at the 3' end using the BamH1 site. This plasmid provides a great deal of flexibility in designing constructs which facilitate ras p21 expression in different cell types, either by transfection in vitro or in transgenic mice in vivo.

  5. Energy use of televisions and video cassette recorders in the U.S.

    Energy Technology Data Exchange (ETDEWEB)

    Meier, Alan; Rosen, Karen

    1999-03-01

    In an effort to more accurately determine nationwide energy consumption, the U.S. Department of Energy has recently commissioned studies with the goal of improving its understanding of the energy use of appliances in the miscellaneous end-use category. This study presents an estimate of the residential energy consumption of two of the most common domestic appliances in the miscellaneous end-use category: color televisions (TVs) and video cassette recorders (VCRs). The authors used a bottom-up approach in estimating national TV and VCR energy consumption. First, they obtained estimates of stock and usage from national surveys, while TV and VCR power measurements and other data were recorded at repair and retail shops. Industry-supplied shipment and sales distributions were then used to minimize bias in the power measurement samples. To estimate national TV and VCR energy consumption values, ranges of power draw and mode usage were created to represent situations in homes with more than one unit. Average energy use values for homes with one unit, two units, etc. were calculated and summed to provide estimates of total national TV and VCR energy consumption.

  6. ATP-Binding Cassette Proteins: Towards a Computational View of Mechanism

    Science.gov (United States)

    Liao, Jielou

    2004-03-01

    Many large machine proteins can generate mechanical force and undergo large-scale conformational changes (LSCC) to perform varying biological tasks in living cells by utilizing ATP. Important examples include ATP-binding cassette (ABC) transporters. They are membrane proteins that couple ATP binding and hydrolysis to the translocation of substrates across membranes [1]. To interpret how the mechanical force generated by ATP binding and hydrolysis is propagated, a coarse-grained ATP-dependent harmonic network model (HNM) [2,3] is applied to the ABC protein, BtuCD. This protein machine transports vitamin B12 across membranes. The analysis shows that subunits of the protein move against each other in a concerted manner. The lowest-frequency modes of the BtuCD protein are found to link the functionally critical domains, and are suggested to be responsible for large-scale ATP-coupled conformational changes. [1] K. P. Locher, A. T. Lee and D. C. Rees. Science 296, 1091-1098 (2002). [2] Atilgan, A. R., S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar. Biophys. J. 80, 505-515(2002); M. M Tirion, Phys. Rev. Lett. 77, 1905-1908 (1996). [3] J. -L. Liao and D. N. Beratan, 2003, to be published.

  7. A novel ATP-binding cassette transporter, ABCG6 is involved in chemoresistance of Leishmania.

    Science.gov (United States)

    BoseDasgupta, Somdeb; Ganguly, Agneyo; Roy, Amit; Mukherjee, Tanmoy; Majumder, Hemanta K

    2008-04-01

    ATP-binding cassette (ABC) transporters constitute the biggest family of membrane proteins involved in drug resistance and other biological activities. Resistance of leishmanial parasites to therapeutic drugs continues to escalate in developing countries and in many instances it is due to overexpressed ABC efflux pumps. Progressively adapted camptothecin (CPT)-resistant parasites show overexpression of a novel ABC transporter, which was classified as ABCG6. Transfection and overexpression of LdABCG6 in wild type parasites, shows its localization primarily in the plasma membrane and flagellar pocket region. Overexpressed LdABCG6 confers substantial CPT resistance to the parasites by rapid drug efflux. Various inhibitors have been tested for their ability to revert the CPT-resistant phenotype to specifically understand the inhibition of LdABCG6 transporter. Transport experiments using everted membrane vesicles were carried out to gain an insight into the kinetics of drug transport. This study provides further knowledge of specific membrane traffic ATPase and its involvement in the chemoresistance of Leishmania. PMID:18243364

  8. False positives observed on the Seratec® PSA SemiQuant Cassette Test with condom lubricants.

    Science.gov (United States)

    Bitner, Sara E

    2012-11-01

    In the course of the validation of a new component of the prostate-specific antigen (PSA) SemiQuant Cassette Test marketed by Seratec(®) , a false-positive reaction was observed when testing samples collected from the surface of unused, lubricated condoms. A variety of personal lubricants and condoms were tested to determine the frequency of the false positive, as well as its potential source. Samples were extracted in both water and the manufacturer-provided buffer, and the test was performed according to the manufacturer's suggested protocol. The false positive was observed intermittently, but occurred consistently with samples containing nonoxynol-9, a strong detergent utilized as a spermicide. The reaction may be attributable to the combination of latex and nonoxynol-9. Because of the unreliability of the test to confirm the presence of PSA in samples collected from condoms, the PSA cassette is an unsuitable method for confirming the presence of seminal fluid in condoms. PMID:22494324

  9. Genome-wide identification and characterization of ATP-binding cassette transporters in the silkworm, Bombyx mori

    Directory of Open Access Journals (Sweden)

    Zhang Jianzhen

    2011-10-01

    Full Text Available Abstract Background The ATP-binding cassette (ABC transporter superfamily is the largest transporter gene family responsible for transporting specific molecules across lipid membranes in all living organisms. In insects, ABC transporters not only have important functions in molecule transport, but also play roles in insecticide resistance, metabolism and development. Results From the genome of the silkworm, Bombyx mori, we have identified 51 putative ABC genes which are classified into eight subfamilies (A-H by phylogenetic analysis. Gene duplication is very evident in the ABCC and ABCG subfamilies, whereas gene numbers and structures are well conserved in the ABCD, ABCE, ABCF, and ABCH subfamilies. Microarray analysis revealed that expression of 32 silkworm ABC genes can be detected in at least one tissue during different developmental stages, and the expression patterns of some of them were confirmed by quantitative real-time PCR. A large number of ABC genes were highly expressed in the testis compared to other tissues. One of the ABCG genes, BmABC002712, was exclusively and abundantly expressed in the Malpighian tubule implying that BmABC002712 plays a tissue-specific role. At least 5 ABCG genes, including BmABC005226, BmABC005203, BmABC005202, BmABC010555, and BmABC010557, were preferentially expressed in the midgut, showing similar developmental expression profiles to those of 20-hydroxyecdysone (20E-response genes. 20E treatment induced the expression of these ABCG genes in the midgut and RNA interference-mediated knockdown of USP, a component of the 20E receptor, decreased their expression, indicating that these midgut-specific ABCG genes are 20E-responsive. Conclusion In this study, a genome-wide analysis of the silkworm ABC transporters has been conducted. A comparison of ABC transporters from 5 insect species provides an overview of this vital gene superfamily in insects. Moreover, tissue- and stage-specific expression data of the

  10. Seismometer array station processors

    International Nuclear Information System (INIS)

    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)

  11. A Novel Multiplex Real-Time PCR Assay for Rapid Typing of Major Staphylococcal Cassette Chromosome mec Elements

    Science.gov (United States)

    Francois, Patrice; Renzi, Gesuele; Pittet, Didier; Bento, Manuela; Lew, Daniel; Harbarth, Stephan; Vaudaux, Pierre; Schrenzel, Jacques

    2004-01-01

    We describe a novel procedure for rapid typing of the staphylococcal cassette chromosome mec element, a molecular marker allowing discrimination between community- and hospital-acquired methicillin-resistant Staphylococcus aureus (MRSA) strains. Oligonucleotides targeting the recombinase genes were type specific and used to type a collection of 399 MRSA isolates recovered during patient screening at admission. This novel assay constitutes a valuable tool for evaluating the molecular epidemiology of MRSA and adjusting infection control strategies against MRSA. PMID:15243102

  12. A Novel Multiplex Real-Time PCR Assay for Rapid Typing of Major Staphylococcal Cassette Chromosome mec Elements

    OpenAIRE

    Francois, Patrice; Renzi, Gesuele; Pittet, Didier; Bento, Manuela; Lew, Daniel; Harbarth, Stephan; Vaudaux, Pierre; Schrenzel, Jacques

    2004-01-01

    We describe a novel procedure for rapid typing of the staphylococcal cassette chromosome mec element, a molecular marker allowing discrimination between community- and hospital-acquired methicillin-resistant Staphylococcus aureus (MRSA) strains. Oligonucleotides targeting the recombinase genes were type specific and used to type a collection of 399 MRSA isolates recovered during patient screening at admission. This novel assay constitutes a valuable tool for evaluating the molecular epidemiol...

  13. Expression of the domain cassette 8 Plasmodium falciparum erythrocyte membrane protein 1 is associated with cerebral malaria in Benin

    DEFF Research Database (Denmark)

    Bertin, Gwladys I; Lavstsen, Thomas; Guillonneau, François;

    2013-01-01

    Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP-1) is a highly polymorphic adherence receptor expressed on the surface of infected erythrocytes. Based on sequence homology PfEMP-1 variants have been grouped into three major groups A-C, the highly conserved VAR2CSA variants, and semi......-conserved types defined by tandem runs of specific domains ("domain cassettes" (DC)). The PfEMP-1 type expressed determines the adherence phenotype, and is associated with clinical outcome of infection....

  14. Staphylococcal Cassette Chromosome mec and Panton-Valentine Leukocidin Characterization of Methicillin-Resistant Staphylococcus aureus Clones▿

    OpenAIRE

    Moroney, Shannon M.; Heller, Loree C.; Arbuckle, Jesse; Talavera, Monica; Widen, Ray H.

    2006-01-01

    Staphylococcal cassette chromosome mec (SCCmec) types and Panton-Valentine leukocidin (PVL) gene carriage were compared among suspected community-associated methicillin-resistant Staphylococcus aureus MRSA (CA-MRSA) and health care-associated MRSA (HA-MRSA) isolates. CA-MRSA isolates carried the SCCmec type IV complex, and most were PVL positive. The HA-MRSA isolates carried the SCCmec type II complex and did not harbor the PVL genes.

  15. Spatial normalization of array-CGH data.

    OpenAIRE

    Brennetot Caroline; Manié Élodie; Liva Stéphane; Brito Isabel; Hupé Philippe; Neuvial Pierre; Radvanyi François; Aurias Alain; Barillot Emmanuel

    2006-01-01

    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: continu...

  16. Spatial normalization of array-CGH data.

    OpenAIRE

    Neuvial, Pierre; Hupé, Philippe; Brito, Isabel; Liva, Stéphane; Manié, Elodie; Brennetot, Caroline; Radvanyi, François; Aurias, Alain; Barillot, Emmanuel

    2006-01-01

    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 spat...

  17. Construction of Synthetic Promoter-Based Expression Cassettes for the Production of Cadaverine in Recombinant Corynebacterium glutamicum.

    Science.gov (United States)

    Oh, Young Hoon; Choi, Jae Woo; Kim, Eun Young; Song, Bong Keun; Jeong, Ki Jun; Park, Kyungmoon; Kim, Il-Kwon; Woo, Han Min; Lee, Seung Hwan; Park, Si Jae

    2015-08-01

    Corynebacterium glutamicum is an important microorganism in the biochemical industry for the production of various platform chemicals. However, despite its importance, a limited number of studies have been conducted on how to constitute gene expression cassettes in engineered C. glutamicum to obtain desired amounts of the target products. Therefore, in this study, six expression cassettes for the expression of the second lysine decarboxylase of Escherichia coli, LdcC, were constructed using six synthetic promoters with different strengths and were examined in C. glutamicum for the production of cadaverine. Among six expression cassettes, the expression of the E. coli ldcC gene under the PH30 promoter supported the highest production of cadaverine in flask and fed-batch cultivations. A fed-batch fermentation of recombinant C. glutamicum expressing E. coli ldcC gene under the PH30 promoter resulted in the production of 40.91 g/L of cadaverine in 64 h. This report is expected to contribute toward developing engineered C. glutamicum strains to have desired features. PMID:26047931

  18. Molecular Events Involved in a Single Cycle of Ligand Transfer from an ATP Binding Cassette Transporter, LolCDE, to a Molecular Chaperone, LolA*

    OpenAIRE

    Taniguchi, Naohiro; Tokuda, Hajime

    2008-01-01

    An ATP binding cassette transporter LolCDE complex releases lipoproteins from the inner membrane of Escherichia coli in an ATP-dependent manner, leading to the formation of a complex between a lipoprotein and a periplasmic chaperone, LolA. LolA is proposed to undergo a conformational change upon the lipoprotein binding. The lipoprotein is then transferred from the LolA-lipoprotein complex to the outer membrane via LolB. Unlike most ATP binding cassette transporters med...

  19. A new method to identify flanking sequence tags in chlamydomonas using 3’-RACE

    OpenAIRE

    Meslet-Cladière Laurence; Vallon Olivier

    2012-01-01

    Abstract Background The green alga Chlamydomonas reinhardtii, although a premier model organism in biology, still lacks extensive insertion mutant libraries with well-identified Flanking Sequence Tags (FSTs). Rapid and efficient methods are needed for FST retrieval. Results Here, we present a novel method to identify FSTs in insertional mutants of Chlamydomonas. Transformants can be obtained with a resistance cassette lacking a 3’ untranslated region (UTR), suggesting that the RNA that is pro...

  20. Hemocompatibility of titania nanotube arrays.

    Science.gov (United States)

    Smith, Barbara S; Yoriya, Sorachon; Grissom, Laura; Grimes, Craig A; Popat, Ketul C

    2010-11-01

    Hemocompatibility is a key consideration for the long-term success of blood contacting biomaterials; hence, there is a critical need to understand the physiological response elicited from blood/nano-biomaterial interactions. In this study, we have investigated the adsorption of key blood serum proteins, in vitro adhesion and activation of platelets, and clotting kinetics of whole blood on titania nanotube arrays. Previous studies have demonstrated improved mesenchymal stem cell functionality, osteoblast phenotypic behavior, localized drug delivery, and the production of endothelial cell ECM on titania nanotube arrays. Furthermore, these titania nanotube arrays have elicited minimal levels of monocyte activation and cytokine secretion, thus exhibiting a very low degree of immunogenicity. Titania nanotube arrays were fabricated using anodization technique and the surface morphology was examined through scanning electron microscopy (SEM). The crystalline phases were identified using glancing angled X-ray diffraction (GAXRD). Nanoindentation and scratch tests were used to characterize the mechanical properties of titania nanotube arrays. The adsorption of key blood proteins (albumin, fibrinogen, and immunoglobulin-g) was evaluated using a micro-BCA assay and X-ray photoelectron spectroscopy (XPS). The adhesion and activation of platelets was investigated using live-cell staining, MTT assay, and SEM. Whole blood clotting kinetics was evaluated by measuring the free hemoglobin concentration, and SEM was used to visualize the clot formation. Our results indicate increased blood serum protein adsorption, platelet adhesion and activation, and whole blood clotting kinetics on titania nanotube arrays. PMID:20629021

  1. The Lophotrochozoan TGF-β signalling cassette - diversification and conservation in a key signalling pathway.

    Science.gov (United States)

    Kenny, Nathan J; Namigai, Erica K O; Dearden, Peter K; Hui, Jerome H L; Grande, Cristina; Shimeld, Sebastian M

    2014-01-01

    TGF-β signalling plays a key role in the patterning of metazoan body plans and growth. It is widely regarded as a 'module' capable of co-option into novel functions. The TGF-β pathway arose in the Metazoan lineage, and while it is generally regarded as well conserved across evolutionary time, its components have been largely studied in the Ecdysozoa and Deuterostomia. The recent discovery of the Nodal molecule in molluscs has underlined the necessity of untangling this signalling network in lophotrochozoans in order to truly comprehend the evolution, conservation and diversification of this key pathway. Three novel genome resources, the mollusc Patella vulgata, annelid Pomatoceros lamarcki and rotifer Brachionus plicatilis, along with other publicly available data, were searched for the presence of TGF-β pathway genes. Bayesian and Maximum Likelihood analyses, along with some consideration of conserved domain structure, was used to confirm gene identity. Analysis revealed conservation of key components within the canonical pathway, allied with extensive diversification of TGF-β ligands and partial loss of genes encoding pathway inhibitors in some lophotrochozoan lineages. We fully describe the TGF-β signalling cassette of a range of lophotrochozoans, allowing firm inference to be drawn as to the ancestral state of this pathway in this Superphylum. The TGF-β signalling cascade's reputation as being highly conserved across the Metazoa is reinforced. Diversification within the activin-like complement, as well as potential wide loss of regulatory steps in some Phyla, hint at specific evolutionary implications for aspects of this cascade's functionality in this Superphylum. PMID:25690968

  2. Endothelial ATP-binding cassette G1 in mouse endothelium protects against hemodynamic-induced atherosclerosis.

    Science.gov (United States)

    Xue, Shanshan; Wang, Jiaxing; Zhang, Xu; Shi, Ying; Li, Bochuan; Bao, Qiankun; Pang, Wei; Ai, Ding; Zhu, Yi; He, Jinlong

    2016-08-19

    Activated vascular endothelium inflammation under persistent hyperlipidemia is the initial step of atherogenesis. ATP-binding cassette G1 (ABCG1) is a crucial factor maintaining sterol and lipid homeostasis by transporting cholesterol efflux to high-density lipoprotein. In this study, we investigated the protective effects of ABCG1 in endothelial inflammation activation during early-stage atherogenesis in mice and the underlying mechanisms. Endothelial cell (EC)-specific ABCG1 transgenic (EC-ABCG1-Tg) mice were generated and cross-bred with low-density lipoprotein receptor-deficient (Ldlr(-/-)) mice. After a 4-week Western-type diet, the mice were sacrificed for assessing atherosclerosis. Human umbilical vein ECs were treated with different flows, and ABCG1 was adenovirally overexpressed to investigate the mechanism in vitro. Compared with Ldlr(-/-) mouse aortas, EC-ABCG1-Tg/Ldlr(-/-) aortas showed decreased early-stage lesions. Furthermore, the lesion area in the EC-ABCG1-Tg/Ldlr(-/-) mouse aortic arch but not thoracic aorta was significantly reduced, which suggests a protective role of ABCG1 under atheroprone flow. In vitro, overexpression of ABCG1 attenuated EC activation caused by oscillatory shear stress. Overexpression of ABCG1 blunted cholesterol-activated ECs in vitro. In exploring the mechanisms of ABCG1 attenuating endothelial inflammation, we found that ABCG1 inhibited oscillatory flow-activated nuclear factor kappa B and NLRP3 inflammasome in ECs. ABCG1 may play a protective role in early-stage atherosclerosis by reducing endothelial activation induced by oscillatory shear stress via suppressing the inflammatory response. PMID:27297110

  3. Development of remote pipe cutting tool for divertor cassettes in JT-60SA

    International Nuclear Information System (INIS)

    Remote pipe cutting tool accessing from inside pipe has been newly developed for JT-60SA. The tool head equips a disk-shaped cutter blade and four rollers which are subjected to the reaction force. The tool pushes out the cutter blade by decreasing the distance between two cams. The tool cuts a cooling pipe by both pushing out the cutter blade and rotating the tool head itself. The roller holder is not pushed out anymore after touching the inner wall of the pipe. In other words, only cutter blade is pushed out after bringing the tool axis into the pipe axis. Outer diameter of the cutting tool head is 44 mm. The cutting tool is able to push out the cutter blade up to 32.5 mm in radius, i.e. 65 mm in diameter, which is enough to cut the pipe having an outer diameter of 59.8 mm. The thickness and material of the cooling pipe are 2.8 mm and SUS316L, respectively. The length of the cutting tool head is about 1 m. The tool is able to cut a pipe locates about 480 mm in depth from the mounting surface on the divertor cassette. The pipe cutting system equips two cutting heads and they are able to cut two pipes at the same time in order to remove the inner target plate. Reproducibility of the cross-sectional shape of the cut pipe is required for re-welding. The degree of reproducibility is inside 0.1 mm except for burr at outside of the pipe, which is enough to re-weld the cut pipe. Some swarf is generated during cutting the double-layered pipe assuming a plug located on the top of the pipe. The swarf is deposited on the bottom of the plug and collected by pulling out the plug in the actual equipment

  4. Population dynamics and current-generation mechanisms in cassette-electrode microbial fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Kazuya [ERATO/JST, Tokyo (Japan). Hashimoto Light Energy Conversion Project; Tokyo Univ. (Japan). Research Center for Advanced Science and Technology; Tokyo Univ. of Pharmacy and Life Sciences (Japan). School of Life Sciences; Miyahara, Morio [ERATO/JST, Tokyo (Japan). Hashimoto Light Energy Conversion Project; Shimoyama, Takefumi [Tokyo Univ. (Japan). Research Center for Advanced Science and Technology; Hashimoto, Kazuhito [ERATO/JST, Tokyo (Japan). Hashimoto Light Energy Conversion Project; Tokyo Univ. (Japan). Dept. of Applied Chemistry

    2011-12-15

    Cassette-electrode microbial fuel cells (CE-MFCs) have been demonstrated useful to treat biomass wastes and recover electric energy from them. In order to reveal electricity-generation mechanisms in CE-MFCs, the present study operated a bench-scale reactor (1 l in capacity; approximately 1,000 cm{sup 2} in anode and cathode areas) for treating a high-strength model organic wastewater (comprised of starch, peptone, and fish extract). Approximately 1 month was needed for the bench reactor to attain a stable performance, after which volumetric maximum power densities persisted between 120 and 150 mW/l throughout the experiment (for over 2 months). Temporal increases in the external resistance were found to induce subsequent increases in power outputs. After electric output became stable, electrolyte and anode were sampled from the reactor for evaluating their current-generation abilities; it was estimated that most of current (over 80%) was generated by microbes in the electrolyte. Cyclic voltammetry of an electrolyte supernatant detected several electron shuttles with different standard redox potentials at high concentrations (equivalent to or more than 100 {mu}M 5-hydroxy-1,4-naphthoquinone). Denaturing gradient gel electrophoresis and quantitative real-time PCR of 16S ribosomal RNA gene fragments showed that bacteria related to the genus Dysgonomonas occurred abundantly in association with the increases in power outputs. These results suggest that mediated electron transfer was the main mechanism for electricity generation in CE-MFC, where high-concentration electron shuttles and Dysgonomonas bacteria played important roles. (orig.)

  5. Oxidized LDL upregulated ATP binding cassette transporter-1 in THP-1 macrophages

    Institute of Scientific and Technical Information of China (English)

    Chao-ke TANG; Guang-hui YI; Jun-hao YANG; Lu-shan LIU; Zuo WANG; Chang-geng RUAN; Yong-zong YANG

    2004-01-01

    AIM: To study the effect of oxidized low density lipoprotein (ox-LDL) on ATP binding cassette transporter A1 (ABCA1) in THP-1 macrophages. METHODS: After exposing the cultured THP-1 macrophages to ox-LDL for different periods, cholesterol efflux was determined by FJ-2107P type liquid scintillator. ABCA1 mRNA and protein level were determined by reverse trancriptase-polymerase chain reaction (RT-PCR) and Western blot, respectively.The cholesterol level in THP-1 macrophage foam cells was detected by high performance liquid chromatography.RESULTS: ox-LDL elevated AB CA1 in both protein and mRNA levels and increased apolipoprotein (apo) A-I-mediated cholesterol efflux in a time- and dose-dependent manner. 22(R)-hydroxyeholesterol and 9-cis-retinoic acid did significantly increase cholesterol efflux in THP-1 macrophage foam cells (P<0.05), respectively. Both of them further promoted cholesterol efflux (P<0.01). As expected, liver X receptor (LXR) agonist decreased content of esterified cholesterol in the macrophage foam cells compared with control, whereas only a slight decrease of free cholesterol was observed. LXR activity was slightly increased by oxidized LDL by 12 % at 12 h compared with 6 h.However, LXR activity was increased about 1.8 times at 24 h, and oxidized LDL further increased LXR activity by about 2.6 times at 48 h. CONCLUSION: ABCA1 gene expression was markedly increased in cholesterol-loaded cells as a result of activation of LXR/RXR. ABCA1 plays an important role in the homeostasis of cholesterol in the macrophages.

  6. ATP Binding Cassette Transporter Mediates Both Heme and Pesticide Detoxification in Tick Midgut Cells.

    Directory of Open Access Journals (Sweden)

    Flavio Alves Lara

    Full Text Available In ticks, the digestion of blood occurs intracellularly and proteolytic digestion of hemoglobin takes place in a dedicated type of lysosome, the digest vesicle, followed by transfer of the heme moiety of hemoglobin to a specialized organelle that accumulates large heme aggregates, called hemosomes. In the present work, we studied the uptake of fluorescent metalloporphyrins, used as heme analogs, and amitraz, one of the most regularly used acaricides to control cattle tick infestations, by Rhipicephalus (Boophilus microplus midgut cells. Both compounds were taken up by midgut cells in vitro and accumulated inside the hemosomes. Transport of both molecules was sensitive to cyclosporine A (CsA, a well-known inhibitor of ATP binding cassette (ABC transporters. Rhodamine 123, a fluorescent probe that is also a recognized ABC substrate, was similarly directed to the hemosome in a CsA-sensitive manner. Using an antibody against conserved domain of PgP-1-type ABC transporter, we were able to immunolocalize PgP-1 in the digest vesicle membranes. Comparison between two R. microplus strains that were resistant and susceptible to amitraz revealed that the resistant strain detoxified both amitraz and Sn-Pp IX more efficiently than the susceptible strain, a process that was also sensitive to CsA. A transcript containing an ABC transporter signature exhibited 2.5-fold increased expression in the amitraz-resistant strain when compared with the susceptible strain. RNAi-induced down-regulation of this ABC transporter led to the accumulation of metalloporphyrin in the digestive vacuole, interrupting heme traffic to the hemosome. This evidence further confirms that this transcript codes for a heme transporter. This is the first report of heme transport in a blood-feeding organism. While the primary physiological function of the hemosome is to detoxify heme and attenuate its toxicity, we suggest that the use of this acaricide detoxification pathway by ticks may

  7. Design of a radiative semi-transparent liner for the ITER divertor cassette

    International Nuclear Information System (INIS)

    The increased safety concern, resulting from the accumulation of tritium in the redeposited carbon-dominated films forming on the surfaces of the ITER divertor private region plasma facing components, has stimulated an important change of the gas box liner design. A significant modification of the ITER divertor cassette design was undertaken in the summer of 1997 with the removal of the so-called 'wings'. This highlighted the necessity to protect the cold (150 deg. C) pumping duct from radiated heat and particle flux from the plasma chamber. A cold duct has the potential to trap unacceptably high levels of tritium in the redeposited carbon films produced from erosion of the vertical target. To provide protection that minimises the uptake of tritium, a new semi-transparent liner operating with hot tungsten (W) tiles was proposed by the ITER Joint Central Team (JCT) and was developed by the RF Home Team. This liner design promises to minimise the amount of tritium trapped in it by operating with the surface temperature of the W in the range 800-1200 deg. C. Radiatively cooled tiles on the surface of the liner maintain the surface temperature between these limits, for a surface heat flux of between 0.1 and 0.35 MW/m2, a range which takes into account the uncertainties in the predicted operational heat loads. This paper reports on the predicted operational regime of the liner which allows effective transformation of incoming atomic tritium and carbon into stable hydrocarbons, that can be pumped safely to the reprocessing plant. The role of hydrocarbons (as molecules and radicals) is assessed. A sensible parametric analysis of tritium retention, on the liner surface and on cold areas behind the liner, was performed for different conditions and operational parameters

  8. The Applicability of Incoherent Array Processing to IMS Seismic Arrays

    Science.gov (United States)

    Gibbons, Steven J.

    2014-03-01

    The seismic arrays of the International Monitoring System (IMS) for the Comprehensive Nuclear-Test-Ban Treaty (CTBT) are highly diverse in size and configuration, with apertures ranging from under 1 km to over 60 km. Large and medium aperture arrays with large inter-site spacings complicate the detection and estimation of high-frequency phases lacking coherence between sensors. Pipeline detection algorithms often miss such phases, since they only consider frequencies low enough to allow coherent array processing, and phases that are detected are often attributed qualitatively incorrect backazimuth and slowness estimates. This can result in missed events, due to either a lack of contributing phases or by corruption of event hypotheses by spurious detections. It has been demonstrated previously that continuous spectral estimation can both detect and estimate phases on the largest aperture arrays, with arrivals identified as local maxima on beams of transformed spectrograms. The estimation procedure in effect measures group velocity rather than phase velocity, as is the case for classical f-k analysis, and the ability to estimate slowness vectors requires sufficiently large inter-sensor distances to resolve time-delays between pulses with a period of the order 4-5 s. Spectrogram beampacking works well on five IMS arrays with apertures over 20 km (NOA, AKASG, YKA, WRA, and KURK) without additional post-processing. Seven arrays with 10-20 km aperture (MJAR, ESDC, ILAR, KSRS, CMAR, ASAR, and EKA) can provide robust parameter estimates subject to a smoothing of the resulting slowness grids, most effectively achieved by convolving the measured slowness grids with the array response function for a 4 or 5 s period signal. Even for medium aperture arrays which can provide high-quality coherent slowness estimates, a complementary spectrogram beampacking procedure could act as a quality control by providing non-aliased estimates when the coherent slowness grids display

  9. Enhancing functional production of a chaperone-dependent lipase in Escherichia coli using the dual expression cassette plasmid

    Directory of Open Access Journals (Sweden)

    Quyen Thi Dinh

    2012-03-01

    Full Text Available Abstracts Background The lipase subfamilies I.1 and I.2 show more than 33% homology in the amino acid sequences and most members share another common property that their genes are clustered with the secondary genes whose protein products are required for folding the lipase into an active conformation and secretion into the culture medium. In previous studies, the lipase (LipA and its chaperone (LipB from Ralstonia sp. M1 were overexpressed in E. coli and the lipase was successfully refolded in vitro. The purpose of this study was to enhance the production of the active lipase LipA from Ralstonia sp. M1 in the heterologous host E. coli without in vitro refolding process, using two-plasmid co-expression systems and dual expression cassette plasmid systems. Results To produce more active lipase from Ralstonia sp. M1 in E. coli without in vitro refolding process but with the help of overexpression of the chaperone (LipB1 and LipB3 corresponding to 56-aa truncated and 26-aa truncated chaperone LipB, six different expression systems including 2 two-plasmid co-expression systems (E. coli BL21/pELipABa + pELipB1k and BL21/pELipABa + pELipB3k and 4 dual expression cassette plasmid systems (BL21/pELipAB-LipB1a, BL21/pELipAB-LipB3a, BL21/pELipA-LipB1a, and BL21/pELipA-LipB3a were constructed. The two-plasmid co-expression systems (E. coli BL21/pELipABa + pELipB1k and BL21/pELipABa + pELipB3k produced the active lipase at a level of 4 times as high as the single expression cassette plasmid system E. coli BL21/pELipABa did. For the first time, the dual expression cassette plasmid systems BL21/pELipAB-LipB1a and BL21/pELipAB-LipB3a yielded 29- and 19-fold production of the active lipase in comparison with the single expression cassette plasmid system E. coli BL21/pELipABa, respectively. Although the lipase amount was equally expressed in all these expression systems (40% of total cellular protein and only a small fraction of the overexpressed lipase was

  10. Role of NH{sub 2}-terminal hydrophobic motif in the subcellular localization of ATP-binding cassette protein subfamily D: Common features in eukaryotic organisms

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Asaka; Asahina, Kota; Okamoto, Takumi; Kawaguchi, Kosuke [Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan); Kostsin, Dzmitry G. [Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan); Institute of Biophysics and Cell Engineering, National Academy of Sciences of Belarus, Academicheskaya Str. 27, Minsk 220072 (Belarus); Kashiwayama, Yoshinori [Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan); Takanashi, Kojiro; Yazaki, Kazufumi [Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoko University, Uji, Kyoto 611-0011 (Japan); Imanaka, Tsuneo, E-mail: imanaka@pha.u-toyama.ac.jp [Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan); Morita, Masashi [Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan)

    2014-10-24

    Highlights: • ABCD proteins classifies based on with or without NH{sub 2}-terminal hydrophobic segment. • The ABCD proteins with the segment are targeted peroxisomes. • The ABCD proteins without the segment are targeted to the endoplasmic reticulum. • The role of the segment in organelle targeting is conserved in eukaryotic organisms. - Abstract: In mammals, four ATP-binding cassette (ABC) proteins belonging to subfamily D have been identified. ABCD1–3 possesses the NH{sub 2}-terminal hydrophobic region and are targeted to peroxisomes, while ABCD4 lacking the region is targeted to the endoplasmic reticulum (ER). Based on hydropathy plot analysis, we found that several eukaryotes have ABCD protein homologs lacking the NH{sub 2}-terminal hydrophobic segment (H0 motif). To investigate whether the role of the NH{sub 2}-terminal H0 motif in subcellular localization is conserved across species, we expressed ABCD proteins from several species (metazoan, plant and fungi) in fusion with GFP in CHO cells and examined their subcellular localization. ABCD proteins possessing the NH{sub 2}-terminal H0 motif were localized to peroxisomes, while ABCD proteins lacking this region lost this capacity. In addition, the deletion of the NH{sub 2}-terminal H0 motif of ABCD protein resulted in their localization to the ER. These results suggest that the role of the NH{sub 2}-terminal H0 motif in organelle targeting is widely conserved in living organisms.

  11. Role of NH2-terminal hydrophobic motif in the subcellular localization of ATP-binding cassette protein subfamily D: Common features in eukaryotic organisms

    International Nuclear Information System (INIS)

    Highlights: • ABCD proteins classifies based on with or without NH2-terminal hydrophobic segment. • The ABCD proteins with the segment are targeted peroxisomes. • The ABCD proteins without the segment are targeted to the endoplasmic reticulum. • The role of the segment in organelle targeting is conserved in eukaryotic organisms. - Abstract: In mammals, four ATP-binding cassette (ABC) proteins belonging to subfamily D have been identified. ABCD1–3 possesses the NH2-terminal hydrophobic region and are targeted to peroxisomes, while ABCD4 lacking the region is targeted to the endoplasmic reticulum (ER). Based on hydropathy plot analysis, we found that several eukaryotes have ABCD protein homologs lacking the NH2-terminal hydrophobic segment (H0 motif). To investigate whether the role of the NH2-terminal H0 motif in subcellular localization is conserved across species, we expressed ABCD proteins from several species (metazoan, plant and fungi) in fusion with GFP in CHO cells and examined their subcellular localization. ABCD proteins possessing the NH2-terminal H0 motif were localized to peroxisomes, while ABCD proteins lacking this region lost this capacity. In addition, the deletion of the NH2-terminal H0 motif of ABCD protein resulted in their localization to the ER. These results suggest that the role of the NH2-terminal H0 motif in organelle targeting is widely conserved in living organisms

  12. Hernandezine, a Bisbenzylisoquinoline Alkaloid with Selective Inhibitory Activity against Multidrug-Resistance-Linked ATP-Binding Cassette Drug Transporter ABCB1.

    Science.gov (United States)

    Hsiao, Sung-Han; Lu, Yu-Jen; Yang, Chun-Chiao; Tuo, Wei-Cherng; Li, Yan-Qing; Huang, Yang-Hui; Hsieh, Chia-Hung; Hung, Tai-Ho; Wu, Chung-Pu

    2016-08-26

    The overexpression of ATP-binding cassette (ABC) drug transporter ABCB1 (P-glycoprotein, MDR1) is the most studied mechanism of multidrug resistance (MDR), which remains a major obstacle in clinical cancer chemotherapy. Consequently, resensitizing MDR cancer cells by inhibiting the efflux function of ABCB1 has been considered as a potential strategy to overcome ABCB1-mediated MDR in cancer patients. However, the task of developing a suitable modulator of ABCB1 has been hindered mostly by the lack of selectivity and high intrinsic toxicity of candidate compounds. Considering the wide range of diversity and relatively nontoxic nature of natural products, developing a potential modulator of ABCB1 from natural sources is particularly valuable. Through screening of a large collection of purified bioactive natural products, hernandezine was identified as a potent and selective reversing agent for ABCB1-mediated MDR in cancer cells. Experimental data demonstrated that the bisbenzylisoquinoline alkaloid hernandezine is selective for ABCB1, effectively inhibits the transport function of ABCB1, and enhances drug-induced apoptosis in cancer cells. More importantly, hernandezine significantly resensitizes ABCB1-overexpressing cancer cells to multiple chemotherapeutic drugs at nontoxic, nanomolar concentrations. Collectively, these findings reveal that hernandezine has great potential to be further developed into a novel reversal agent for combination therapy in MDR cancer patients. PMID:27504669

  13. IMB2026791, a Xanthone, Stimulates Cholesterol Efflux by Increasing the Binding of Apolipoprotein A-I to ATP-Binding Cassette Transporter A1

    Directory of Open Access Journals (Sweden)

    Zijian Xie

    2012-03-01

    Full Text Available It is known that the ATP-binding cassette transporter A1 (ABCA1 plays a major role in cholesterol homeostasis and high density lipoprotein (HDL metabolism. Several laboratories have demonstrated that ABCA1 binding to lipid-poor apolipoprotein A-I (apoA-I will mediate the assembly of nascent HDL and cellular cholesterol efflux, which suggests a possible receptor-ligand interaction between ABCA1 and apoA-I. In this study, a cell-based-ELISA-like high-throughput screening (HTS method was developed to identify the synthetic and natural compounds that can regulate binding activity of ABCA1 to apoA-I. The cell-based-ELISA-like high-throughput screen was conducted in a 96-well format using Chinese hamster ovary (CHO cells stably transfected with ABCA1 pIRE2-EGFP (Enhanced Green Fluorecence Protein expression vector and the known ABCA1 inhibitor glibenclamide as the antagonist control. From 2,600 compounds, a xanthone compound (IMB 2026791 was selected using this HTS assay, and it was proved as an apoA-I binding agonist to ABCA1 by a flow cytometry assay and western blot analysis. The [3H] cholesterol efflux assay of IMB2026791 treated ABCA1-CHO cells and PMA induced THP-1 macrophages (human acute monocytic leukemia cell further confirmed the compound as an accelerator of cholesterol efflux in a dose-dependent manner with an EC50 of 25.23 μM.

  14. Assembling the Streptococcus thermophilus clustered regularly interspaced short palindromic repeats (CRISPR) array for multiplex DNA targeting.

    Science.gov (United States)

    Guo, Lijun; Xu, Kun; Liu, Zhiyuan; Zhang, Cunfang; Xin, Ying; Zhang, Zhiying

    2015-06-01

    In addition to the advantages of scalable, affordable, and easy to engineer, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) technology is superior for multiplex targeting, which is laborious and inconvenient when achieved by cloning multiple gRNA expressing cassettes. Here, we report a simple CRISPR array assembling method which will facilitate multiplex targeting usage. First, the Streptococcus thermophilus CRISPR3/Cas locus was cloned. Second, different CRISPR arrays were assembled with different crRNA spacers. Transformation assays using different Escherichia coli strains demonstrated efficient plasmid DNA targeting, and we achieved targeting efficiency up to 95% with an assembled CRISPR array with three crRNA spacers. PMID:25748774

  15. The Design Concept of a Steam Generator Cassette Mock-Up for ISI of Helical Tubes in SMART Steam Generator

    International Nuclear Information System (INIS)

    The SMART reactor steam generator is composed of 8 Steam Generator Cassettes (SGC) and each the SGC has a once-through-type, helical-coil-tube bundle structure using INCONEL alloy 690 tubes. The SGC installed in reactor vessel is a kind of heat exchanger made of INCONEL alloy 690 tubes. This paper introduces the design concepts of an SGC mock-up for the test probe insertion ability of In- Service Inspection (ISI). The backgrounds of selected tube material, size and tube composition are described

  16. The Design Concept of a Steam Generator Cassette Mock-Up for ISI of Helical Tubes in SMART Steam Generator

    Energy Technology Data Exchange (ETDEWEB)

    Choung, Yun Hang; Kim, Dong Ok; Park, Jin Seok; Lee, Won Jae [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2009-10-15

    The SMART reactor steam generator is composed of 8 Steam Generator Cassettes (SGC) and each the SGC has a once-through-type, helical-coil-tube bundle structure using INCONEL alloy 690 tubes. The SGC installed in reactor vessel is a kind of heat exchanger made of INCONEL alloy 690 tubes. This paper introduces the design concepts of an SGC mock-up for the test probe insertion ability of In- Service Inspection (ISI). The backgrounds of selected tube material, size and tube composition are described.

  17. Investigation of integrons/cassettes in antimicrobial-resistant Escherichia coli isolated from food animals in China

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    In this study,326 Escherichia coli isolates from food animals collected during the last four decades in China were characterized using antimicrobial susceptibility testing and screening for integrons/cassettes.Minimum inhibitory concentration(MIC) testing indicated that the antimicrobial resistance of E.coli has increased since the 1970s.The findings of this study present a warning to veterinary practitioners about the excessive use of antimicrobials,and suggest the necessity for surveillance and control of antimicrobial resistance in veterinary clinical medicine in China.

  18. Partial Excision of the Chromosomal Cassette Containing the Methicillin Resistance Determinant Results in Methicillin-Susceptible Staphylococcus aureus

    Science.gov (United States)

    Donnio, Pierre-Yves; Oliveira, Duarte C.; Faria, Nuno A.; Wilhelm, Nathalie; Le Coustumier, Alain; de Lencastre, Herminia

    2005-01-01

    We report a detailed characterization of methicillin-susceptible Staphylococcus aureus isolates from five French hospitals negative for both the mecA and the ccrAB loci but positive for the IS431::pUB110::IS431::dcs structure, present in some Staphylococcus cassette chromosome mec (SCCmec) types. The presence of SCCmec-associated elements suggests that this unusual resistant phenotype is due to a partial excision of SCCmec from epidemic methicillin-resistant S. aureus. The hypothesis of a genetic relatedness is strengthened by common sequence and spa types and similar susceptibility patterns. PMID:16081974

  19. An Array-Based Method to Identify Multivalent Inhibitors

    OpenAIRE

    Zhang, Yalong; Li, Qian; Rodriguez, Luis G.; Gildersleeve, Jeffrey C.

    2010-01-01

    Carbohydrate-protein interactions play a critical role in a variety of biological processes, and agonists/antagonists of these interactions are useful as biological probes and therapeutic agents. Most carbohydrate-binding proteins achieve tight binding through formation of a multivalent complex. Therefore, both ligand structure and presentation contribute to recognition. Since there are many potential combinations of structure, spacing, and orientation to consider and the optimal one cannot b...

  20. Concept design of the DEMO divertor cassette-to-vacuum vessel locking system adopting a systems engineering approach

    Energy Technology Data Exchange (ETDEWEB)

    Di Gironimo, G., E-mail: giuseppe.digironimo@unina.it [Università degli Studi di Napoli “Federico II”, Dipartimento di Ingegneria Industriale, Piazzale Tecchio 80, 80135 Napoli (Italy); Carfora, D. [Tampere University of Technology, Korkeakoulunkatu 6, 33720 Tampere (Finland); VTT Technical Research Centre of Finland, Tekniikankatu 1, PO Box 1300, FI-33101 Tampere (Finland); Università degli Studi di Napoli “Federico II”, Dipartimento di Ingegneria Industriale, Piazzale Tecchio 80, 80135 Napoli (Italy); Esposito, G.; Lanzotti, A.; Marzullo, D. [Università degli Studi di Napoli “Federico II”, Dipartimento di Ingegneria Industriale, Piazzale Tecchio 80, 80135 Napoli (Italy); Siuko, M. [VTT Technical Research Centre of Finland, Tekniikankatu 1, PO Box 1300, FI-33101 Tampere (Finland)

    2015-05-15

    Highlights: • An iterative and incremental design process for cassette-to-VV locking system of DEMO divertor is presented. • Three different concepts have been developed with a systematic design approach. • The final concept has been selected with Fuzzy-Analytic Hierarchy Process in virtual reality. - Abstract: This paper deals with pre-concept studies of DEMO divertor cassette-to-vacuum vessel locking system under the work program WP13-DAS-07-T06: Divertor Remote Maintenance System pre-concept study. An iterative design process, consistent with Systems Engineering guidelines and named Iterative and Participative Axiomatic Design Process (IPADeP), is used in this paper to propose new innovative solutions for divertor locking system, which can overcome the difficulties in applying the ITER principles to DEMO. The solutions conceived have been analysed from the structural point of view using the software Ansys and, eventually, evaluated using the methodology known as Fuzzy-Analytic Hierarchy Process. Due to the lack and the uncertainty of the requirements in this early conceptual design stage, the aim is to cover a first iteration of an iterative and incremental process to propose an innovative design concept to be developed in more details as the information will be completed.

  1. ATP-binding cassette-like transporters are involved in the transport of lignin precursors across plasma and vacuolar membranes

    Energy Technology Data Exchange (ETDEWEB)

    Miao, Y.C.; Liu, C.

    2010-12-28

    Lignin is a complex biopolymer derived primarily from the condensation of three monomeric precursors, the monolignols. The synthesis of monolignols occurs in the cytoplasm. To reach the cell wall where they are oxidized and polymerized, they must be transported across the cell membrane. However, the molecular mechanisms underlying the transport process are unclear. There are conflicting views about whether the transport of these precursors occurs by passive diffusion or is an energized active process; further, we know little about what chemical forms are required. Using isolated plasma and vacuolar membrane vesicles prepared from Arabidopsis, together with applying different transporter inhibitors in the assays, we examined the uptake of monolignols and their derivatives by these native membrane vesicles. We demonstrate that the transport of lignin precursors across plasmalemma and their sequestration into vacuoles are ATP-dependent primary-transport processes, involving ATP-binding cassette-like transporters. Moreover, we show that both plasma and vacuolar membrane vesicles selectively transport different forms of lignin precursors. In the presence of ATP, the inverted plasma membrane vesicles preferentially take up monolignol aglycones, whereas the vacuolar vesicles are more specific for glucoconjugates, suggesting that the different ATP-binding cassette-like transporters recognize different chemical forms in conveying them to distinct sites, and that glucosylation of monolignols is necessary for their vacuolar storage but not required for direct transport into the cell wall in Arabidopsis.

  2. Generation of minipigs with targeted transgene insertion by recombinase-mediated cassette exchange (RMCE) and somatic cell nuclear transfer (SCNT)

    DEFF Research Database (Denmark)

    Jakobsen, Jannik Ejnar; Johansen, Marianne G; Schmidt, Mette;

    2013-01-01

    Targeted transgenesis using site-specific recombinases is an attractive method to create genetically modified animals as it allows for integration of the transgene in a pre-selected transcriptionally active genomic site. Here we describe the application of recombinase-mediated cassette exchange (...... enhanced human UbiC promoter, had an expression profile in various tissues similar to that of the GFP marker gene. The results show that RMCE can be done in a pre-selected transcriptionally active acceptor locus for targeted transgenesis in pigs.......Targeted transgenesis using site-specific recombinases is an attractive method to create genetically modified animals as it allows for integration of the transgene in a pre-selected transcriptionally active genomic site. Here we describe the application of recombinase-mediated cassette exchange...... (RMCE) in cells from a Göttingen minipig with four RMCE acceptor loci, each containing a green fluorescence protein (GFP) marker gene driven by a human UbiC promoter. The four RMCE acceptor loci segregated independent of each other, and expression profiles could be determined in various tissues. Using...

  3. Concept design of the DEMO divertor cassette-to-vacuum vessel locking system adopting a systems engineering approach

    International Nuclear Information System (INIS)

    Highlights: • An iterative and incremental design process for cassette-to-VV locking system of DEMO divertor is presented. • Three different concepts have been developed with a systematic design approach. • The final concept has been selected with Fuzzy-Analytic Hierarchy Process in virtual reality. - Abstract: This paper deals with pre-concept studies of DEMO divertor cassette-to-vacuum vessel locking system under the work program WP13-DAS-07-T06: Divertor Remote Maintenance System pre-concept study. An iterative design process, consistent with Systems Engineering guidelines and named Iterative and Participative Axiomatic Design Process (IPADeP), is used in this paper to propose new innovative solutions for divertor locking system, which can overcome the difficulties in applying the ITER principles to DEMO. The solutions conceived have been analysed from the structural point of view using the software Ansys and, eventually, evaluated using the methodology known as Fuzzy-Analytic Hierarchy Process. Due to the lack and the uncertainty of the requirements in this early conceptual design stage, the aim is to cover a first iteration of an iterative and incremental process to propose an innovative design concept to be developed in more details as the information will be completed

  4. Super phase array

    Energy Technology Data Exchange (ETDEWEB)

    Wee, W H; Pendry, J B [Condensed Matter Theory Group Department of Physics Imperial College London London SW7 2AZ (United Kingdom)], E-mail: w.wee07@imperial.ac.uk

    2010-03-15

    For a long time phase arrays have been used in a variety of wave transmission applications because of their simplicity and versatility. Conventionally there is a trade-off between the compactness of a phase array and its directivity. In this paper we demonstrate how by embedding a normal phase array within a superlens (made of negative refractive index material) we can overcome this constraint and create compact phase arrays with a virtual extent much larger than the physical size of the array. In this paper we also briefly discuss the apparent unphysical field divergences in superlenses and how to resolve this issue.

  5. Super phase array

    International Nuclear Information System (INIS)

    For a long time phase arrays have been used in a variety of wave transmission applications because of their simplicity and versatility. Conventionally there is a trade-off between the compactness of a phase array and its directivity. In this paper we demonstrate how by embedding a normal phase array within a superlens (made of negative refractive index material) we can overcome this constraint and create compact phase arrays with a virtual extent much larger than the physical size of the array. In this paper we also briefly discuss the apparent unphysical field divergences in superlenses and how to resolve this issue.

  6. Construction of deletion mutants in the phosphotransferase transport system and adenosine triphosphate-binding cassette transporters in Listeria monocytogenes and analysis of their growth under different stress conditions

    Directory of Open Access Journals (Sweden)

    Marina Ceruso

    2013-10-01

    Full Text Available Functional genomics approaches enable us to investigate the biochemical, cellular, and physiological properties of each gene product and are nowadays applied to enhance food safety by understanding microbial stress responses in food and host-pathogen interactions. Listeria monocytogenes is a food-borne pathogen that causes listeriosis and is difficult to eliminate this pathogen since it can survive under multiple stress conditions such as low pH and low temperature. Detailed studies are needed to determine its mode of action and to understand the mechanisms that protect the pathogen when it is subjected to stress. In this study, deletion mutants of phosphotransferase transport system genes (PTS and adenosine triphosphate(ATP-binding cassette transporters (ABC of Listeria monocytogenes F2365 were created using molecular techniques. These mutants and the wild-type were tested under different stress conditions, such as in solutions with different NaCl concentration, pH value and for nisin resistance. Results demonstrate that the behaviour of these deletion mutants is different from the wild type. In particular, deleted genes may be involved in L. monocytogenes resistance to nisin and to acid and salt concentrations. Functional genomics research on L. monocytogenes allows a better understanding of the genes related to stress responses and this knowledge may help in intervention strategies to control this food-borne pathogen. Furthermore, specific gene markers can be used to identify and subtype L. monocytogenes. Thus, future development of this study will focus on additional functional analyses of important stress response-related genes, as well as on methods for rapid and sensitive detection of L. monocytogenes such as using DNA microarrays.

  7. Emergence of sequence type 779 methicillin-resistant Staphylococcus aureus harboring a novel pseudo staphylococcal cassette chromosome mec (SCCmec)-SCC-SCCCRISPR composite element in Irish hospitals.

    LENUS (Irish Health Repository)

    Kinnevey, Peter M

    2013-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) has been a major cause of nosocomial infection in Irish hospitals for 4 decades, and replacement of predominant MRSA clones has occurred several times. An MRSA isolate recovered in 2006 as part of a larger study of sporadic MRSA exhibited a rare spa (t878) and multilocus sequence (ST779) type and was nontypeable by PCR- and DNA microarray-based staphylococcal cassette chromosome mec (SCCmec) element typing. Whole-genome sequencing revealed the presence of a novel 51-kb composite island (CI) element with three distinct domains, each flanked by direct repeat and inverted repeat sequences, including (i) a pseudo SCCmec element (16.3 kb) carrying mecA with a novel mec class region, a fusidic acid resistance gene (fusC), and two copper resistance genes (copB and copC) but lacking ccr genes; (ii) an SCC element (17.5 kb) carrying a novel ccrAB4 allele; and (iii) an SCC element (17.4 kb) carrying a novel ccrC allele and a clustered regularly interspaced short palindromic repeat (CRISPR) region. The novel CI was subsequently identified by PCR in an additional 13 t878\\/ST779 MRSA isolates, six from bloodstream infections, recovered between 2006 and 2011 in 11 hospitals. Analysis of open reading frames (ORFs) carried by the CI showed amino acid sequence similarity of 44 to 100% to ORFs from S. aureus and coagulase-negative staphylococci (CoNS). These findings provide further evidence of genetic transfer between S. aureus and CoNS and show how this contributes to the emergence of novel SCCmec elements and MRSA strains. Ongoing surveillance of this MRSA strain is warranted and will require updating of currently used SCCmec typing methods.

  8. Identification of Dehydroxytrichostatin A as a Novel Up-Regulator of the ATP-Binding Cassette Transporter A1 (ABCA1

    Directory of Open Access Journals (Sweden)

    Shuyi Si

    2011-08-01

    Full Text Available The ATP-binding cassette transporter A1 (ABCA1 mediates the cellular efflux of excess cholesterol and phospholipids to lipid-poor apolipoprotein A-I (apoA-I. ABCA1 plays an important role in high-density lipoprotein (HDL biogenesis and reverse cholesterol transport. By using a cell-based screening model for the ABCA1 up-regulator and column chromatography, an active compound, 9179B, was isolated. Through analysis of its NMR data, 9179B was identified as dehydroxytrichostatin A. We found that 9179B increased the transcription of ABCA1 in a cell-based reporter assay, with an EC50 value of 2.65 μM. 9179B up-regulated ABCA1 expression at both mRNA and protein levels in HepG2 and RAW264.7 cells. It also up-regulated the expression of scavenger receptor class B type I (SR-BI as well as the uptake of DiI-HDL in RAW264.7 cells. This compound stimulated ApoA-I-mediated cellular cholesterol efflux from RAW 264.7 cells. We further found that 9179B was a potent histone deacetylase (HDAC inhibitor with an IC50 value of 0.08 μM. Reporter gene assays showed that the regulation of ABCA1 transcription by 9179B was mainly mediated by the −171/−75 bp promoter region. Together, our results indicate that 9179B is an ABCA1 up-regulator and dehydroxytrichostatin A may be a novel anti-atherogenic compound.

  9. Spreading of genes encoding enterotoxins, haemolysins, adhesin and biofilm among methicillin resistant Staphylococcus aureus strains with staphylococcal cassette chromosome mec type IIIA isolated from burn patients.

    Science.gov (United States)

    Motallebi, Mitra; Jabalameli, Fereshteh; Asadollahi, Kheirollah; Taherikalani, Morovat; Emaneini, Mohammad

    2016-08-01

    The emergence of antibiotic-resistant Staphylococcus aureus in particular methicillin-resistant S. aureus (MRSA) is an important concern in burn medical centers either in Iran or worldwide. A total of 128 S. aureus isolates were collected from wound infection of burn patients during June 2013 to June 2014. Multiplex-polymerase chain reaction (MPCR) assay was performed for the characterization of the staphylococcal cassette chromosome mec (SCCmec). Genes encoding virulence factors and biofilm were targeted by PCR. Of 128 S. aureus isolates, 77 (60.1%) isolates were MRSA. Fifty four (70.1%) isolates were identified as SCCmec type IIIA. The most frequently detected toxin genes among MRSA isolates with SCCmec type IIIA were sea (64.1%) and hla (51.8%). The rate of coexistence of sea with hla and sea with hla and hlb was 37% and12.9%, respectively. The sec, eta, tst, pvl, hla and hlb genes were not detected in any of the MRSA isolates. The most prevalent genes encoding biofilm was eno, found in 61.1% of isolates, followed by fib and icaA found in 48.1% and 38.8% of the isolates, respectively. The rate of coexistence of fib + eno + icaA + icaD and fib + eno was 20.3% and 9.2%, respectively. The ebps gene was not detected in any of the isolates. In conclusion, our study indicated that the sea, hla, fib and icaA were most frequent genes encoding virulence factors among MRSA with SCCmec type IIIA isolated from burn wound infection. Moreover, the results of this study shows that the rate of coexistence of genes encoding different virulence factor were high. PMID:27238459

  10. 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.

  11. WBC27, an Adenosine Tri-phosphate-binding Cassette Protein, Controls Pollen Wall Formation and Patterning in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Xiao-Ying Dou; Ke-Zhen Yang; Yi Zhang; Wei Wang; Xiao-Lei Liu; Li-Qun Chen; Xue-Qin Zhang; De Ye

    2011-01-01

    In flowering plants, the exine components are derived from tapetum. Despite its importance to sexual plant reproduction, little is known about the translocation of exine materials from tapetum to developing microspores. Here we report functional characterization of the arabidopsis WBC27 gene. WBC27 encodes an adenosine tri-phosphate binding cassette (ABC) transporter and is expressed preferentially in tapetum. Mutation of WBC27 disrupted the exine formation. The wbc27 mutant microspores began to degenerate once released from tetrads and most of the microspores collapsed at the uninucleate stage. Only a small number of wbc27-1 microspores could develop into tricellular pollen grains. These survival pollen grains lacked exine and germinated in the anther before anthesis. All of these results suggest that the ABC transporter, WBC27 plays important roles in the formation of arabidopsis exine, possibly by translocation of lipidic precursors of sporopollenin from tapetum to developing microspores.

  12. In Vivo Bioluminescent Imaging of ATP-Binding Cassette Transporter-Mediated Efflux at the Blood-Brain Barrier.

    Science.gov (United States)

    Bakhsheshian, Joshua; Wei, Bih-Rong; Hall, Matthew D; Simpson, R Mark; Gottesman, Michael M

    2016-01-01

    We provide a detailed protocol for imaging ATP-binding cassette subfamily G member 2 (ABCG2) function at the blood-brain barrier (BBB) of transgenic mice. D-Luciferin is specifically transported by ABCG2 found on the apical side of endothelial cells at the BBB. The luciferase-luciferin enzymatic reaction produces bioluminescence, which allows a direct measurement of ABCG2 function at the BBB. Therefore bioluminescence imaging (BLI) correlates with ABCG2 function at the BBB and this can be measured by administering luciferin in a mouse model that expresses luciferase in the brain parenchyma. BLI allows for a relatively low-cost alternative for studying transporter function in vivo compared to other strategies such as positron emission tomography. This method for imaging ABCG2 function at the BBB can be used to investigate pharmacokinetic inhibition of the transporter. PMID:27424909

  13. Functions of the conserved thrombospondin carboxy-terminal cassette in cell-extracellular matrix interactions and signaling.

    Science.gov (United States)

    Adams, Josephine C

    2004-06-01

    Thrombospondins (TSPs) are extracellular, multidomain, calcium-binding glycoproteins that function at cell surfaces, in extracellular matrix (ECM) and as bridging molecules in cell-cell interactions. TSPs are multifunctional and modulate cell behavior during development, wound-healing, immune response, tumor growth and in the homeostasis of adult tissues. TSPs are assembled as oligomers that are composed of homologous polypeptides. In all the TSP polypeptides, the most highly-conserved region is the carboxyl-region, which contains a characteristic set of domains comprising EGF domains, TSP type 3 repeats and a globular carboxy-terminal domain. This large region is termed here the thrombospondin carboxy-terminal cassette (TSP-CTC). The strong conservation of the TSP-CTC suggests that it may mediate ancestral functions that are shared by all TSPs. This review summarizes the current knowledge of the TSP-CTC and areas of future interest. PMID:15094125

  14. Plasmodium falciparum Expressing Domain Cassette 5 Type PfEMP1 (DC5-PfEMP1) Bind PECAM1

    DEFF Research Database (Denmark)

    Berger, Sanne S; Turner, Louise; Wang, Christian W;

    2013-01-01

    Members of the Plasmodium falciparum Erythrocyte Membrane protein 1 (PfEMP1) family expressed on the surface of malaria-infected erythrocytes mediate binding of the parasite to different receptors on the vascular lining. This process drives pathologies, and severe childhood malaria has been...... associated with the expression of particular subsets of PfEMP1 molecules. PfEMP1 are grouped into subtypes based on upstream sequences and the presence of semi-conserved PfEMP1 domain compositions named domain cassettes (DCs). Earlier studies have indicated that DC5-containing PfEMP1 (DC5-PfEMP1) are more...... likely to be expressed in children with severe malaria disease than in children with uncomplicated malaria, but these PfEMP1 subtypes only dominate in a relatively small proportion of the children with severe disease. In this study, we have characterised the genomic sequence characteristic for DC5, and...

  15. An Optimized GD2-Targeting Retroviral Cassette for More Potent and Safer Cellular Therapy of Neuroblastoma and Other Cancers.

    Science.gov (United States)

    Thomas, Simon; Straathof, Karin; Himoudi, Nourredine; Anderson, John; Pule, Martin

    2016-01-01

    Neuroblastoma is the commonest extra cranial solid cancer of childhood. Despite escalation of treatment regimens, a significant minority of patients die of their disease. Disialoganglioside (GD2) is consistently expressed at high-levels in neuroblastoma tumors, which have been targeted with some success using therapeutic monoclonal antibodies. GD2 is also expressed in a range of other cancer but with the exception of some peripheral nerves is largely absent from non-transformed tissues. Chimeric Antigen Receptors (CARs) are artificial type I proteins which graft the specificity of a monoclonal antibody onto a T-cell. Clinical data with early CAR designs directed against GD2 have shown some promise in Neuroblastoma. Here, we describe a GD2-targeting CAR retroviral cassette, which has been optimized for CAR T-cell persistence, efficacy and safety. PMID:27030986

  16. Remote detection of human toxicants in real time using a human-optimized, bioluminescent bacterial luciferase gene cassette bioreporter

    Science.gov (United States)

    Close, Dan; Webb, James; Ripp, Steven; Patterson, Stacey; Sayler, Gary

    2012-06-01

    Traditionally, human toxicant bioavailability screening has been forced to proceed in either a high throughput fashion using prokaryotic or lower eukaryotic targets with minimal applicability to humans, or in a more expensive, lower throughput manner that uses fluorescent or bioluminescent human cells to directly provide human bioavailability data. While these efforts are often sufficient for basic scientific research, they prevent the rapid and remote identification of potentially toxic chemicals required for modern biosecurity applications. To merge the advantages of high throughput, low cost screening regimens with the direct bioavailability assessment of human cell line use, we re-engineered the bioluminescent bacterial luciferase gene cassette to function autonomously (without exogenous stimulation) within human cells. Optimized cassette expression provides for fully endogenous bioluminescent production, allowing continuous, real time monitoring of the bioavailability and toxicology of various compounds in an automated fashion. To access the functionality of this system, two sets of bioluminescent human cells were developed. The first was programed to suspend bioluminescent production upon toxicological challenge to mimic the non-specific detection of a toxicant. The second induced bioluminescence upon detection of a specific compound to demonstrate autonomous remote target identification. These cells were capable of responding to μM concentrations of the toxicant n-decanal, and allowed for continuous monitoring of cellular health throughout the treatment process. Induced bioluminescence was generated through treatment with doxycycline and was detectable upon dosage at a 100 ng/ml concentration. These results demonstrate that leveraging autonomous bioluminescence allows for low-cost, high throughput direct assessment of toxicant bioavailability.

  17. 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.

  18. Sterol transporter adenosine triphosphate-binding cassette transporter G8, gallstones, and biliary cancer in 62,000 individuals from the general population

    DEFF Research Database (Denmark)

    Stender, Stefan; Frikke-Schmidt, Ruth; Nordestgaard, Børge G; Tybjærg-Hansen, Anne

    2011-01-01

    Gallstone disease, a risk factor for biliary cancer, has a strong heritable component, but the underlying genes are largely unknown. To test the hypothesis that ABCG8 (adenosine triphosphate-binding cassette transporter G8) Asp19His (D19H) genotype predicted risk of gallstones and biliary cancer ...

  19. Application of Cassette Ultracentrifugation Using Non-labeled Compounds and Liquid Chromatography-Tandem Mass Spectrometry Analysis for High-Throughput Protein Binding Determination.

    Science.gov (United States)

    Kieltyka, Kasia; McAuliffe, Brian; Cianci, Christopher; Drexler, Dieter M; Shou, Wilson; Zhang, Jun

    2016-03-01

    Membrane-based devices typically used for serum protein binding determination are not fully applicable to highly lipophilic compounds because of nonspecific binding to the device membrane. Ultracentrifugation, however, completely eliminates the issue by using a membrane-free approach, although its wide application has been limited. This lack of utilization is mainly attributed to 2 factors: the high cost in acquiring and handling of radiolabeled compounds and low assay throughput owing to the difficulties in process automation. To overcome these challenges, we report a high-throughput workflow by cassette ultracentrifugation of nonradiolabeled compounds followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Twenty compounds with diverse physicochemical and protein binding properties were selected for the evaluation of the workflow. To streamline the working process, approaches of matrix balancing for all the samples for LC-MS/MS analysis and determining free fraction without analytical calibration curves were adopted. Both the discrete ultracentrifugation of individual compounds and cassette ultracentrifugation of all the test compounds followed by simultaneous LC-MS/MS analysis exhibited a linear correlation with literature values, demonstrating respectively the validity of the ultracentrifugation process and the cassette approach. The cassette ultracentrifugation using nonradiolabeled compounds followed by LC-MS/MS analysis has greatly facilitated its application for high-throughput protein binding screening in drug discovery. PMID:26886323

  20. The homodimeric ATP-binding cassette transporter LmrA mediates multidrug transport by an alternating two-site (two-cylinder engine) mechanism

    NARCIS (Netherlands)

    van Veen, HW; Margolles, A; Muller, M; Higgins, CF; Konings, WN

    2000-01-01

    The bacterial LmrA protein and the mammalian multidrug resistance P-glycoprotein are closely related ATP-binding cassette (ABC) transporters that confer multidrug resistance on cells by mediating the extrusion of drugs at the expense of ATP hydrolysis. The mechanisms by which transport is mediated,

  1. Regulation of ATP-binding cassette transporters and cholesterol efflux by glucose in primary human monocytes and murine bone marrow-derived macrophages

    Science.gov (United States)

    Individuals with type 2 diabetes mellitus are at increased risk of developing atherosclerosis. This may be partially attributable to suppression of macrophage ATP-binding cassette (ABC) transporter mediated cholesterol efflux by sustained elevated blood glucose concentrations. Two models were used...

  2. 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.

  3. ABCB5 Identifies Immunoregulatory Dermal Cells

    Directory of Open Access Journals (Sweden)

    Tobias Schatton

    2015-09-01

    Full Text Available Cell-based strategies represent a new frontier in the treatment of immune-mediated disorders. However, the paucity of markers for isolation of molecularly defined immunomodulatory cell populations poses a barrier to this field. Here, we show that ATP-binding cassette member B5 (ABCB5 identifies dermal immunoregulatory cells (DIRCs capable of exerting therapeutic immunoregulatory functions through engagement of programmed cell death 1 (PD-1. Purified Abcb5+ DIRCs suppressed T cell proliferation, evaded immune rejection, homed to recipient immune tissues, and induced Tregs in vivo. In fully major-histocompatibility-complex-mismatched cardiac allotransplantation models, allogeneic DIRCs significantly prolonged allograft survival. Blockade of DIRC-expressed PD-1 reversed the inhibitory effects of DIRCs on T cell activation, inhibited DIRC-dependent Treg induction, and attenuated DIRC-induced prolongation of cardiac allograft survival, indicating that DIRC immunoregulatory function is mediated, at least in part, through PD-1. Our results identify ABCB5+ DIRCs as a distinct immunoregulatory cell population and suggest promising roles of this expandable cell subset in cellular immunotherapy.

  4. 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.

  5. Micromachined electrode array

    Energy Technology Data Exchange (ETDEWEB)

    Okandan, Murat (Edgewood, NM); Wessendorf, Kurt O. (Albuquerque, NM)

    2007-12-11

    An electrode array is disclosed which has applications for neural stimulation and sensing. The electrode array, in certain embodiments, can include a plurality of electrodes each of which is flexibly attached to a common substrate using a plurality of springs to allow the electrodes to move independently. In other embodiments of the electrode array, the electrodes can be fixed to the substrate. The electrode array can be formed from a combination of bulk and surface micromachining, and can include electrode tips having an electroplated metal (e.g. platinum, iridium, gold or titanium) or a metal oxide (e.g. iridium oxide) for biocompatibility. The electrode array can be used to form a part of a neural prosthesis, and is particularly well adapted for use in an implantable retinal prosthesis.

  6. Diode Laser Arrays

    Science.gov (United States)

    Botez, Dan; Scifres, Don R.

    1994-08-01

    This book provides a comprehensive overview of the fundamental principles and applications of semiconductor diode laser arrays. All of the major types of arrays are discussed in detail, including coherent, incoherent, edge- and surface-emitting, horizontal- and vertical-cavity, individually addressed, lattice- matched and strained-layer systems. The initial chapters cover such topics as lasers, amplifiers, external-cavity control, theoretical modeling, and operational dynamics. Spatially incoherent arrays are then described in detail, and the uses of vertical-cavity surface emitter and edge-emitting arrays in parallel optical-signal processing and multi-channel optical recording are discussed. Researchers and graduate students in solid state physics and electrical engineering studying the properties and applications of such arrays will find this book invaluable.

  7. Microfabricated ion trap array

    Science.gov (United States)

    Blain, Matthew G.; Fleming, James G.

    2006-12-26

    A microfabricated ion trap array, comprising a plurality of ion traps having an inner radius of order one micron, can be fabricated using surface micromachining techniques and materials known to the integrated circuits manufacturing and microelectromechanical systems industries. Micromachining methods enable batch fabrication, reduced manufacturing costs, dimensional and positional precision, and monolithic integration of massive arrays of ion traps with microscale ion generation and detection devices. Massive arraying enables the microscale ion traps to retain the resolution, sensitivity, and mass range advantages necessary for high chemical selectivity. The reduced electrode voltage enables integration of the microfabricated ion trap array with on-chip circuit-based rf operation and detection electronics (i.e., cell phone electronics). Therefore, the full performance advantages of the microfabricated ion trap array can be realized in truly field portable, handheld microanalysis systems.

  8. DNA microarray profiling of a diverse collection of nosocomial methicillin-resistant staphylococcus aureus isolates assigns the majority to the correct sequence type and staphylococcal cassette chromosome mec (SCCmec) type and results in the subsequent identification and characterization of novel SCCmec-SCCM1 composite islands.

    LENUS (Irish Health Repository)

    Shore, Anna C

    2012-10-01

    One hundred seventy-five isolates representative of methicillin-resistant Staphylococcus aureus (MRSA) clones that predominated in Irish hospitals between 1971 and 2004 and that previously underwent multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec (SCCmec) typing were characterized by spa typing (175 isolates) and DNA microarray profiling (107 isolates). The isolates belonged to 26 sequence type (ST)-SCCmec types and subtypes and 35 spa types. The array assigned all isolates to the correct MLST clonal complex (CC), and 94% (100\\/107) were assigned an ST, with 98% (98\\/100) correlating with MLST. The array assigned all isolates to the correct SCCmec type, but subtyping of only some SCCmec elements was possible. Additional SCCmec\\/SCC genes or DNA sequence variation not detected by SCCmec typing was detected by array profiling, including the SCC-fusidic acid resistance determinant Q6GD50\\/fusC. Novel SCCmec\\/SCC composite islands (CIs) were detected among CC8 isolates and comprised SCCmec IIA-IIE, IVE, IVF, or IVg and a ccrAB4-SCC element with 99% DNA sequence identity to SCC(M1) from ST8\\/t024-MRSA, SCCmec VIII, and SCC-CI in Staphylococcus epidermidis. The array showed that the majority of isolates harbored one or more superantigen (94%; 100\\/107) and immune evasion cluster (91%; 97\\/107) genes. Apart from fusidic acid and trimethoprim resistance, the correlation between isolate antimicrobial resistance phenotype and the presence of specific resistance genes was ≥97%. Array profiling allowed high-throughput, accurate assignment of MRSA to CCs\\/STs and SCCmec types and provided further evidence of the diversity of SCCmec\\/SCC. In most cases, array profiling can accurately predict the resistance phenotype of an isolate.

  9. A versatile transreplication-based system to identify cellular proteins involved in geminivirus replication.

    Science.gov (United States)

    Morilla, Gabriel; Castillo, Araceli G; Preiss, Werner; Jeske, Holger; Bejarano, Eduardo R

    2006-04-01

    A versatile green fluorescent protein (GFP) expression cassette containing the replication origins of the monopartite begomovirus Tomato yellow leaf curl Sardinia virus (TYLCSV) is described. Transgenic Nicotiana benthamiana plants containing one copy of the cassette stably integrated into their genome were superinfected with TYLCSV, which mobilized and replicated the cassette as an episomal replicon. The expression of the reporter gene (the GFP gene) was thereby modified. Whereas GFP fluorescence was dimmed in the intercostal areas, an increase of green fluorescence in veins of all leaves placed above the inoculation site, as well as in transport tissues of roots and stems, was observed. The release of episomal trans replicons from the transgene and the increase in GFP expression were dependent on the cognate geminiviral replication-associated protein (Rep) and required interaction between Rep and the intergenic region of TYLCSV. This expression system is able to monitor the replication status of TYLCSV in plants, as induction of GFP expression is only produced in those tissues where Rep is present. To further confirm this notion, the expression of a host factor required for geminivirus replication, the proliferating cellular nuclear antigen (PCNA) was transiently silenced. Inhibition of PCNA prevented GFP induction in veins and reduced viral DNA. We propose that these plants could be widely used to easily identify host factors required for geminivirus replication by virus-induced gene silencing. PMID:16537630

  10. Science with the Murchison Widefield Array

    CERN Document Server

    Bowman, Judd D; Kaplan, David L; Murphy, Tara; Oberoi, Divya; Staveley-Smith, Lister; Arcus, Wayne; Barnes, David G; Bernardi, Gianni; Briggs, Frank H; Brown, Shea; Bunton, John D; Burgasser, Adam J; Cappallo, Roger J; Chatterjee, Shami; Corey, Brian E; Coster, Anthea; Deshpande, Avinash; deSouza, Ludi; Emrich, David; Erickson, Philip; Goeke, Robert F; Gaensler, B M; Greenhill, Lincoln J; Harvey-Smith, Lisa; Hazelton, Bryna J; Herne, David; Hewitt, Jacqueline N; Johnston-Hollitt, Melanie; Kasper, Justin C; Kincaid, Barton B; Koenig, Ronald; Kratzenberg, Eric; Lonsdale, Colin J; Lynch, Mervyn J; Matthews, Lynn D; McWhirter, S Russell; Mitchell, Daniel A; Morales, Miguel F; Morgan, Edward H; Ord, Stephen M; Pathikulangara, Joseph; Thiagaraj, Prabu; Remillard, Ronald A; Robishaw, Timothy; Rogers, Alan E E; Roshi, Anish A; Salah, Joseph E; Sault, Robert J; Shankar, N Udaya; Srivani, K S; Stevens, Jamie B; Subrahmanyan, Ravi; Tingay, Steven J; Wayth, Randall B; Waterson, Mark; Webster, Rachel L; Whitney, Alan R; Williams, Andrew J; Williams, Christopher L; Wyithe, J Stuart B

    2012-01-01

    Significant new opportunities for astrophysics and cosmology have been identified at low radio frequencies. The Murchison Widefield Array is the first telescope in the Southern Hemisphere designed specifically to explore the low-frequency astronomical sky between 80 and 300 MHz with arcminute angular resolution and high survey efficiency. The telescope will enable new advances along four key science themes, including searching for redshifted 21 cm emission from the epoch of reionisation in the early Universe; Galactic and extragalactic all-sky southern hemisphere surveys; time-domain astrophysics; and solar, heliospheric, and ionospheric science and space weather. The Murchison Widefield Array is located in Western Australia at the site of the planned Square Kilometre Array (SKA) low-band telescope and is the only low-frequency SKA precursor facility. In this paper, we review the performance properties of the Murchison Widefield Array and describe its primary scientific objectives.

  11. Improving yeast strains using recyclable integration cassettes, for the production of plant terpenoids

    DEFF Research Database (Denmark)

    Ignea, Codruta; Cvetkovic, Ivana; Loupassaki, Sofia; Kefalas, Panagiotis; Johnson, Christopher B; Kampranis, Sotirios C; Makris, Antonios M

    2011-01-01

    the sage species Salvia fruticosa and S. pomifera (SfCinS1, SpP330) in the modified yeast cells identified a range of terpenoids which are also present in the plant essential oils. Co-expression of the putative interacting protein HSP90 with cineole synthase 1 (SfCinS1) also improved production levels...

  12. Cassette Series Designed for Live-Cell Imaging of Proteins and High Resolution Techniques in Yeast

    OpenAIRE

    Young, Carissa L.; Raden, David L.; Caplan, Jeffrey; Czymmek, Kirk; Robinson, Anne S.

    2012-01-01

    During the past decade, it has become clear that protein function and regulation are highly dependent upon intracellular localization. Although fluorescent protein variants are ubiquitously used to monitor protein dynamics, localization, and abundance; fluorescent light microscopy techniques often lack the resolution to explore protein heterogeneity and cellular ultrastructure. Several approaches have been developed to identify, characterize, and monitor the spatial localization of proteins a...

  13. Anomalous effects of moderation in transportation and storage arrays - revisited

    International Nuclear Information System (INIS)

    A number of anomalies have been observed for fissile material arrays. This paper will review anomalous behavior associated with interstitial array moderation and correct one previously-mis-identified anomaly. Most arrays show a maximum keff with low-density water moderation. An earlier study, however, did not show this maximum for unreflected 5x5x5 and 10x10x10 arrays of 15-kg 235U spheres. Our present calculations with MCNP and KENO V.a, however, show low-density maximums for both unreflected and reflected arrays of these units. We conclude that the earlier calculations for unreflected arrays were in error -- perhaps due to problem setup or code errors. The reactivity enhancement due to fissile material density reductions, however, still exits and is now seen to occur for both unreflected and water-reflected arrays

  14. 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

  15. Self-Steering Antenna Arrays for Distributed Picosatellite Networks

    OpenAIRE

    Murakami, Blaine; Ohta, Aaron; Tamamoto, Michael; Shiroma, Grant; Miyamoto, Ryan; Shiroma, Wayne

    2003-01-01

    The potential for using self-steering arrays for secure crosslinks in picosatellite networks is investigated. The principle of operation and methods of characterization of these so-called retrodirective arrays is reviewed, and examples developed by our group are presented. New challenges for the space environment are identified, specifically the development of two-dimensional, circularly polarized retrodirective arrays optimized for size and power consumption.

  16. Generalized Narayana Polynomials, Riordan Arrays and Lattice Paths

    OpenAIRE

    Barry, Paul; Hennessy, Aoife

    2012-01-01

    We study a family of polynomials in two variables, identifying them as the moments of a two-parameter family of orthogonal polynomials. The coefficient array of these orthogonal polynomials is shown to be an ordinary Riordan array. We express the generating function of the sequence of polynomials under study as a continued fraction, and determine the corresponding Hankel transform. An alternative characterization of the polynomials in terms of a related Riordan array is also given. This Riord...

  17. 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.

  18. Permutations of cubical arrays

    International Nuclear Information System (INIS)

    The structure constants of an algebra determine a cube called the cubical array associated with the algebra. The permuted indices of the cubical array associated with a finite semifield generate new division algebras. We do not not require that the algebra be finite and ask 'Is it possible to choose a basis for the algebra such any permutation of the indices of the structure constants leaves the algebra unchanged?' What are the associated algebras? Author shows that the property 'weakly quadratic' is invariant under all permutations of the indices of the corresponding cubical array and presents two algebras for which the cubical array is invariant under all permutations of the indices.

  19. Flexible retinal electrode array

    Energy Technology Data Exchange (ETDEWEB)

    Okandan, Murat (Albuquerque, NM); Wessendorf, Kurt O. (Albuquerque, NM); Christenson, Todd R. (Albuquerque, NM)

    2006-10-24

    An electrode array which has applications for neural stimulation and sensing. The electrode array can include a large number of electrodes each of which is flexibly attached to a common substrate using a plurality of springs to allow the electrodes to move independently. The electrode array can be formed from a combination of bulk and surface micromachining, with electrode tips that can include an electroplated metal (e.g. platinum, iridium, gold or titanium) or a metal oxide (e.g. iridium oxide) for biocompatibility. The electrode array can be used to form a part of a neural prosthesis, and is particularly well adapted for use in an implantable retinal prosthesis where the electrodes can be tailored to provide a uniform gentle contact pressure with optional sensing of this contact pressure at one or more of the electrodes.

  20. Expandable LED array interconnect

    Science.gov (United States)

    Yuan, Thomas Cheng-Hsin; Keller, Bernd

    2011-03-01

    A light emitting device that can function as an array element in an expandable array of such devices. The light emitting device comprises a substrate that has a top surface and a plurality of edges. Input and output terminals are mounted to the top surface of the substrate. Both terminals comprise a plurality of contact pads disposed proximate to the edges of the substrate, allowing for easy access to both terminals from multiple edges of the substrate. A lighting element is mounted to the top surface of the substrate. The lighting element is connected between the input and output terminals. The contact pads provide multiple access points to the terminals which allow for greater flexibility in design when the devices are used as array elements in an expandable array.

  1. Aligators for arrays

    OpenAIRE

    Henzinger, Thomas A.; Hottelier, Thibaud; Kovács, Laura; Rybalchenko, Andrey

    2010-01-01

    This paper presents Aligators, a tool for the generation of universally quantified array invariants. Aligators leverages recurrence solving and algebraic techniques to carry out inductive reasoning over array content. The Aligators’ loop extraction module allows treatment of multi-path loops by exploiting their commutativity and serializability properties. Our experience in applying Aligators on a collection of loops from open source software projects indicates the applicability of recurren...

  2. RFID array sensing

    OpenAIRE

    Capdevila Cascante, Santiago; Jofre Roca, Lluís; Romeu Robert, Jordi; Bolomey, J.Ch

    2010-01-01

    In this paper the use of RFID tags for the measurement of physical parameters in a distributed set of points is presented. Experimental results for two different scenarios are presented; the first uses a 2D RFID array to measure the field distribution of a radiating aperture, while the second detects the change in the close environment of an array of RFID tags to determine the water level of a container.

  3. Subtyping of Chilean Methicillin-Resistant Staphylococcus aureus strains carrying the staphylococcal cassette chromosome mec type I

    Directory of Open Access Journals (Sweden)

    Gustavo Medina

    2012-09-01

    Full Text Available The cassette chromosome mec (SCCmec present in methicillin-resistant Staphylococcus aureus (MRSA has two essential components, the ccr gene complex and the mec gene complex. Additionally, SCCmec has non-essential components called J regions which are used for MRSA subtyping. This study was performed to determine subtypes MRSA strains carrying SCCmec type I based on polymorphism of regions located downstream of the mecA gene. A total of 98 MRSA strains carrying SCCmec type I isolated from patients hospitalized at the County Hospital of Valdivia (Chile between May 2007 and May 2008, were analyzed by multiplex PCR designed to amplify the mecA gene and 7 DNA hypervariable regions located around the mecA gene. MRSA strains were classified into seventeen genotypes accordingly to amplification patterns of DNA hypervariable regions. Five genotypes showed amplification patterns previously described. The remaining twelve genotypes showed new amplification patterns. Genotypes 18 and Genotype 19 were the most frequently detected. Regions HVR, Ins117 and pI258 stand out as being present in more than 60% of tested isolates. The acquisition of hypervariable regions by MRSA is a continuous horizontal transfer process through which the SCCmec have been preserved intact, or even may give rise to new types and subtypes of SCCmec. Therefore it is possible to infer that most MRSA strains isolated at the County Hospital of Valdivia (Chile were originated from two local clones which correspond to Genotype 18 and Genotype 19.

  4. Diversity of staphylococcal cassette chromosome mec elements in predominant methicillin-resistant Staphylococcus aureus clones in a small geographic area.

    Science.gov (United States)

    Basset, Patrick; Senn, Laurence; Vogel, Valérie; Zanetti, Giorgio; Blanc, Dominique S

    2010-11-01

    Recent population genetic studies suggest that staphylococcal cassette chromosome mec (SCCmec) was acquired much more frequently than previously thought. In the present study, we aimed to investigate the diversity of SCCmec elements in a local methicillin-resistant Staphylococcus aureus (MRSA) population. Each MRSA isolate (one per patient) recovered in the Vaud canton of Switzerland from January 2005 to December 2008 was analyzed by the double-locus sequence typing (DLST) method and SCCmec typing. DLST analysis indicated that 1,884/2,036 isolates (92.5%) belong to four predominant clones. As expected from the local spread of a clone, most isolates within clones harbored an identical SCCmec type. However, three to seven SCCmec types have been recovered in every predominant DLST clone, suggesting that some of these elements might have been acquired locally. This pattern could also be explained by distinct importations of related isolates into the study region. The addition of a third highly variable locus to further increase the discriminatory power of typing as well as epidemiological data suggested that most ambiguous situations were explained by the second hypothesis. In conclusion, our study showed that even if the acquisition of new SCCmec elements at a local level likely occurs, it does not explain all the diversity observed in the study region. PMID:20713672

  5. Novel Cellulase Profile of Trichoderma reesei Strains Constructed by cbh1 Gene Replacement with eg3 Gene Expression Cassette

    Institute of Scientific and Technical Information of China (English)

    Tian-Hong WANG; Ti LIU; Zhi-Hong WU; Shi-Li LIU; Yi LU; Yin-Bo QU

    2004-01-01

    To construct strains of the filamentous fungus Trichoderma reesei with low cellobiohydrolases while high endoglucanase activity, the Pcbh1-eg3-Tcbh1 cassette was constructed and the coding sequence of the cellobiohydrolase I (CBHI) gene was replaced with the coding sequence of the eg3 gene by homologous recombination. Disruption of the cbh1 gene was confirmed by PCR, Southern dot blot and Western hybridization analysis in two transforments denoted as L 13 and L29. The filter paper-hydrolyzing activity of strain L29 was 60% of the parent strain Rut C30, and the CMCase activity was increased by 33%. This relatively modest increase suggested that the eg3 cDNA under the control of the cbh1 promoter was not efficiently transcribed as the wild type cbhl gene. However our results confirmed that homologous recombination could be used to construct strains of the filamentous fungus Trichoderma reesei with novel cellulase profile. Such strains are of interest from the basic science perspective and also have potential industrial applications.

  6. Subcellular distribution of small interfering RNA: directed delivery through RNA polymerase III expression cassettes and localization by in situ hybridization.

    Science.gov (United States)

    Paul, Cynthia P

    2005-01-01

    Reduction in the expression of specific genes through small interfering RNAs (siRNAs) is dependent on the colocalization of siRNAs with other components of the RNA interference (RNAi) pathways within the cell. The expression of siRNAs within cells from cassettes that are derived from genes transcribed by RNA polymerase III (pol III) and provide for selective subcellular distribution of their products can be used to direct siRNAs to the cellular pathways. Expression from the human U6 promoter, resulting in siRNA accumulation in the nucleus, is effective in reducing gene expression, whereas cytoplasmic and nucleolar localization of the siRNA when expressed from the 5S or 7 SL promoters is not effective. The distribution of siRNA within the cell is determined by fluorescence in situ hybridization. Although the long uninterrupted duplex of siRNA makes it difficult to detect with DNA oligonucleotide probes, labeled oligonucleotide probes with 2'-O-methyl RNA backbones provide the stability needed for a strong signal. These methods contribute to studies of the interconnected cellular RNAi pathways and are useful in adapting RNAi as a tool to determine gene function and develop RNA-based therapeutics. PMID:15644179

  7. Recombinations in staphylococcal cassette chromosome mec elements compromise the molecular detection of methicillin resistance in Staphylococcus aureus

    KAUST Repository

    Hill-Cawthorne, Grant A.

    2014-06-27

    Clinical laboratories are increasingly using molecular tests for methicillin-resistant Staphylococcus aureus (MRSA) screening. However, primers have to be targeted to a variable chromosomal region, the staphylococcal cassette chromosome mec (SCCmec). We initially screened 726 MRSA isolates from a single UK hospital trust by recombinase polymerase amplification (RPA), a novel, isothermal alternative to PCR. Undetected isolates were further characterised using multilocus sequence, spa typing and whole genome sequencing. 96% of our tested phenotypically MRSA isolates contained one of the six orfX-SCCmec junctions our RPA test and commercially available molecular tests target. However 30 isolates could not be detected. Sequencing of 24 of these isolates demonstrated recombinations within the SCCmec element with novel insertions that interfered with the RPA, preventing identification as MRSA. This result suggests that clinical laboratories cannot rely solely upon molecular assays to reliably detect all methicillin-resistance. The presence of significant recombinations in the SCCmec element, where the majority of assays target their primers, suggests that there will continue to be isolates that escape identification. We caution that dependence on amplification-based molecular assays will continue to result in failure to diagnose a small proportion (?4%) of MRSA isolates, unless the true level of SCCmec natural diversity is determined by whole genome sequencing of a large collection of MRSA isolates. © 2014 Hill-Cawthorne et al.

  8. Recombinations in staphylococcal cassette chromosome mec elements compromise the molecular detection of methicillin resistance in Staphylococcus aureus.

    Directory of Open Access Journals (Sweden)

    Grant A Hill-Cawthorne

    Full Text Available Clinical laboratories are increasingly using molecular tests for methicillin-resistant Staphylococcus aureus (MRSA screening. However, primers have to be targeted to a variable chromosomal region, the staphylococcal cassette chromosome mec (SCCmec. We initially screened 726 MRSA isolates from a single UK hospital trust by recombinase polymerase amplification (RPA, a novel, isothermal alternative to PCR. Undetected isolates were further characterised using multilocus sequence, spa typing and whole genome sequencing. 96% of our tested phenotypically MRSA isolates contained one of the six orfX-SCCmec junctions our RPA test and commercially available molecular tests target. However 30 isolates could not be detected. Sequencing of 24 of these isolates demonstrated recombinations within the SCCmec element with novel insertions that interfered with the RPA, preventing identification as MRSA. This result suggests that clinical laboratories cannot rely solely upon molecular assays to reliably detect all methicillin-resistance. The presence of significant recombinations in the SCCmec element, where the majority of assays target their primers, suggests that there will continue to be isolates that escape identification. We caution that dependence on amplification-based molecular assays will continue to result in failure to diagnose a small proportion (∼4% of MRSA isolates, unless the true level of SCCmec natural diversity is determined by whole genome sequencing of a large collection of MRSA isolates.

  9. Stickleback embryos use ATP-binding cassette transporters as a buffer against exposure to maternally derived cortisol.

    Science.gov (United States)

    Paitz, Ryan T; Bukhari, Syed Abbas; Bell, Alison M

    2016-03-16

    Offspring from females that experience stressful conditions during reproduction often exhibit altered phenotypes and many of these effects are thought to arise owing to increased exposure to maternal glucocorticoids. While embryos of placental vertebrates are known to regulate exposure to maternal glucocorticoids via placental steroid metabolism, much less is known about how and whether egg-laying vertebrates can control their steroid environment during embryonic development. We tested the hypothesis that threespine stickleback (Gasterosteus aculeatus) embryos can regulate exposure to maternal steroids via active efflux of maternal steroids from the egg. Embryos rapidly (within 72 h) cleared intact steroids, but blocking ATP-binding cassette (ABC) transporters inhibited cortisol clearance. Remarkably, this efflux of cortisol was sufficient to prevent a transcriptional response of embryos to exogenous cortisol. Taken together, these findings suggest that, much like their placental counterparts, developing fish embryos can actively regulate their exposure to maternal cortisol. These findings highlight the fact that even in egg-laying vertebrates, the realized exposure to maternal steroids is mediated by both maternal and embryonic processes and this has important implications for understanding how maternal stress influences offspring development. PMID:26984623

  10. Rice Stomatal Closure Requires Guard Cell Plasma Membrane ATP-Binding Cassette Transporter RCN1/OsABCG5.

    Science.gov (United States)

    Matsuda, Shuichi; Takano, Sho; Sato, Moeko; Furukawa, Kaoru; Nagasawa, Hidetaka; Yoshikawa, Shoko; Kasuga, Jun; Tokuji, Yoshihiko; Yazaki, Kazufumi; Nakazono, Mikio; Takamure, Itsuro; Kato, Kiyoaki

    2016-03-01

    Water stress is one of the major environmental stresses that affect agricultural production worldwide. Water loss from plants occurs primarily through stomatal pores. Here, we report that an Oryza sativa half-size ATP-binding cassette (ABC) subfamily G protein, RCN1/OsABCG5, is involved in stomatal closure mediated by phytohormone abscisic acid (ABA) accumulation in guard cells. We found that the GFP-RCN1/OsABCG5-fusion protein was localized at the plasma membrane in guard cells. The percentage of guard cell pairs containing both ABA and GFP-RCN1/OsABCG5 increased after exogenous ABA treatment, whereas they were co-localized in guard cell pairs regardless of whether exogenous ABA was applied. ABA application resulted in a smaller increase in the percentage of guard cell pairs containing ABA in rcn1 mutant (A684P) and RCN1-RNAi than in wild-type plants. Furthermore, polyethylene glycol (drought stress)-inducible ABA accumulation in guard cells did not occur in rcn1 mutants. Stomata closure mediated by exogenous ABA application was strongly reduced in rcn1 mutants. Finally, rcn1 mutant plants had more rapid water loss from detached leaves than the wild-type plants. These results indicate that in response to drought stress, RCN1/OsABCG5 is involved in accumulation of ABA in guard cells, which is indispensable for stomatal closure. PMID:26708605

  11. 多重PCR检测MRSA的SCCmec基因分型%Staphylococcal chromosome cassette typing in MRSA by multiplex PCR

    Institute of Scientific and Technical Information of China (English)

    韩玉涛; 蒋燕群

    2008-01-01

    目的 了解我院MRSA的流行状况.方法 收集2005年1-6月65株社区感染MRSA及60株医院感染MRSA,应用多重PCR对MRSA染色体mec基因盒(Staphylococcal cassette chromosome SCCmec)分型及杀白细胞毒素(PVL)基因检测,应用K-B纸片法进行药敏分析.结果 125株MRSA的mecA基因阳性,其中SCCmecⅡ型1株,SCCmecⅢ型120株,SCCmecⅣ型3株,未分型1株;未发现携带PVL基因的MRSA.携带SCCmecⅡ型、SCCmecⅢ型的菌株均为多重耐药株,而携带SCCmecⅣ型的菌株除对β内酰胺类药物耐药外,对其他类别的抗菌药敏感.结论 本院分离的MRSA以SCCmecⅢ型为主,发现SCCmecⅣ型CA-MRSA,但不携带PVL基因;携带SCCmecⅡ、SCCmecⅢ的临床分离株耐药严重.

  12. Effect of genomic location on horizontal transfer of a recombinant gene cassette between Pseudomonas strains in the rhizosphere and spermosphere of barley seedlings

    DEFF Research Database (Denmark)

    Sengelov, G.; Kristensen, K. J.; Sørensen, Anders Morten Hay;

    2001-01-01

    , horizontal transfer of a recombinant gene cassette inserted into the chromosome of a Pseudomonas strutzeri strain, into a mobilizable plasmid (pAGM42), and into a conjugative plasmid (pKJK5) isolated from barley rhizosphere was investigated. Horizontal transfer efficiencies of the gene cassette inserted into...... a conjugative plasmid was 8.20 x 10(-3) transconjugants/(donors x recipients)(1/2) in the rhizosphere and 4.57 x 10(-2) transconjugants/(donors x recipients)(1/2) in the spermosphere. Mobilization of the plasmid pAGM42 by the plasmids RP4 and pKJK5 was also detected at high levels in the microcosms...

  13. Effect of genomic location on horizontal transfer of a recombinant gene cassette between Pseudomonas strains in the rhizosphere and spermosphere of barley seedlings

    DEFF Research Database (Denmark)

    Sengelov, G.; Kristensen, K. J.; Sørensen, Anders Morten Hay; Kroer, N.; Sørensen, S. J.

    2001-01-01

    The use of genetically engineered bacteria in natural environments constitutes a risk of transfer of recombinant DNA to the indigenous bacteria. However, chromosomal genes are believed to be less likely to transfer than genes on mobilizable and conjugative plasmids. To study this assumption......, horizontal transfer of a recombinant gene cassette inserted into the chromosome of a Pseudomonas strutzeri strain, into a mobilizable plasmid (pAGM42), and into a conjugative plasmid (pKJK5) isolated from barley rhizosphere was investigated. Horizontal transfer efficiencies of the gene cassette inserted into...... a conjugative plasmid was 8.20 x 10(-3) transconjugants/(donors x recipients)(1/2) in the rhizosphere and 4.57 x 10(-2) transconjugants/(donors x recipients)(1/2) in the spermosphere. Mobilization of the plasmid pAGM42 by the plasmids RP4 and pKJK5 was also detected at high levels in the microcosms...

  14. Multidrug efflux pumps: the structures of prokaryotic ATP-binding cassette transporter efflux pumps and implications for our understanding of eukaryotic P-glycoproteins and homologues.

    Science.gov (United States)

    Kerr, Ian D; Jones, Peter M; George, Anthony M

    2010-02-01

    One of the Holy Grails of ATP-binding cassette transporter research is a structural understanding of drug binding and transport in a eukaryotic multidrug resistance pump. These transporters are front-line mediators of drug resistance in cancers and represent an important therapeutic target in future chemotherapy. Although there has been intensive biochemical research into the human multidrug pumps, their 3D structure at atomic resolution remains unknown. The recent determination of the structure of a mouse P-glycoprotein at subatomic resolution is complemented by structures for a number of prokaryotic homologues. These structures have provided advances into our knowledge of the ATP-binding cassette exporter structure and mechanism, and have provided the template data for a number of homology modelling studies designed to reconcile biochemical data on these clinically important proteins. PMID:19961540

  15. Production of transgenic cashmere goat embryos expressing red fluorescent protein and containing IGF1 hair-follicle-cell specific expression cassette by somatic cell nuclear transfer

    Institute of Scientific and Technical Information of China (English)

    BOU; ShorGan

    2009-01-01

    In the present study, cashmere goat fetal fibroblasts were transfected with pCDsR-KI, a hair-follicle-cell specific expression vector for insulin-like growth factor 1 (IGF1) that contains two markers for selection (red fluorescent protein gene and neomycin resistant gene). The transgenic fibroblasts cell lines were obtained after G418 selection. Prior to the somatic cell nuclear transfer (SCNT), the maturation rate of caprine cumulus oocytes complexes (COCs) was optimized to an in vitro maturation time of 18 h. Parthenogenetic ooctyes were used as a model to investigate the effect of two activation methods, one with calcium ionophore IA23187 plus 6-DMAP and the other with ethanol plus 6-DMAP. The cleavage rates after 48 h were respectively 88.7% and 86.4%, with no significant difference (P>0.05). There was no significant difference between the cleavage rate and the blastocyst rate in two different media (SO- Faa and CR1aa; 86.3% vs 83.9%, P>0.05 and 23.1% vs 17.2%,P>0.05). The fusion rate of a 190 V/mm group (62.4%) was significantly higher than 130 V/mm (32.8%) and 200 V/mm (42.9%), groups (P<0.05). After transgenic somatic cell nuclear transfer (TSCNT) manipulation, 203 reconstructed embryos were obtained in which the cleavage rate after in vitro development (IVD) for 48 h was 79.3% (161/203). The blastocyst rate after IVD for 7 to 9 d was 15.3% (31/203). There were 17 embryos out of 31 strongly ex- pressing red fluorescence. Two of the red fluorescent blastocysts were randomly selected to identify transgene by polymerase chain reaction. Both were positive. These results showed that: (i) RFP and Neor genes were correctly expressed indicating that transgenic somatic cell lines and positive trans- genic embryos were obtained; (ii) one more selection at the blastocyst stage was necessary although the donor cells were transgenic positive, because only partially transgenic embryos expressing red fluorescence were obtained; and (iii) through TSCNT manipulation and

  16. Production of transgenic cashmere goat embryos expressing red fluorescent protein and containing IGF1 hair-follicle-cell specific expression cassette by somatic cell nuclear transfer

    Institute of Scientific and Technical Information of China (English)

    GUO XuDong; YANG DongShan; Ao XuDong; WU Xia; LI GuangPeng; WANG LingLing; BAO MingTao; XUE Lian; BOU ShorGan

    2009-01-01

    In the present study, cashmere goat fetal flbroblasta were transfected with pCDsR-KI, a hair-follicle-cell specific expression vector for insulin-like growth factor 1(IGF1) that contains two markers for selection (red fluorescent protein gene and neomycin resistant gene). The transgenic fibroblasta cell lines were obtained after G418 selection. Prior to the somatic cell nuclear transfer (SCNT), the maturation rate of caprine cumulus oocytes complexes (COCs) was optimized to an in vitro maturation time of 18 h.Parthenogenetic ooctyes were used as a model to Investigate the effect of two activation methods, one with calcium ionophore IA23187 plus 6-DMAP and the other with ethanol plus 6-DMAP. The cleavage rates after 48 h were respectively 88.7% and 86.4%, with no significant difference (P>0.05). There was no significant difference between the cleavage rate and the blastocyst rate in two different media (SO-Faa and CR1aa; 86.3% va 83.9%, P>0.05 and 23.1% vs 17.2%, P>0.05). The fusion rate of a 190 V/mm group (62.4%) was significantly higher than 130 V/mm (32.8%) and 200 V/mm (42.9%), groups (P<0.05).After transgenic somatic cell nuclear transfer (TSCNT) manipulation, 203 reconstructed embryos were obtained in which the cleavage rate after in vitro development (IVD) for 48 h was 79.3% (161/203). The blastocyst rate after IVD for 7 to 9 d was 15.3% (31/203). There were 17 embryos out of 31 strongly ex-pressing red fluorescence. Two of the red fluorescent blastocysta were randomly selected to identify transgene by polymeraee chain reaction. Both were positive. These results showed that: (i) RFP and Neo genes were correctly expressed indicating that transgenlc somatic cell lines and positive trans-genic embryos were obtained; (ii) one more selection at the blastocyst stage was necessary although the donor cells were transgenic positive, because only partially transgenic embryos expressing red fluorescence were obtained; and (iii) through TSCNT manipulation and

  17. CNPC makes major breakthrough in array lateral logging technology

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    On October 12, 2011, the array lateral logging tool independently developed by CNPC Well Logging Company was successfully put to use at two production wells at Changqing Oilfield, obtaining high quality logging information. CNPC becomes the second company after Schlumberger in the world to master the array lateral logging technology, which can effectively identify layers as thin as 0.3 meter.

  18. Prenatal Ethanol Exposure Up-Regulates the Cholesterol Transporters ATP-Binding Cassette A1 and G1 and Reduces Cholesterol Levels in the Developing Rat Brain

    OpenAIRE

    Zhou, Chunyan; Chen, Jing; Zhang, Xiaolu; Costa, Lucio G.; Guizzetti, Marina

    2014-01-01

    Aims: Cholesterol plays a pivotal role in many aspects of brain development; reduced cholesterol levels during brain development, as a consequence of genetic defects in cholesterol biosynthesis, leads to severe brain damage, including microcephaly and mental retardation, both of which are also hallmarks of the fetal alcohol syndrome. We had previously shown that ethanol up-regulates the levels of two cholesterol transporters, ABCA1 (ATP binding cassette-A1) and ABCG1, leading to increased cho...

  19. Diversity of Staphylococcal Cassette Chromosome mec Elements in Predominant Methicillin-Resistant Staphylococcus aureus Clones in a Small Geographic Area ▿

    OpenAIRE

    Basset, Patrick; Senn, Laurence; Vogel, Valérie; Zanetti, Giorgio; Blanc, Dominique S.

    2010-01-01

    Recent population genetic studies suggest that staphylococcal cassette chromosome mec (SCCmec) was acquired much more frequently than previously thought. In the present study, we aimed to investigate the diversity of SCCmec elements in a local methicillin-resistant Staphylococcus aureus (MRSA) population. Each MRSA isolate (one per patient) recovered in the Vaud canton of Switzerland from January 2005 to December 2008 was analyzed by the double-locus sequence typing (DLST) method and SCCmec t...

  20. Homologous Recombination-Independent Large Gene Cassette Knock-in in CHO Cells Using TALEN and MMEJ-Directed Donor Plasmids

    OpenAIRE

    Tetsushi Sakuma; Mitsumasa Takenaga; Yoshinori Kawabe; Takahiro Nakamura; Masamichi Kamihira; Takashi Yamamoto

    2015-01-01

    Gene knock-in techniques have rapidly evolved in recent years, along with the development and maturation of genome editing technology using programmable nucleases. We recently reported a novel strategy for microhomology-mediated end-joining-dependent integration of donor DNA by using TALEN or CRISPR/Cas9 and optimized targeting vectors, named PITCh (Precise Integration into Target Chromosome) vectors. Here we describe TALEN and PITCh vector-mediated integration of long gene cassettes, includi...

  1. Staphylococcal Cassette Chromosome mec (SCCmec) Typing of Methicillin-Resistant Staphylococcus aureus Strains Isolated in 11 Asian Countries: a Proposal for a New Nomenclature for SCCmec Elements

    OpenAIRE

    Chongtrakool, Piriyaporn; Ito, Teruyo; Ma, Xiao Xue; Kondo, Yoko; Trakulsomboon, Suwanna; Tiensasitorn, Chuntima; Jamklang, Mantana; Chavalit, Tavinun; Song, Jae-Hoon; Hiramatsu, Keiichi

    2006-01-01

    A description of staphylococcal cassette chromosome mec (SCCmec) elements carried by 615 methicillin-resistant Staphylococcus aureus (MRSA) strains isolated in 11 Asian countries is reported, and a novel nomenclatural system based on their structures is proposed. The 615 strains were classified as type 3A (370 strains), type 2A (207 strains), type 2B (32 strains), type 1B (1 strain), and nontypeable (5 strains). The previously reported type III SCCmec (DDBJ/EMBL/GenBank accession no. AB037671...

  2. A Selective ATP-binding Cassette Sub-family G Member 2 Efflux Inhibitor Revealed Via High-Throughput Flow Cytometry

    OpenAIRE

    Strouse, J. Jacob; Ivnitski-Steele, Irena; Khawaja, Hadya M.; Perez, Dominique; Ricci, Jerec; Yao, Tuanli; Weiner, Warren S.; Schroeder, Chad E.; Simpson, Denise S.; Maki, Brooks E.; Li, Kelin; Golden, Jennifer E.; Foutz, Terry D.; Waller, Anna; Evangelisti, Annette M.

    2012-01-01

    Chemotherapeutics tumor resistance is a principal reason for treatment failure and clinical and experimental data indicate that multidrug transporters such as ATP-binding Cassette (ABC) B1 and ABCG2 play a leading role by preventing cytotoxic intracellular drug concentrations. Functional efflux inhibition of existing chemotherapeutics by these pumps continues to present a promising approach for treatment. A contributing factor to the failure of existing inhibitors in clinical applications is ...

  3. Novel Multiplex PCR Assay for Characterization and Concomitant Subtyping of Staphylococcal Cassette Chromosome mec Types I to V in Methicillin-Resistant Staphylococcus aureus

    OpenAIRE

    Zhang, Kunyan; McClure, Jo-Ann; Elsayed, Sameer; Louie, Thomas; Conly, John M

    2005-01-01

    Staphylococcal cassette chromosome mec (SCCmec) typing is essential for understanding the molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA). SCCmec elements are currently classified into types I to V based on the nature of the mec and ccr gene complexes, and are further classified into subtypes according to their junkyard region DNA segments. Previously described traditional SCCmec PCR typing schemes require multiple primer sets and PCR experiments, while a previous...

  4. Influence of ATP-Binding Cassette Transporter 1 R219K and M883I Polymorphisms on Development of Atherosclerosis: A Meta-Analysis of 58 Studies

    OpenAIRE

    Yin, Yan-Wei; Li, Jing-Cheng; Gao, Dong; Chen, Yan-Xiu; Li, Bing-Hu; Wang, Jing-Zhou; Liu, Yun; Liao, Shao-Qiong; Zhang, Ming-Jie; Chang-yue GAO; Zhang, Li-li

    2014-01-01

    Background Numerous epidemiological studies have evaluated the associations between ATP-binding cassette transporter 1 (ABCA1) R219K (rs2230806) and M883I (rs4149313) polymorphisms and atherosclerosis (AS), but results remain controversial. The purpose of the present study is to investigate whether these two polymorphisms facilitate the susceptibility to AS using a meta-analysis. Methods PubMed, Embase, Web of Science, Medline, Cochrane database, Clinicaltrials.gov, Current Controlled Trials,...

  5. ATP and AMP Mutually Influence Their Interaction with the ATP-binding Cassette (ABC) Adenylate Kinase Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) at Separate Binding Sites*

    OpenAIRE

    Randak, Christoph O.; Dong, Qian; Ver Heul, Amanda R.; Elcock, Adrian H.; Welsh, Michael J.

    2013-01-01

    Cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel in the ATP-binding cassette (ABC) transporter protein family. In the presence of ATP and physiologically relevant concentrations of AMP, CFTR exhibits adenylate kinase activity (ATP + AMP ⇆ 2 ADP). Previous studies suggested that the interaction of nucleotide triphosphate with CFTR at ATP-binding site 2 is required for this activity. Two other ABC proteins, Rad50 and a structural maintenance of chromosome protein, ...

  6. Optimizing Chemical Sensor Array Sizes

    International Nuclear Information System (INIS)

    Optimal selection of array sensors for a chemical sensing application is a nontrivial task. It is commonly believed that ''more is better'' when choosing the number of sensors required to achieve good chemical selectivity. However, cost and system complexity issues point towards the choice of small arrays. A quantitative array optimization is carried out to explore the selectivity of arrays of partially-selective chemical sensors as a function of array size. It is shown that modest numbers (dozens) of target analytes are completely distinguished with a range of arrays sizes. However, the array selectivity and the robustness against sensor sensitivity variability are significantly degraded if the array size is increased above a certain number of sensors, so that relatively small arrays provide the best performance. The results also suggest that data analyses for very large arrays of partially-selective sensors will be optimized by separately anal yzing small sensor subsets

  7. Characterization of a novel arginine catabolic mobile element (ACME) and staphylococcal chromosomal cassette mec composite island with significant homology to Staphylococcus epidermidis ACME type II in methicillin-resistant Staphylococcus aureus genotype ST22-MRSA-IV.

    LENUS (Irish Health Repository)

    Shore, Anna C

    2011-05-01

    The arginine catabolic mobile element (ACME) is prevalent among methicillin-resistant Staphylococcus aureus (MRSA) isolates of sequence type 8 (ST8) and staphylococcal chromosomal cassette mec (SCCmec) type IVa (USA300) (ST8-MRSA-IVa isolates), and evidence suggests that ACME enhances the ability of ST8-MRSA-IVa to grow and survive on its host. ACME has been identified in a small number of isolates belonging to other MRSA clones but is widespread among coagulase-negative staphylococci (CoNS). This study reports the first description of ACME in two distinct strains of the pandemic ST22-MRSA-IV clone. A total of 238 MRSA isolates recovered in Ireland between 1971 and 2008 were investigated for ACME using a DNA microarray. Twenty-three isolates (9.7%) were ACME positive, and all were either MRSA genotype ST8-MRSA-IVa (7\\/23, 30%) or MRSA genotype ST22-MRSA-IV (16\\/23, 70%). Whole-genome sequencing and comprehensive molecular characterization revealed the presence of a novel 46-kb ACME and staphylococcal chromosomal cassette mec (SCCmec) composite island (ACME\\/SCCmec-CI) in ST22-MRSA-IVh isolates (n=15). This ACME\\/SCCmec-CI consists of a 12-kb DNA region previously identified in ACME type II in S. epidermidis ATCC 12228, a truncated copy of the J1 region of SCCmec type I, and a complete SCCmec type IVh element. The composite island has a novel genetic organization, with ACME located within orfX and SCCmec located downstream of ACME. One PVL locus-positive ST22-MRSA-IVa isolate carried ACME located downstream of SCCmec type IVa, as previously described in ST8-MRSA-IVa. These results suggest that ACME has been acquired by ST22-MRSA-IV on two independent occasions. At least one of these instances may have involved horizontal transfer and recombination events between MRSA and CoNS. The presence of ACME may enhance dissemination of ST22-MRSA-IV, an already successful MRSA clone.

  8. Imaging antenna arrays

    Science.gov (United States)

    Rutledge, D. B.; Muha, M. S.

    1982-01-01

    Many millimeter and far-infrared imaging systems are limited in sensitivity and speed because they depend on a single scanned element. Because of recent advances in planar detectors such as Schottky diodes, superconducting tunnel junctions, and microbolometers, an attractive approach to this problem is a planar antenna array with integrated detectors. A planar line antenna array and optical system for imaging has been developed. The significant advances are a 'reverse-microscope' optical configuration and a modified bow-tie antenna design. In the 'reverse-microscope' configuration, a lens is attached to the bottom of the substrate containing the antennas. Imaging is done through the substrate. This configuration eliminates the troublesome effects of substrate surface waves. The substrate lens has only a single refracting surface, making possible a virtually aplanatic system, with little spherical aberration or coma. The array is characterized by an optical transfer function that is easily measured. An array with 19 dB crosstalk levels between adjacent antennas has been tested and it was found that the array captured 50 percent of the available power. This imaging system was diffraction limited.

  9. EAS selection in the EMMA underground array

    DEFF Research Database (Denmark)

    Sarkamo, J.; Bezrukov, L.; Enqvist, T.;

    2013-01-01

    The first measurements of the Experiment with MultiMuon Array (EMMA) have been analyzed for the selection of the Extensive Air Showers (EAS). Test data were recorded with an underground muon tracking station and a satellite station separated laterally by 10 metres. Events with tracks distributed...... over all of the tracking detector area and even extending over to the satellite station are identified as EAS. The recorded multiplicity spectrum of the events is in general agreement with CORSIKA EAS simulation and demonstrates the array's capability of EAS detection....

  10. Array-based techniques for fingerprinting medicinal herbs

    Directory of Open Access Journals (Sweden)

    Xue Charlie

    2011-05-01

    Full Text Available Abstract Poor quality control of medicinal herbs has led to instances of toxicity, poisoning and even deaths. The fundamental step in quality control of herbal medicine is accurate identification of herbs. Array-based techniques have recently been adapted to authenticate or identify herbal plants. This article reviews the current array-based techniques, eg oligonucleotides microarrays, gene-based probe microarrays, Suppression Subtractive Hybridization (SSH-based arrays, Diversity Array Technology (DArT and Subtracted Diversity Array (SDA. We further compare these techniques according to important parameters such as markers, polymorphism rates, restriction enzymes and sample type. The applicability of the array-based methods for fingerprinting depends on the availability of genomics and genetics of the species to be fingerprinted. For the species with few genome sequence information but high polymorphism rates, SDA techniques are particularly recommended because they require less labour and lower material cost.

  11. FEL phased array configurations

    Science.gov (United States)

    Shellan, Jeffrey B.

    1986-01-01

    The advantages and disadvantages of various phased array and shared aperture concepts for FEL configurations are discussed. Consideration is given to the characteristics of intra- and inter-micropulse phasing; intra-macropulse phasing; an internal coupled resonator configuration; and an injection locked oscillator array. The use of a master oscillator power amplifier (MOPA) configuration with multiple or single master oscillators for FELs is examined. The venetian blind, rotating plate, single grating, and grating rhomb shared aperture concepts are analyzed. It is noted that the shared aperture approach using a grating rhomb and the MOPA concept with a single master oscillator and a coupled resonator are useful for FEL phased array configurations; and the MOPA concept is most applicable.

  12. MODELLING AND CONTROL OF PARTIALLY SHADED PHOTOVOLTAIC ARRAYS

    Directory of Open Access Journals (Sweden)

    Chia Seet Chin

    2013-01-01

    Full Text Available The photovoltaic (PV array controlled by Maximum Power Point Tracking (MPPT method for optimum PV power generation, particularly when the PV array is under partially shaded condition is presented in this paper. The system modelling is carried out in MATLAB-SIMULINK where the PV array is formed by five series connected identical PV modules. Under uniform solar irradiance conditions, the PV module and the PV array present nonlinear P-V characteristic but the maximum power point (MPP can be easily identified. However, when the PV array is under shaded conditions, the P-V characteristic becomes more complex with the present of multiple MPP. While the PV array operated at local MPP, the generated power is limited. Thus, the investigation on MPPT approach is carried out to maximize the PV generated power even when the PV array is under partially shaded conditions (PSC. Fuzzy logic is adopted into the conventional MPPT to form fuzzy logic based MPPT (FMPPT for better performance. The developed MPPT and FMPPT are compared, particularly the performances on the transient response and the steady state response when the array is under various shaded conditions. FMPPT shows better performance where the simulation results demonstrate FMPPT is able to facilitate the PV array to reach the MPP faster while it helps the PV array to produce a more stable output power.

  13. SNP Array in Hematopoietic Neoplasms: A Review

    Science.gov (United States)

    Song, Jinming; Shao, Haipeng

    2015-01-01

    Cytogenetic analysis is essential for the diagnosis and prognosis of hematopoietic neoplasms in current clinical practice. Many hematopoietic malignancies are characterized by structural chromosomal abnormalities such as specific translocations, inversions, deletions and/or numerical abnormalities that can be identified by karyotype analysis or fluorescence in situ hybridization (FISH) studies. Single nucleotide polymorphism (SNP) arrays offer high-resolution identification of copy number variants (CNVs) and acquired copy-neutral loss of heterozygosity (LOH)/uniparental disomy (UPD) that are usually not identifiable by conventional cytogenetic analysis and FISH studies. As a result, SNP arrays have been increasingly applied to hematopoietic neoplasms to search for clinically-significant genetic abnormalities. A large numbers of CNVs and UPDs have been identified in a variety of hematopoietic neoplasms. CNVs detected by SNP array in some hematopoietic neoplasms are of prognostic significance. A few specific genes in the affected regions have been implicated in the pathogenesis and may be the targets for specific therapeutic agents in the future. In this review, we summarize the current findings of application of SNP arrays in a variety of hematopoietic malignancies with an emphasis on the clinically significant genetic variants.

  14. Deployable Structural Booms for Large Deployable Solar Arrays Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The development of a new generation of large, high power deployable solar arrays has been identified as the most significant challenge facing the development of...

  15. Design and Analysis Tools for Deployable Solar Array Systems Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Large, lightweight, deployable solar array structures have been identified as a key enabling technology for NASA with analysis and design of these structures being...

  16. Atacama Compact Array Antennas

    OpenAIRE

    Saito, Masao; Inatani, Junji; Nakanishi, Kouichiro; Naoi, Takahiro; Yamada, Masumi; Saito, Hiro; Ikenoue, Bungo; Kato, Yoshihiro; Morita, Kou-ichiro; Mizuno, Norikazu; Iguchi, Satoru

    2011-01-01

    We report major performance test results of the Atacama Compact Array (ACA) 7-m and 12-m antennas of ALMA (Atacama Large Millimeter/submillimeter Array). The four major performances of the ACA antennas are all-sky pointing (to be not more than 2.0 arcsec), offset pointing (to be < 0.6 arcsec) surface accuracy (< 25(20) micrometer for 12(7)m-antenna), stability of path-length (15 micrometer over 3 min), and high servo capability (6 degrees/s for Azimuth and 3 degrees/s for Elevation). The high...

  17. 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

  18. Overexpression of the ATP binding cassette gene ABCA1 determines resistance to Curcumin in M14 melanoma cells

    Directory of Open Access Journals (Sweden)

    Angelini Giovanna

    2009-12-01

    Full Text Available Abstract Background Curcumin induces apoptosis in many cancer cells and it reduces xenograft growth and the formation of lung metastases in nude mice. Moreover, the plant derived polyphenol has been reported to be able to overcome drug resistance to classical chemotherapy. These features render the drug a promising candidate for tumor therapy especially for cancers known for their high rates concerning therapy resistance like melanoma. Results We show here that the melanoma cell line M14 is resistant to Curcumin induced apoptosis, which correlates with the absence of any effect on NFκB signaling. We show that CXCL1 a chemokine that is down regulated in breast cancer cells by Curcumin in an NFκB dependant manner is expressed at variable levels in human melanomas. Yet in M14 cells, CXCL1 expression did not change upon Curcumin treatment. Following the hypothesis that Curcumin is rapidly removed from the resistant cells, we analyzed expression of known multi drug resistance genes and cellular transporters in M14 melanoma cells and in the Curcumin sensitive breast cancer cell line MDA-MB-231. ATP-binding cassette transporter ABCA1, a gene involved in the cellular lipid removal pathway is over-expressed in resistant M14 melanoma as compared to the sensitive MDA-MB-231 breast cancer cells. Gene silencing of ABCA1 by siRNA sensitizes M14 cells to the apoptotic effect of Curcumin most likely as a result of reduced basal levels of active NFκB. Moreover, ABCA1 silencing alone also induces apoptosis and reduces p65 expression. Conclusion Resistance to Curcumin thus follows classical pathways and ABCA1 expression should be considered as response marker.

  19. Ablation of the ATP-binding cassette transporter, Abca2 modifies response to estrogen-based therapies.

    Science.gov (United States)

    Mack, Jody T; Brown, Carol B; Garrett, Tracy E; Uys, Joachim D; Townsend, Danyelle M; Tew, Kenneth D

    2012-09-01

    The ATP-binding cassette transporter 2 (ABCA2) is an endolysosomal protein expressed in oligodendrocytes and Schwann cells, prostate, ovary and macrophages. In cell cultures, ABCA2 over-expression has been linked with resistance to the anticancer agent, estramustine phosphate (EMP; a nor-nitrogen mustard conjugate of estradiol). The present study shows that Abca2 knockout (KO) mice have greater sensitivity to a variety of side effects induced by EMP treatment. Chronic EMP (12×100 mg/kg body weight) produced mortality in 36% of KO mice, but only 7% of age-matched wild type (WT). Side effects of the drug were also more prevalent in the KO mouse. For example, during the first week of EMP treatments, 67% of KO males (compared to 6% of WT males) responded with episodic erectile events. In WT mice, ABCA2 protein localized within pene corpuscles, (which rely on modified Schwann cells for amplification of tactile signals) suggesting that the transporter may function in the erectile process. Endothelial nitric oxide synthase (eNOS; a source of nitric oxide during erectile response) levels were similar in WT and KO male penile tissue. Treatment with 100 mg/kg EMP (once daily for four days) elevated serum estradiol and estrone in both WT and KO. However, the circulating levels of these estrogens were higher in KO mice implying a reduced plasma clearance of estrogens as a consequence of ABCA2 ablation. Consistent with the pro-convulsant effects of estrogens, KO mice also displayed an increased incidence of seizures following EMP (14% vs. 0%). Taken together, these data indicate that ABCA2 deficiency renders mice more sensitive to EMP treatment-induced effects implying that the transporter has a role in regulating EMP transport and/or metabolism. PMID:22898081

  20. Rapid Emergence and Evolution of Staphylococcus aureus Clones Harboring fusC-Containing Staphylococcal Cassette Chromosome Elements.

    Science.gov (United States)

    Baines, Sarah L; Howden, Benjamin P; Heffernan, Helen; Stinear, Timothy P; Carter, Glen P; Seemann, Torsten; Kwong, Jason C; Ritchie, Stephen R; Williamson, Deborah A

    2016-04-01

    The prevalence of fusidic acid (FA) resistance amongStaphylococcus aureusstrains in New Zealand (NZ) is among the highest reported globally, with a recent study describing a resistance rate of approximately 28%. Three FA-resistantS. aureusclones (ST5 MRSA, ST1 MSSA, and ST1 MRSA) have emerged over the past decade and now predominate in NZ, and in all three clones FA resistance is mediated by thefusCgene. In particular, ST5 MRSA has rapidly become the dominant MRSA clone in NZ, although the origin of FA-resistant ST5 MRSA has not been explored, and the genetic context offusCin FA-resistant NZ isolates is unknown. To better understand the rapid emergence of FA-resistantS. aureus, we used population-based comparative genomics to characterize a collection of FA-resistant and FA-susceptible isolates from NZ. FA-resistant NZ ST5 MRSA displayed minimal genetic diversity and represented a phylogenetically distinct clade within a global population model of clonal complex 5 (CC5)S. aureus In all lineages,fusCwas invariably located within staphylococcal cassette chromosome (SCC) elements, suggesting that SCC-mediated horizontal transfer is the primary mechanism offusCdissemination. The genotypic association offusCwithmecAhas important implications for the emergence of MRSA clones in populations with high usage of fusidic acid. In addition, we found thatfusCwas colocated with a recently described virulence factor (tirS) in dominant NZS. aureusclones, suggesting a fitness advantage. This study points to the likely molecular mechanisms responsible for the successful emergence and spread of FA-resistantS. aureus. PMID:26856837

  1. Osimertinib (AZD9291) Attenuates the Function of Multidrug Resistance-Linked ATP-Binding Cassette Transporter ABCB1 in Vitro.

    Science.gov (United States)

    Hsiao, Sung-Han; Lu, Yu-Jen; Li, Yan-Qing; Huang, Yang-Hui; Hsieh, Chia-Hung; Wu, Chung-Pu

    2016-06-01

    The effectiveness of cancer chemotherapy is often circumvented by multidrug resistance (MDR) caused by the overexpression of ATP-binding cassette (ABC) drug transporter ABCB1 (MDR1, P-glycoprotein). Several epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) have been shown previously capable of modulating the function of ABCB1 and reversing ABCB1-mediated MDR in human cancer cells. Furthermore, some TKIs are transported by ABCB1, which results in low oral bioavailability, reduced distribution, and the development of acquired resistance to these TKIs. In this study, we investigated the interaction between ABCB1 and osimertinib, a novel selective, irreversible third-generation EGFR TKI that has recently been approved by the U.S. Food and Drug Administration. We also evaluated the potential impact of ABCB1 on the efficacy of osimertinib in cancer cells, which can present a therapeutic challenge to clinicians in the future. We revealed that although osimertinib stimulates the ATPase activity of ABCB1, overexpression of ABCB1 does not confer resistance to osimertinib. Our results suggest that it is unlikely that the overexpression of ABCB1 can be a major contributor to the development of osimertinib resistance in cancer patients. More significantly, we revealed an additional action of osimertinib that directly inhibits the function of ABCB1 without affecting the expression level of ABCB1, enhances drug-induced apoptosis, and reverses the MDR phenotype in ABCB1-overexpressing cancer cells. Considering that osimertinib is a clinically approved third-generation EGFR TKI, our findings suggest that a combination therapy with osimertinib and conventional anticancer drugs may be beneficial to patients with MDR tumors. PMID:27169328

  2. Influenza A vaccines using linear expression cassettes delivered via electroporation afford full protection against challenge in a mouse model.

    Science.gov (United States)

    Shen, Xuefei; Söderholm, Jonas; Lin, Feng; Kobinger, Gary; Bello, Alexander; Gregg, Derek A; Broderick, Kate E; Sardesai, Niranjan Y

    2012-11-01

    Alternative DNA vaccine constructs such as fully synthetic linear expressing cassettes (LECs) offer the advantage of accelerated manufacturing techniques as well as the lack of both antibiotic resistance genes and bacterial contaminants. The speed of manufacture makes LEC technology a possible future vaccination strategy for pandemic influenza outbreaks. Previously, we reported on a novel concept of DNA delivery to dermal tissue by a minimally invasive electroporation (EP) surface device powered using low voltage parameters. This device allows electroporation without penetration of electrodes into the skin. In addition to enhancing the delivery of traditional plasmid DNA vaccines, this device may also offer a safe, tolerable and efficient method to administer LECs. To assess immunogenicity and efficacy of EP-enhanced LEC delivery in mice, we designed and tested two influenza antigens in the form of LEC constructs delivered using the newly developed surface dermal EP device. Strong CTL and antibody responses were induced by the LEC versions of the DNA vaccine. When challenged with A/Canada/AB/RV1532/2009 viruses, mice immunized with LEC encoding the M2 and NP antigens recovered faster than naïve or mice immunized ID without EP. Mice immunized with equal-molar doses of LEC encoding the M2 and NP antigens demonstrated 100% survival following a lethal (100× LD50) challenge of the heterologuos and highly pathogenic H5N1 influenza virus (A/Vietnam/1203/04). These results suggest that influenza DNA vaccines based on LEC technology combined with the surface delivery platform are capable of fully protecting mice in a lethal challenge and the LEC based DNA constructs may serve as viable vaccine candidates. PMID:22406460

  3. Mission applications for advanced photovoltaic solar arrays

    International Nuclear Information System (INIS)

    The compatibility of the advanced photovoltaic solar array (APSA) for future space missions was examined by considering the impact on the spacecraft system in general. The lightweight flexible blanket array system (> 130 w/kG) was compared to rigid arrays and an RTG (radio-isotope thermoelectric generator) static power source for a wide range of assumed future Earth orbiting and interplanetary mission applications. The study approach was to establish assessment criteria and a rating scheme, identify a reference mission set, perform the power system assessment for each mission, and develop conclusions and recommendations to guide future APSA technology development. This paper discusses the three selected power sources, the assessment criteria and rating definitions, the reference missions, and presents the assessment results in a tabular format

  4. Turbulent chimeras in large semiconductor laser arrays

    CERN Document Server

    Shena, Joniald; Kovanis, Vassilios; Tsironis, George P

    2016-01-01

    Semiconductor laser arrays have been investigated experimentally and theoretically from the viewpoint of temporal and spatial coherence for the past forty years. In this work, we are focusing on a rather novel complex collective behavior, namely chimera states, where synchronized clusters of emitters coexist with unsynchronized ones. For the first time, we find such states exist in large diode arrays based on quantum well gain media with nearest-neighbor interactions. The crucial parameters are the evanescent coupling strength and the relative optical frequency detuning between the emitters of the array. By employing a recently proposed figure of merit for classifying chimera states, we provide quantitative and qualitative evidence for the observed dynamics. The corresponding chimeras are identified as turbulent according to the irregular temporal behavior of the classification measure. Such studies may be the springboard for designing next generation photonic emitters providing on demand diverse waveforms.

  5. Array processors in chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Ostlund, N.S.

    1980-01-01

    The field of attached scientific processors (''array processors'') is surveyed, and an attempt is made to indicate their present and possible future use in computational chemistry. The current commercial products from Floating Point Systems, Inc., Datawest Corporation, and CSP, Inc. are discussed.

  6. 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...

  7. Detector array and method

    International Nuclear Information System (INIS)

    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

  8. The Murchison Widefield Array

    NARCIS (Netherlands)

    Mitchell, Daniel A.; Greenhill, Lincoln J.; Ord, Stephen M.; Bernardi, Gianni

    2010-01-01

    It is shown that the excellent Murchison Radio-astronomy Observatory site allows the Murchison Widefield Array to employ a simple RFI blanking scheme and still calibrate visibilities and form images in the FM radio band. The techniques described are running autonomously in our calibration and imagin

  9. Cantilever array sensors

    Directory of Open Access Journals (Sweden)

    Hans Peter Lang

    2005-04-01

    Full Text Available Miniaturized microfabricated sensors have enormous potential in gas detection, biochemical analysis, medical applications, quality and process control, and product authenticity issues. Here, we highlight an ultrasensitive mechanical way of converting (bio-chemical or physical processes into a recordable signal using microfabricated cantilever arrays.

  10. Novel immune-modulator identified by a rapid, functional screen of the parapoxvirus ovis (Orf virus genome

    Directory of Open Access Journals (Sweden)

    McGuire Michael J

    2012-01-01

    Full Text Available Abstract Background The success of new sequencing technologies and informatic methods for identifying genes has made establishing gene product function a critical rate limiting step in progressing the molecular sciences. We present a method to functionally mine genomes for useful activities in vivo, using an unusual property of a member of the poxvirus family to demonstrate this screening approach. Results The genome of Parapoxvirus ovis (Orf virus was sequenced, annotated, and then used to PCR-amplify its open-reading-frames. Employing a cloning-independent protocol, a viral expression-library was rapidly built and arrayed into sub-library pools. These were directly delivered into mice as expressible cassettes and assayed for an immune-modulating activity associated with parapoxvirus infection. The product of the B2L gene, a homolog of vaccinia F13L, was identified as the factor eliciting immune cell accumulation at sites of skin inoculation. Administration of purified B2 protein also elicited immune cell accumulation activity, and additionally was found to serve as an adjuvant for antigen-specific responses. Co-delivery of the B2L gene with an influenza gene-vaccine significantly improved protection in mice. Furthermore, delivery of the B2L expression construct, without antigen, non-specifically reduced tumor growth in murine models of cancer. Conclusion A streamlined, functional approach to genome-wide screening of a biological activity in vivo is presented. Its application to screening in mice for an immune activity elicited by the pathogen genome of Parapoxvirus ovis yielded a novel immunomodulator. In this inverted discovery method, it was possible to identify the adjuvant responsible for a function of interest prior to a mechanistic study of the adjuvant. The non-specific immune activity of this modulator, B2, is similar to that associated with administration of inactivated particles to a host or to a live viral infection. Administration

  11. Concurrent array-based queue

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. 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

  13. 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

  14. INHIBITION OF ACTIVATED K-RAS GENE BY SIRNA EXPRESSION CASSETTES IN HUMAN PANCREATIC CARCINOMA CELL LINE MIAPACA-2

    Institute of Scientific and Technical Information of China (English)

    WANG Wei; WANG Chun-you; DONG Ji-hua; CHEN Xiong; ZHANG Min; ZHAO Gang

    2005-01-01

    Objective: To construct the small interfering RNA(siRNA) expression cassettes (SECs) targeting activated K-ras gene sequence and investigate the effects of SECs on K-ras gene in human pancreatic cancer cell line MIAPaCa-2. Methods: Three different sites of SECs were constructed by PCR. The K1/siRNA, K2/siRNA and K3/siRNA were located at the site 194, 491 and 327, respectively. They were transfected into MiaPaCa-2 cells by liposome to inhibit the expression of activated K-ras. In the interfering groups of site 194,491, we observed the cytopathic effect of confluent MiaPaCa-2 cells after they were incubated for 48 hours, and detected the apoptosis in cells by FACS, then we tested the alternation of K-ras gene in confluent MiaPaCa-2 cells by RT-PCR,immunofluorescence and western blot, respectively. Results: Introductions of the K1/siRNA and K2/siRNA against K-ras into MiaPaCa-2 cells led to cytopathic effect, slower proliferation and increased apoptosis, while the appearances of control MiaPaCa-2 cells remained well. The number of apoptotic cells increased compared with control cells. RT-PCR,immunofluorescence and western blot showed the effects of inhibited expression of activated K-ras gene by RNA interference in the K1/siRNA and K2/siRNA groups. We also found that the introduction of K3/siRNA had no effect on MiaPaCa-2 cells. Conclusion: K1/siRNA and K2/siRNA can inhibit the expression of activated K-ras and decrease the growth of MiaPaCa-2 cells, while K3/siRNA has no such effect, demonstrating that the suppression of tumor growth by siRNA is sequence-specific. We conclude that K-ras is involved in maintenance of tumor growth of human pancreatic cancer, and SECs against K-ras expression may be a powerful tool to be used therapeutically against human pancreatic cancer.

  15. Mobile insertion cassette elements found in small non-transmissible plasmids in Proteeae may explain qnrD mobilization.

    Directory of Open Access Journals (Sweden)

    Thomas Guillard

    Full Text Available qnrD is a plasmid mediated quinolone resistance gene from unknown origin, recently described in Enterobacteriaceae. It encodes a pentapeptide repeat protein 36-60% different from the other Qnr (A, B, C, S and VC. Since most qnrD-positive strains were described as strains belonging to Proteus or Providencia genera, we hypothesized that qnrD originated in Proteeae before disseminating to other enterobacterial species. We screened 317 strains of Proteeae for qnrD and its genetic support by PCR. For all the seven qnrD-positive strains (4 Proteus mirabilis, 1 Proteus vulgaris and 2 Providencia rettgeri the gene was carried onto a small non-transmissible plasmid, contrarily to other qnr genes that are usually carried onto large multi-resistant plasmids. Nucleotide sequences of the qnrD-bearing plasmids were 96% identical. Plasmids contained 3 ORFs apart from qnrD and belonged to an undescribed incompatibility group. Only one plasmid, in P. vulgaris, was slightly different with a 1,568-bp insertion between qnrD and its promoter, leading to absence of quinolone resistance. We sought for similar plasmids in 15 reference strains of Proteeae, but which were tested negative for qnrD, and found a 48% identical plasmid (pVERM in Providencia vermicola. In order to explain how qnrD could have been inserted into such native plasmid, we sought for gene mobilization structures. qnrD was found to be located within a mobile insertion cassette (mic element which sequences are similar to one mic also found in pVERM. Our conclusions are that (i the small non-transmissible qnrD-plasmids described here may result from the recombination between an as-yet-unknown progenitor of qnrD and pVERM, (ii these plasmids are maintained in Proteeae being a qnrD reservoir (iii the mic element may explain qnrD mobilization from non-transmissible plasmids to mobilizable or conjugative plasmids from other Enterobacteriaceae, (iv they can recombined with larger multiresistant plasmids

  16. Microreactor Array Device

    Science.gov (United States)

    Wiktor, Peter; Brunner, Al; Kahn, Peter; Qiu, Ji; Magee, Mitch; Bian, Xiaofang; Karthikeyan, Kailash; Labaer, Joshua

    2015-03-01

    We report a device to fill an array of small chemical reaction chambers (microreactors) with reagent and then seal them using pressurized viscous liquid acting through a flexible membrane. The device enables multiple, independent chemical reactions involving free floating intermediate molecules without interference from neighboring reactions or external environments. The device is validated by protein expressed in situ directly from DNA in a microarray of ~10,000 spots with no diffusion during three hours incubation. Using the device to probe for an autoantibody cancer biomarker in blood serum sample gave five times higher signal to background ratio compared to standard protein microarray expressed on a flat microscope slide. Physical design principles to effectively fill the array of microreactors with reagent and experimental results of alternate methods for sealing the microreactors are presented.

  17. Optically interconnected phased arrays

    Science.gov (United States)

    Bhasin, Kul B.; Kunath, Richard R.

    1988-01-01

    Phased-array antennas are required for many future NASA missions. They will provide agile electronic beam forming for communications and tracking in the range of 1 to 100 GHz. Such phased arrays are expected to use several hundred GaAs monolithic integrated circuits (MMICs) as transmitting and receiving elements. However, the interconnections of these elements by conventional coaxial cables and waveguides add weight, reduce flexibility, and increase electrical interference. Alternative interconnections based on optical fibers, optical processing, and holography are under evaluation as possible solutions. In this paper, the current status of these techniques is described. Since high-frequency optical components such as photodetectors, lasers, and modulators are key elements in these interconnections, their performance and limitations are discussed.

  18. Atacama Compact Array Antennas

    CERN Document Server

    Saito, Masao; Nakanishi, Kouichiro; Naoi, Takahiro; Yamada, Masumi; Saito, Hiro; Ikenoue, Bungo; Kato, Yoshihiro; Morita, Kou-ichiro; Mizuno, Norikazu; Iguchi, Satoru

    2011-01-01

    We report major performance test results of the Atacama Compact Array (ACA) 7-m and 12-m antennas of ALMA (Atacama Large Millimeter/submillimeter Array). The four major performances of the ACA antennas are all-sky pointing (to be not more than 2.0 arcsec), offset pointing (to be < 0.6 arcsec) surface accuracy (< 25(20) micrometer for 12(7)m-antenna), stability of path-length (15 micrometer over 3 min), and high servo capability (6 degrees/s for Azimuth and 3 degrees/s for Elevation). The high performance of the ACA antenna has been extensively evaluated at the Site Erection Facility area at an altitude of about 2900 meters. Test results of pointing performance, surface performance, and fast motion capability are demonstrated.

  19. The Murchison Widefield Array

    CERN Document Server

    Mitchell, Daniel A; Ord, Stephen M; Bernardi, Gianni; Wayth, Randall B; Edgar, Richard G; Clark, Michael A; Dal, Kevin; Pfister, Hanspeter; Gleadow, Stewart J; Arcus, W; Briggs, F H; Benkevitch, L; Bowman, J D; Bunton, J D; Burns, S; Cappallo, R J; Corey, B E; de Oliveira-Costa, A; Desouza, L; Doeleman, S S; Derome, M F; Emrich, D; Glossop, M; Goeke, R; Krishna, M R Gopala; Hazelton, B; Herne, D E; Hewitt, J N; Kamini, P A; Kaplan, D L; Kasper, J C; Kincaid, B B; Kocz, J; Kowald, E; Kratzenberg, E; Kumar, D; Lonsdale, C J; Lynch, M J; Madhavi, S; Matejek, M; McWhirter, S R; Morales, M F; Morgan, E; Oberoi, D; Pathikulangara, J; Prabu, T; Rogers, A; Salah, J E; Sault, R J; Shankar, N Udaya; Srivani, K S; Stevens, J; Tingay, S J; Vaccarella, A; Waterson, M; Webster, R L; Whitney, A R; Williams, A; Williams, C

    2010-01-01

    It is shown that the excellent Murchison Radio-astronomy Observatory site allows the Murchison Widefield Array to employ a simple RFI blanking scheme and still calibrate visibilities and form images in the FM radio band. The techniques described are running autonomously in our calibration and imaging software, which is currently being used to process an FM-band survey of the entire southern sky.

  20. The Square Kilometre Array

    OpenAIRE

    Lazio, Joseph

    2009-01-01

    The Square Kilometre Array (SKA) is intended as the next-generation radio telescope and will address fundamental questions in astrophysics, physics, and astrobiology. The international science community has developed a set of Key Science Programs: (1) Emerging from the Dark Ages and the Epoch of Reionization, (2) Galaxy Evolution, Cosmology, and Dark Energy, (3) The Origin and Evolution of Cosmic Magnetism, (4) Strong Field Tests of Gravity Using Pulsars and Black Holes, and (5) The Cradle of...

  1. The Cherenkov Telescope Array

    OpenAIRE

    Bigongiari, Ciro

    2016-01-01

    The Cherenkov Telescope Array (CTA) is planned to be the next generation ground based observatory for very high energy (VHE) gamma-ray astronomy. Gamma-rays provide a powerful insight into the non-thermal universe and hopefully a unique probe for new physics. Imaging Cherenkov telescopes have already discovered more than 170 VHE gamma-ray emitters providing plentiful of valuable data and clearly demonstrating the power of this technique. In spite of the impressive results there are indication...

  2. The Submillimeter Array Polarimeter

    OpenAIRE

    Marrone, Daniel P.; Rao, Ramprasad

    2008-01-01

    We describe the Submillimeter Array (SMA) Polarimeter, a polarization converter and feed multiplexer installed on the SMA. The polarimeter uses narrow-band quarter-wave plates to generate circular polarization sensitivity from the linearly-polarized SMA feeds. The wave plates are mounted in rotation stages under computer control so that the polarization handedness of each antenna is rapidly selectable. Positioning of the wave plates is found to be highly repeatable, better than 0.2 degrees. A...

  3. 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.

  4. Supersymetric laser arrays

    OpenAIRE

    El-Ganainy, Ramy; Ge, Li; Khajavikhan, Mercedeh; Christodoulides, Demetrios

    2015-01-01

    We introduce the concept of supersymmetric laser arrays that consists of a main optical lattice and its superpartner structure, and we investigate the onset of their lasing oscillations. Due to the coupling of the two constituent lattices, their degenerate optical modes form doublets, while the extra mode associated with unbroken supersymmetry forms a singlet state. Singlet lasing can be achieved for a wide range of design parameters either by introducing stronger loss in the partner lattice ...

  5. Microphone array proccesing

    OpenAIRE

    Navarro Contreras, Héctor Ángel

    2010-01-01

    Microphone arrays consist of multiple microphones functioning as a single directional input device: essentially, an acoustic antenna. Using sound propagation principles, the principal sound sources in an environment can be spatially located. Distinguishing sounds based on the spatial location of their source is achieved by filtering and combining the individual microphone signals. The location of the principal sounds sources may be determined dynamically by analyzing peaks i...

  6. Sequencing of IncX-plasmids suggests ubiquity of mobile forms of a biofilm-promoting gene cassette recruited from Klebsiella pneumoniae.

    Directory of Open Access Journals (Sweden)

    Mette Burmølle

    Full Text Available Plasmids are a highly effective means with which genetic traits that influence human health, such as virulence and antibiotic resistance, are disseminated through bacterial populations. The IncX-family is a hitherto sparsely populated group of plasmids that are able to thrive within Enterobacteriaceae. In this study, a replicon-centric screening method was used to locate strains from wastewater sludge containing plasmids belonging to the IncX-family. A transposon aided plasmid capture method was then employed to transport IncX-plasmids from their original hosts (and co-hosted plasmids into a laboratory strain (Escherichia coli Genehogs® for further study. The nucleotide sequences of the three newly isolated IncX-plasmids (pLN126_33, pMO17_54, pMO440_54 and the hitherto un-sequenced type-plasmid R485 revealed a remarkable occurrence of whole or partial gene cassettes that promote biofilm-formation in Klebsiella pneumonia or E. coli, in all four instances. Two of the plasmids (R485 and pLN126_33 were shown to directly induce biofilm formation in a crystal violet retention assay in E. coli. Sequence comparison revealed that all plasmid-borne forms of the type 3 fimbriae encoding gene cassette mrkABCDF were variations of a composite transposon Tn6011 first described in the E. coli IncX plasmid pOLA52. In conclusion, IncX-plasmids isolated from Enterobacteriaceae over almost 40 years and on three different continents have all been shown to carry a type 3 fimbriae gene cassette mrkABCDF stemming from pathogenic K. pneumoniae. Apart from contributing general knowledge about IncX-plasmids, this study also suggests an apparent ubiquity of a mobile form of an important virulence factor and is an illuminating example of the recruitment, evolution and dissemination of genetic traits through plasmid-mediated horizontal gene transfer.

  7. Spaceborne Processor Array

    Science.gov (United States)

    Chow, Edward T.; Schatzel, Donald V.; Whitaker, William D.; Sterling, Thomas

    2008-01-01

    A Spaceborne Processor Array in Multifunctional Structure (SPAMS) can lower the total mass of the electronic and structural overhead of spacecraft, resulting in reduced launch costs, while increasing the science return through dynamic onboard computing. SPAMS integrates the multifunctional structure (MFS) and the Gilgamesh Memory, Intelligence, and Network Device (MIND) multi-core in-memory computer architecture into a single-system super-architecture. This transforms every inch of a spacecraft into a sharable, interconnected, smart computing element to increase computing performance while simultaneously reducing mass. The MIND in-memory architecture provides a foundation for high-performance, low-power, and fault-tolerant computing. The MIND chip has an internal structure that includes memory, processing, and communication functionality. The Gilgamesh is a scalable system comprising multiple MIND chips interconnected to operate as a single, tightly coupled, parallel computer. The array of MIND components shares a global, virtual name space for program variables and tasks that are allocated at run time to the distributed physical memory and processing resources. Individual processor- memory nodes can be activated or powered down at run time to provide active power management and to configure around faults. A SPAMS system is comprised of a distributed Gilgamesh array built into MFS, interfaces into instrument and communication subsystems, a mass storage interface, and a radiation-hardened flight computer.

  8. 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.

  9. Synthetic Genetic Array Analysis.

    Science.gov (United States)

    Kuzmin, Elena; Costanzo, Michael; Andrews, Brenda; Boone, Charles

    2016-01-01

    Genetic interaction studies have been used to characterize unknown genes, assign membership in pathway and complex, and build a comprehensive functional map of a eukaryotic cell. Synthetic genetic array (SGA) methodology automates yeast genetic analysis and enables systematic mapping of genetic interactions. In its simplest form, SGA consists of a series of replica pinning steps that enable construction of haploid double mutants through automated mating and meiotic recombination. Using this method, a strain carrying a query mutation, such as a deletion allele of a nonessential gene or a conditional temperature-sensitive allele of an essential gene, can be crossed to an input array of yeast mutants, such as the complete set of approximately 5000 viable deletion mutants. The resulting output array of double mutants can be scored for genetic interactions based on estimates of cellular fitness derived from colony-size measurements. The SGA score method can be used to analyze large-scale data sets, whereas small-scale data sets can be analyzed using SGAtools, a simple web-based interface that includes all the necessary analysis steps for quantifying genetic interactions. PMID:27037072

  10. The optimal configuration of photovoltaic module arrays based on adaptive switching controls

    International Nuclear Information System (INIS)

    Highlights: • We propose a strategy for determining the optimal configuration of a PV array. • The proposed strategy was based on particle swarm optimization (PSO) method. • It can identify the optimal module array connection scheme in the event of shading. • It can also find the optimal connection of a PV array even in module malfunctions. - Abstract: This study proposes a strategy for determining the optimal configuration of photovoltaic (PV) module arrays in shading or malfunction conditions. This strategy was based on particle swarm optimization (PSO). If shading or malfunctions of the photovoltaic module array occur, the module array immediately undergoes adaptive reconfiguration to increase the power output of the PV power generation system. First, the maximal power generated at various irradiation levels and temperatures was recorded during normal array operation. Subsequently, the irradiation level and module temperature, regardless of operating conditions, were used to recall the maximal power previously recorded. This previous maximum was compared with the maximal power value obtained using the maximum power point tracker to assess whether the PV module array was experiencing shading or malfunctions. After determining that the array was experiencing shading or malfunctions, PSO was used to identify the optimal module array connection scheme in abnormal conditions, and connection switches were used to implement optimal array reconfiguration. Finally, experiments were conducted to assess the strategy for identifying the optimal reconfiguration of a PV module array in the event of shading or malfunctions

  11. Genetic Analysis of the Mode of Interplay between an ATPase Subunit and Membrane Subunits of the Lipoprotein-Releasing ATP-Binding Cassette Transporter LolCDE†

    OpenAIRE

    Ito, Yasuko; Matsuzawa, Hitomi; Matsuyama, Shin-ichi; Narita, Shin-ichiro; Tokuda, Hajime

    2006-01-01

    The LolCDE complex, an ATP-binding cassette (ABC) transporter, releases lipoproteins from the inner membrane, thereby initiating lipoprotein sorting to the outer membrane of Escherichia coli. The LolCDE complex is composed of two copies of an ATPase subunit, LolD, and one copy each of integral membrane subunits LolC and LolE. LolD hydrolyzes ATP on the cytoplasmic side of the inner membrane, while LolC and/or LolE recognize and release lipoproteins anchored to the periplasmic leaflet of the i...

  12. Evaluation of the role of ATP-binding cassette transporters as a defence mechanism against temephos in populations of Aedes aegypti

    OpenAIRE

    Estelita Pereira Lima; Marília Oliveira Fonseca Goulart; Modesto Leite Rolim Neto

    2014-01-01

    The role of ATP-binding cassette (ABC) transporters in the efflux of the insecticide, temephos, was assessed in the larvae of Aedes aegypti. Bioassays were conducted using mosquito populations that were either susceptible or resistant to temephos by exposure to insecticide alone or in combination with sublethal doses of the ABC transporter inhibitor, verapamil (30, 35 and 40 μM). The best result in the series was obtained with the addition of verapamil (40 μM), which led to a 2x increase in t...

  13. Evaluation of the role of ATP-binding cassette transporters as a defence mechanism against temephos in populations of Aedes aegypti.

    Science.gov (United States)

    Lima, Estelita Pereira; Goulart, Marília Oliveira Fonseca; Rolim Neto, Modesto Leite

    2014-11-01

    The role of ATP-binding cassette (ABC) transporters in the efflux of the insecticide, temephos, was assessed in the larvae of Aedes aegypti. Bioassays were conducted using mosquito populations that were either susceptible or resistant to temephos by exposure to insecticide alone or in combination with sublethal doses of the ABC transporter inhibitor, verapamil (30, 35 and 40 μM). The best result in the series was obtained with the addition of verapamil (40 μM), which led to a 2x increase in the toxicity of temephos, suggesting that ABC transporters may be partially involved in conferring resistance to the populations evaluated. PMID:25411004

  14. Evaluation of the role of ATP-binding cassette transporters as a defence mechanism against temephos in populations of Aedes aegypti

    Directory of Open Access Journals (Sweden)

    Estelita Pereira Lima

    2014-11-01

    Full Text Available The role of ATP-binding cassette (ABC transporters in the efflux of the insecticide, temephos, was assessed in the larvae of Aedes aegypti. Bioassays were conducted using mosquito populations that were either susceptible or resistant to temephos by exposure to insecticide alone or in combination with sublethal doses of the ABC transporter inhibitor, verapamil (30, 35 and 40 μM. The best result in the series was obtained with the addition of verapamil (40 μM, which led to a 2x increase in the toxicity of temephos, suggesting that ABC transporters may be partially involved in conferring resistance to the populations evaluated.

  15. Cloning and Characterization of the Pseudomonas fluorescens ATP-Binding Cassette Exporter, HasDEF, for the Heme Acquisition Protein HasA

    OpenAIRE

    Idei, Akiko; Kawai, Eri; Akatsuka, Hiroyuki; Omori, Kenji

    1999-01-01

    Two ATP-binding cassette (ABC) exporters are present in Pseudomonas fluorescens no. 33; one is the recently reported AprDEF system and the other is HasDEF, which exports a heme acquisition protein, HasA. The hasDEF genes were cloned by DNA hybridization with a DNA probe coding for the LipB protein, one of the components of the Serratia marcescens ABC exporter Lip system. P. fluorescens HasA showed sequence identity of 40 to 49% with HasA proteins from Pseudomonas aeruginosa and Serratia marce...

  16. Science with the Murchison Widefield Array

    OpenAIRE

    Bowman, Judd D.; Cairns, Iver; Kaplan, David L.; Murphy, Tara; Oberoi, Divya; Staveley-Smith, Lister; Arcus, Wayne; Barnes, David G.; Bernardi, Gianni; Briggs, Frank H.; Brown, Shea; Bunton, John D.; Burgasser, Adam J.; Cappallo, Roger J.; Chatterjee, Shami

    2012-01-01

    Significant new opportunities for astrophysics and cosmology have been identified at low radio frequencies. The Murchison Widefield Array is the first telescope in the Southern Hemisphere designed specifically to explore the low-frequency astronomical sky between 80 and 300 MHz with arcminute angular resolution and high survey efficiency. The telescope will enable new advances along four key science themes, including searching for redshifted 21 cm emission from the epoch of reionisation in th...

  17. UAVSAR Phased Array Aperture

    Science.gov (United States)

    Chamberlain, Neil; Zawadzki, Mark; Sadowy, Greg; Oakes, Eric; Brown, Kyle; Hodges, Richard

    2009-01-01

    This paper describes the development of a patch antenna array for an L-band repeat-pass interferometric synthetic aperture radar (InSAR) instrument that is to be flown on an unmanned aerial vehicle (UAV). The antenna operates at a center frequency of 1.2575 GHz and with a bandwidth of 80 MHz, consistent with a number of radar instruments that JPL has previously flown. The antenna is designed to radiate orthogonal linear polarizations in order to facilitate fully-polarimetric measurements. Beam-pointing requirements for repeat-pass SAR interferometry necessitate electronic scanning in azimuth over a range of -20degrees in order to compensate for aircraft yaw. Beam-steering is accomplished by transmit/receive (T/R) modules and a beamforming network implemented in a stripline circuit board. This paper, while providing an overview of phased array architecture, focuses on the electromagnetic design of the antenna tiles and associated interconnects. An important aspect of the design of this antenna is that it has an amplitude taper of 10dB in the elevation direction. This is to reduce multipath reflections from the wing that would otherwise be detrimental to interferometric radar measurements. This taper is provided by coupling networks in the interconnect circuits as opposed to attenuating the output of the T/R modules. Details are given of material choices and fabrication techniques that meet the demanding environmental conditions that the antenna must operate in. Predicted array performance is reported in terms of co-polarized and crosspolarized far-field antenna patterns, and also in terms of active reflection coefficient.

  18. Weak Algebraic Monge Arrays

    OpenAIRE

    Rudolf, Rüdiger; Fortin, Dominique

    1995-01-01

    An $n\\times n$ matrix $C$ is called a {\\em weak Monge\\/} matrix iff $c_{ii}+c_{rs}\\le c_{is}+c_{ri}$ for all $1\\le i\\le r,s\\le n$. It is well known that the classical linear assignment problem is optimally solved by the identity permutation if the underlying cost-matrix fulfills the weak Monge property. In this paper we introduce higher dimensional weak Monge arrays and prove that higher dimensional axial assignment problems can be solved efficiently if the cost-structure is a higher dimensio...

  19. The Square Kilometre Array

    CERN Document Server

    Rawlings, Steve

    2011-01-01

    We review the current status of the Square Kilometre Array (SKA) by outlining the science drivers for its Phase-1 (SKA1) and setting out the timeline for the key decisions and milestones on the way to the planned start of its construction in 2016. We explain how Phase-2 SKA (SKA2) will transform the research scope of the SKA infrastructure, placing it amongst the great astronomical observatories and survey instruments of the future, and opening up new areas of discovery, many beyond the confines of conventional astronomy.

  20. Inclusion of Moloney murine leukemia virus elements upstream of the transgene cassette in an E1-deleted adenovirus leads to an unusual genomic integration in epithelial cells

    International Nuclear Information System (INIS)

    Classically, the 5' and 3' long terminal repeats (LTRs) are considered necessary but not sufficient for retroviral integration. Recently, we reported that inclusion of these and additional elements from Moloney murine leukemia virus (MoMLV) facilitated transgene integration, without retroviral integrase, when placed in an adenoviral context (AdLTR-luc vector) (Nat. Biotech. 18 (2000), 176; Biochem. Biophys. Res. Commun. 300 (2003), 115). To help understand this nonhomologous DNA recombination event, we constructed another vector, AdELP-luc, with 2.7 kb of MoMLV elements identically placed into an E1-deleted adenovirus type 5 backbone upstream of a luciferase cDNA reporter gene. Unlike AdLTR-luc, no MoMLV elements were placed downstream of the expression cassette. AdELP-luc readily infected epithelial cells in vitro. Southern hybridizations with DNA from cloned cells showed that disruption of the MoMLV sequences occurred. One cell clone, grown in vitro without any special selection medium for 9 months, exhibited stable vector integration and luciferase activity. Importantly, both Southern hybridization and FISH analyses showed that in addition to the MoMLV elements and expression cassette, substantial adenoviral sequence downstream of the luciferase cDNA was genomically integrated. These results suggest that the 2.7 kb of MoMLV sequence included in AdELP-luc have cis-acting functions and mediates an unusual integration event

  1. ATP-binding cassette subfamily B member 1 (ABCB1) and subfamily C member 10 (ABCC10) are not primary resistance factors for cabazitaxel

    Institute of Scientific and Technical Information of China (English)

    Rishil J Kathawala; Yi-Jun Wang; Suneet Shukla; Yun-Kai Zhang; Saeed Alqahtani; Amal Kaddoumi; Suresh V Ambudkar; Charles R Ashby Jr; Zhe-Sheng Chen

    2015-01-01

    Introduction:ATP-binding cassette subfamily B member 1 (ABCB1) and subfamily C member 10 (ABCC10) proteins are efflux transporters that couple the energy derived from ATP hydrolysis to the translocation of toxic substances and chemotherapeutic drugs out of cells. Cabazitaxel is a novel taxane that differs from paclitaxel by its lower affinity for ATP-binding cassette (ABC) transporters. Methods:We determined the effects of cabazitaxel, a novel tubulin-binding taxane, and paclitaxel on paclitaxel-resistant, ABCB1-overexpressing KB-C2 and LLC-MDR1-WT cells and paclitaxel-resistant, ABCC10-overexpressing HEK293/ABCC10 cells by calculating the degree of drug resistance and measuring ATPase activity of the ABCB1 transporter. Results:Decreased resistance to cabazitaxel compared with paclitaxel was observed in KB-C2, LLC-MDR1-WT, and HEK293/ABCC10 cells. Moreover, cabazitaxel had low efficacy, whereas paclitaxel had high efficacy in stimulating the ATPase activity of ABCB1, indicating a direct interaction of both drugs with the transporter. Conclusion:ABCB1 and ABCC10 are not primary resistance factors for cabazitaxel compared with paclitaxel, suggesting that cabazitaxel may have a low affinity for these efflux transporters.

  2. Identifiability in stochastic models

    CERN Document Server

    1992-01-01

    The problem of identifiability is basic to all statistical methods and data analysis, occurring in such diverse areas as Reliability Theory, Survival Analysis, and Econometrics, where stochastic modeling is widely used. Mathematics dealing with identifiability per se is closely related to the so-called branch of ""characterization problems"" in Probability Theory. This book brings together relevant material on identifiability as it occurs in these diverse fields.

  3. 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....

  4. Electromagnetically Clean Solar Arrays

    Science.gov (United States)

    Stem, Theodore G.; Kenniston, Anthony E.

    2008-01-01

    The term 'electromagnetically clean solar array' ('EMCSA') refers to a panel that contains a planar array of solar photovoltaic cells and that, in comparison with a functionally equivalent solar-array panel of a type heretofore used on spacecraft, (1) exhibits less electromagnetic interferences to and from other nearby electrical and electronic equipment and (2) can be manufactured at lower cost. The reduction of electromagnetic interferences is effected through a combination of (1) electrically conductive, electrically grounded shielding and (2) reduction of areas of current loops (in order to reduce magnetic moments). The reduction of cost is effected by designing the array to be fabricated as a more nearly unitary structure, using fewer components and fewer process steps. Although EMCSAs were conceived primarily for use on spacecraft they are also potentially advantageous for terrestrial applications in which there are requirements to limit electromagnetic interference. In a conventional solar panel of the type meant to be supplanted by an EMCSA panel, the wiring is normally located on the back side, separated from the cells, thereby giving rise to current loops having significant areas and, consequently, significant magnetic moments. Current-loop geometries are chosen in an effort to balance opposing magnetic moments to limit far-0field magnetic interactions, but the relatively large distances separating current loops makes full cancellation of magnetic fields problematic. The panel is assembled from bare photovoltaic cells by means of multiple sensitive process steps that contribute significantly to cost, especially if electomagnetic cleanliness is desired. The steps include applying a cover glass and electrical-interconnect-cell (CIC) sub-assemble, connecting the CIC subassemblies into strings of series-connected cells, laying down and adhesively bonding the strings onto a panel structure that has been made in a separate multi-step process, and mounting the

  5. Array processing——a new method to detect and correct errors on array resistivity logging tool measurements

    Institute of Scientific and Technical Information of China (English)

    Philip D.RABINOWITZ; Zhiqiang ZHOU

    2007-01-01

    In recent years more and more multi-array logging tools, such as the array induction and the array lateralog, are applied in place of conventional logging tools resulting in increased resolution, better radial and vertical sounding capability and other features. Multi-array logging tools acquire several times more individual measurements than conventional logging tools. In addition to new information contained in these data, there is a certain redundancy among the measurements. The sum of the measurements actually composes a large matrix. Providing the measurements are error-free, the elements of this matrix show certain consistencies. Taking advantage of these consistencies, an innovative method is developed to detect and correct errors in the array resistivity logging tool raw measurements, and evaluate the quality of the data. The method can be described in several steps. First, data consistency patterns are identified based onthe physics of the measurements. Second, the measurements are compared against the consistency patterns for error and bad data detection. Third, the erroneous data are eliminated and the measurements are re-constructed according to the consistency patterns. Finally, the data quality is evaluated by comparing the raw measurements with the re-constructed measurements. The method can be applied to all array type logging tools, such as array induction tool and array resistivity tool. This paper describes the method and illustrates its application with the High Definition Lateral Log (HDLL, Baker Atlas) instrument. To demonstrate the efficiency of the method, several field examples are shown and discussed.

  6. Commercial/industrial photovoltaic module and array requirement study. Low-cost solar array project engineering area

    Science.gov (United States)

    1981-01-01

    Design requirements for photovoltaic modules and arrays used in commercial and industrial applications were identified. Building codes and referenced standards were reviewed for their applicability to commercial and industrial photovoltaic array installation. Four general installation types were identified - integral (replaces roofing), direct (mounted on top of roofing), stand-off (mounted away from roofing), and rack (for flat or low slope roofs, or ground mounted). Each of the generic mounting types can be used in vertical wall mounting systems. This implies eight mounting types exist in the commercial/industrial sector. Installation costs were developed for these mounting types as a function of panel/module size. Cost drivers were identified. Studies were performed to identify optimum module shapes and sizes and operating voltage cost drivers. The general conclusion is that there are no perceived major obstacles to the use of photovoltaic modules in commercial/industrial arrays.

  7. Electrode array for neural stimulation

    Energy Technology Data Exchange (ETDEWEB)

    Wessendorf, Kurt O. (Albuquerque, NM); Okandan, Murat (Edgewood, NM); Stein, David J. (Albuquerque, NM); Yang, Pin (Albuquerque, NM); Cesarano, III, Joseph (Albuquerque, NM); Dellinger, Jennifer (Albuquerque, NM)

    2011-08-16

    An electrode array for neural stimulation is disclosed which has particular applications for use in a retinal prosthesis. The electrode array can be formed as a hermetically-sealed two-part ceramic package which includes an electronic circuit such as a demultiplexer circuit encapsulated therein. A relatively large number (up to 1000 or more) of individually-addressable electrodes are provided on a curved surface of a ceramic base portion the electrode array, while a much smaller number of electrical connections are provided on a ceramic lid of the electrode array. The base and lid can be attached using a metal-to-metal seal formed by laser brazing. Electrical connections to the electrode array can be provided by a flexible ribbon cable which can also be used to secure the electrode array in place.

  8. The Murchison Widefield Array Correlator

    OpenAIRE

    Ord, S. M.; Crosse, B.; Emrich, D.; Pallot, D.; Wayth, R. B.; Clark, M. A.; Tremblay, S. E.; Arcus, W.; Barnes, D; Bell, M.; Bernardi, G.; Bhat, N. D. R.; Bowman, J.D.; Briggs, F.; Bunton, J. D.

    2014-01-01

    The Murchison Widefield Array (MWA) is a Square Kilometre Array (SKA) Precursor. The telescope is located at the Murchison Radio--astronomy Observatory (MRO) in Western Australia (WA). The MWA consists of 4096 dipoles arranged into 128 dual polarisation aperture arrays forming a connected element interferometer that cross-correlates signals from all 256 inputs. A hybrid approach to the correlation task is employed, with some processing stages being performed by bespoke hardware, based on Fiel...

  9. Aligators for Arrays (Tool Paper)

    Science.gov (United States)

    Henzinger, Thomas A.; Hottelier, Thibaud; Kovács, Laura; Rybalchenko, Andrey

    This paper presents Aligators, a tool for the generation of universally quantified array invariants. Aligators leverages recurrence solving and algebraic techniques to carry out inductive reasoning over array content. The Aligators' loop extraction module allows treatment of multi-path loops by exploiting their commutativity and serializability properties. Our experience in applying Aligators on a collection of loops from open source software projects indicates the applicability of recurrence and algebraic solving techniques for reasoning about arrays.

  10. Electrodynamic Arrays Having Nanomaterial Electrodes

    Science.gov (United States)

    Trigwell, Steven (Inventor); Biris, Alexandru S. (Inventor); Calle, Carlos I. (Inventor)

    2013-01-01

    An electrodynamic array of conductive nanomaterial electrodes and a method of making such an electrodynamic array. In one embodiment, a liquid solution containing nanomaterials is deposited as an array of conductive electrodes on a substrate, including rigid or flexible substrates such as fabrics, and opaque or transparent substrates. The nanomaterial electrodes may also be grown in situ. The nanomaterials may include carbon nanomaterials, other organic or inorganic nanomaterials or mixtures.

  11. Developing an Inflatable Solar Array

    OpenAIRE

    Malone, Patrick; Crawford, Larry; Williams, Geoffrey,

    1993-01-01

    L'Garde is developing a light weight deployable solar array wing in the 200-1000 watt range, on the Inflatable Torus Solar Array Technology Demonstration (ITSAT Demo) Project. The power density goal is 90-100 W/Kg for a 200 W wing, including structure and deployment mechanisms. In Phase 1, a proof of concept torus and array was constructed and deployed in the laboratory. A revised Phase 2 Torus and Array are now being fabricated. Phase 3 will be a space flight test. The current design uses cr...

  12. Wave propagation in waveguide arrays with alternating positive and negative couplings

    International Nuclear Information System (INIS)

    We introduce a waveguide array model with alternating positive and negative couplings between adjacent waveguides. Two different settings where such a model can be realized are identified as arrays of defects in Bragg gratings and arrays with propagation constants that periodically vary along the propagation direction. We analyze the properties of wave propagation in such waveguide arrays and find several interesting properties that have no counterpart in the case of arrays with constant couplings. These include the beam self-splitting, self-induced Talbot oscillations, symmetric evolution of Bloch oscillations, and new families of lattice solitons.

  13. Array-A-Lizer: A serial DNA microarray quality analyzer

    Directory of Open Access Journals (Sweden)

    Matthiessen Mads

    2004-02-01

    Full Text Available Abstract Background The proliferate nature of DNA microarray results have made it necessary to implement a uniform and quick quality control of experimental results to ensure the consistency of data across multiple experiments prior to actual data analysis. Results Array-A-Lizer is a small and convenient stand-alone tool providing the necessary initial analysis of hybridization quality of an unlimited number of microarray experiments. The experiments are analyzed for even hybridization across the slide and between fluorescent dyes in two-color experiments in spotted DNA microarrays. Conclusions Array-A-Lizer allows the expedient determination of the quality of multiple DNA microarray experiments allowing for a rapid initial screening of results before progressing to further data analysis. Array-A-Lizer is directed towards speed and ease-of-use allowing both the expert and non-expert microarray researcher to rapidly assess the quality of multiple microarray hybridizations. Array-A-Lizer is available from the Internet as both source code and as a binary installation package.

  14. 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....... Numerical results for the capacities are presented....

  15. Solitons in optomechanical arrays.

    Science.gov (United States)

    Gan, Jing-Hui; Xiong, Hao; Si, Liu-Gang; Lü, Xin-You; Wu, Ying

    2016-06-15

    We show that optical solitons can be obtained with a one-dimensional optomechanical array that consists of a chain of periodically spaced identical optomechanical systems. Unlike conventional optical solitons, which originate from nonlinear polarization, the optical soliton here stems from a new mechanism, namely, phonon-photon interaction. Under proper conditions, the phonon-photon induced nonlinearity that refers to the optomechanical nonlinearity will exactly compensate the dispersion caused by photon hopping of adjacent optomechanical systems. Moreover, the solitons are capable of exhibiting very low group velocity, depending on the photon hopping rate, which may lead to many important applications, including all-optical switches and on-chip optical architecture. This work may extend the range of optomechanics and nonlinear optics and provide a new field to study soliton theory and develop corresponding applications. PMID:27304261

  16. GERmanium detector array, GERDA

    International Nuclear Information System (INIS)

    The GERmanium Detector Array, GERDA, is designed to search for 'neutrinoless double beta decay' (0ν2β) in 76Ge. The high-purity segmented Ge detectors will be directly submerged and operated in liquid N2 or Ar. The measurement of the half-life time of 0ν2β decay will provide information about the absolute neutrino mass scale and indirectly, the hierarchy. The design goal of GERDA is to reach a sensitivity of 0.2 eV on the effective Majorana neutrino mass (mββ). The GERDA experiment is located in hall A of the Grand Sasso national lab (LNGS) and the construction will start in 2006

  17. The Square Kilometre Array

    Science.gov (United States)

    Huynh, Minh; Lazio, Joseph

    2011-01-01

    The Square Kilometre Array (SKA) will be the premier instrument to study radiation at centimetre and metre wavelengths from the cosmos, and in particular neutral hydrogen, the most abundant element in the universe. The SKA will probe the dawn of galaxy formation as well as allow advances in many other areas of astronomy, such as fundamental physics, astro-biology and cosmology. The SKA will have a collecting area of up to one million square metres spread over at least 3000 km, providing a collecting area more than twenty times greater than the current largest radio telescope. Its field of view on the sky will be several tens of square degrees with potentially several large (100 square degrees) independent beams at the lower frequencies, providing a survey speed many thousands of times greater than current facilities. This paper summarises the key science drivers of the SKA and provides an update on the international project.

  18. 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.

  19. Scintillator detector array

    International Nuclear Information System (INIS)

    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)

  20. Networked Sensor Arrays

    International Nuclear Information System (INIS)

    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

  1. First Staphylococcal Cassette Chromosome mec Containing a mecB-Carrying Gene Complex Independent of Transposon Tn6045 in a Macrococcus caseolyticus Isolate from a Canine Infection.

    Science.gov (United States)

    Gómez-Sanz, Elena; Schwendener, Sybille; Thomann, Andreas; Gobeli Brawand, Stefanie; Perreten, Vincent

    2015-08-01

    A methicillin-resistant mecB-positive Macrococcus caseolyticus (strain KM45013) was isolated from the nares of a dog with rhinitis. It contained a novel 39-kb transposon-defective complete mecB-carrying staphylococcal cassette chromosome mec element (SCCmecKM45013). SCCmecKM45013 contained 49 coding sequences (CDSs), was integrated at the 3' end of the chromosomal orfX gene, and was delimited at both ends by imperfect direct repeats functioning as integration site sequences (ISSs). SCCmecKM45013 presented two discontinuous regions of homology (SCCmec coverage of 35%) to the chromosomal and transposon Tn6045-associated SCCmec-like element of M. caseolyticus JCSC7096: (i) the mec gene complex (98.8% identity) and (ii) the ccr-carrying segment (91.8% identity). The mec gene complex, located at the right junction of the cassette, also carried the β-lactamase gene blaZm (mecRm-mecIm-mecB-blaZm). SCCmecKM45013 contained two cassette chromosome recombinase genes, ccrAm2 and ccrBm2, which shared 94.3% and 96.6% DNA identity with those of the SCCmec-like element of JCSC7096 but shared less than 52% DNA identity with the staphylococcal ccrAB and ccrC genes. Three distinct extrachromosomal circularized elements (the entire SCCmecKM45013, ΨSCCmecKM45013 lacking the ccr genes, and SCCKM45013 lacking mecB) flanked by one ISS copy, as well as the chromosomal regions remaining after excision, were detected. An unconventional circularized structure carrying the mecB gene complex was associated with two extensive direct repeat regions, which enclosed two open reading frames (ORFs) (ORF46 and ORF51) flanking the chromosomal mecB-carrying gene complex. This study revealed M. caseolyticus as a potential disease-associated bacterium in dogs and also unveiled an SCCmec element carrying mecB not associated with Tn6045 in the genus Macrococcus. PMID:25987634

  2. Identifying Unknown Proteins

    OpenAIRE

    Barker, Winona C.; Dayhoff, Margaret O.

    1983-01-01

    In this paper we discuss ways to identify a protein, both when its amino acid sequence is known and, particularly, prior to the determination of the complete sequence. If a similar sequence is in the Protein Sequence Database, an unknown may be identified on the basis of partial or ambiguous sequence data, or on the basis of amino acid composition. Identification in the early stages of structural determination can save time and scarce resources by preventing duplicate effort or by suggesting ...

  3. A microbial detection array (MDA for viral and bacterial detection

    Directory of Open Access Journals (Sweden)

    McLoughlin Kevin S

    2010-11-01

    Full Text Available Abstract Background Identifying the bacteria and viruses present in a complex sample is useful in disease diagnostics, product safety, environmental characterization, and research. Array-based methods have proven utility to detect in a single assay at a reasonable cost any microbe from the thousands that have been sequenced. Methods We designed a pan-Microbial Detection Array (MDA to detect all known viruses (including phages, bacteria and plasmids and developed a novel statistical analysis method to identify mixtures of organisms from complex samples hybridized to the array. The array has broader coverage of bacterial and viral targets and is based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms, and to have no significant matches to the human genome sequence. Results In blinded testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR. Conclusions The MDA can be used to identify the suite of viruses and bacteria present in complex samples.

  4. Array tomography: semiautomated image alignment.

    Science.gov (United States)

    Micheva, Kristina D; O'Rourke, Nancy; Busse, Brad; Smith, Stephen J

    2010-11-01

    Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. Successful array tomography requires that the captured images be properly stacked and aligned, and the software to achieve these ends is freely available. This protocol describes the construction of volumetric image stacks from images of fluorescently labeled arrays for three-dimensional image visualization, analysis, and archiving. PMID:21041400

  5. Cyclotron-Resonance-Maser Arrays

    International Nuclear Information System (INIS)

    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

  6. Passive microfluidic array card and reader

    Energy Technology Data Exchange (ETDEWEB)

    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.

  7. 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.

  8. A Human t-PA Mutant cDNA Cassette Knocked in the Murine fgfr-4 Locus Targeting for Mammary Gland Expression

    Institute of Scientific and Technical Information of China (English)

    Fu-Yu LIN; Hong-Xing CHEN; Xuan CHENG; Xiao YANG; Ji-Xian DENG; Pei-Tang HUANG

    2004-01-01

    The expression of foreign gene in transgenic animals produced by pronuclear microinjection is often confounded by the position effects caused by not only the nature of chromosomal integration site but also the number and arrangement of multiple transgene copies. Gene targeting provides a new way to overcome these inhibitions by introducing single-copy transgene into a chosen site. The choice of a good chromosomal site will favor transgene expression in a predictable fashion. In this study, we tested a new site (fgfr-4) for foreign gene integration and expression. A t-PA mutant (t-PAm) expression cassette under bovine αs1-casein regulatory sequences was efficiently knocked-infgfr-4 site through homologous recombination. The t-PAm was expressed in the milk of all targeted mice. Our experiment indicates that the fgfr-4 may be a candidate site for knocking foreign gene to make transgenic animals.

  9. Overexpression of the ATP-binding cassette half-transporter, ABCG2 (Mxr/BCrp/ABCP1), in flavopiridol-resistant human breast cancer cells

    DEFF Research Database (Denmark)

    Robey, R W; Medina-Pérez, W Y; Nishiyama, K;

    2001-01-01

    We sought to characterize the interactions of flavopiridol with members of the ATP-binding cassette (ABC) transporter family. Cells overexpressing multidrug resistance-1 (MDR-1) and multidrug resistance-associated protein (MRP) did not exhibit appreciable flavopiridol resistance, whereas cell lines...... overexpressing the ABC half-transporter, ABCG2 (MXR/BCRP/ABCP1), were found to be resistant to flavopiridol. Flavopiridol at a concentration of 10 microM was able to prevent MRP-mediated calcein efflux, whereas Pgp-mediated transport of rhodamine 123 was unaffected at flavopiridol concentrations of up to 100...... microM. To determine putative mechanisms of resistance to flavopiridol, we exposed the human breast cancer cell line MCF-7 to incrementally increasing concentrations of flavopiridol. The resulting resistant subline, MCF-7 FLV1000, is maintained in 1,000 nM flavopiridol and was found to be 24-fold...

  10. Seismo-acoustic array installed in Vrancea seismogenic area

    Science.gov (United States)

    Ionescu, Constantin; Moldovan, Adrian-Septimiu; Moldovan, Iren-Adelina; Ghica, Daniela

    2010-05-01

    The National Institute for Earth Physics (NIEP) has installed two infrasound networks: a four-element seismo-acoustic array with an 1.2 km aperture (IPLOR) and a three-element array with a 400m aperture (IOANE). Both arrays are installed in Vrancea seismogenic area. Each array element of IPLOR consists of three sensors (a seismic 3C broad-band instrument with 1000V/m/s sensitivity, an accelerometer +/-2g EpiSensor type, and an infrasound Chaparral type sensor) and a 24-bit digitizer (Quanterra Q330). The BB sensors and accelerometers are located in 3 meters deep boreholes, while the infrasound sensors are installed in a plastic 1 mc container connected to a porous flexible pipe or plastic tube (for the central element). Inter-array communication is achieved by radio link (2.4 GHz frequency band) which transmits the data from the six-channel digitizers to the local acquisition system. Each power array element consisted of a 12 V DC source powered by the commercial power line or solar panels. The data acquisition system is based on the Seiscomp3 software; a sampling rate of 100 samples per second is applied for BB seismic instruments and accelerometers, whilst for the infrasound sensor a 20 sps rate is used. Each array element of IPLOR consists of a MBAZEL2007 microbarometer and a 24-bit digitizer. Inter-array communication is achieved by a fiber optic link. The sampling rate is 10 sps. The Vrancea seismo-acoustic array is used to identify and locate events associated with industrial blasts, to detect local and regional events, as well for the complex studies on the Vrancea seismogenic area. Moreover, the array data accelerometers are used in the early warning system for Bucharest. At NIEP, several programs are running to analyze each type of data (seismic and acoustic): for BB seismic data, a software for event detection and characterization, kindly provided by NORSAR, is applied, acceleration data recorded by the episensors are processed with a software developed

  11. Identifying Knowledge and Communication

    Directory of Open Access Journals (Sweden)

    Eduardo Coutinho Lourenço de Lima

    2006-12-01

    Full Text Available In this paper, I discuss how the principle of identifying knowledge which Strawson advances in ‘Singular Terms and Predication’ (1961, and in ‘Identifying Reference and Truth-Values’ (1964 turns out to constrain communication. The principle states that a speaker’s use of a referring expression should invoke identifying knowledge on the part of the hearer, if the hearer is to understand what the speaker is saying, and also that, in so referring, speakers are attentive to hearers’ epistemic states. In contrasting it with Russell’s Principle (Evans 1982, as well as with the principle of identifying descriptions (Donnellan 1970, I try to show that the principle of identifying knowledge, ultimately a condition for understanding, makes sense only in a situation of conversation. This allows me to conclude that the cooperative feature of communication (Grice 1975 and reference (Clark andWilkes-Gibbs 1986 holds also at the understanding level. Finally, I discuss where Strawson’s views seem to be unsatisfactory, and suggest how they might be improved.

  12. IncP-1ε plasmids are important vectors of antibiotic resistance genes in agricultural systems: diversification driven by class 1 integron gene cassettes

    Directory of Open Access Journals (Sweden)

    HolgerHeuer

    2012-01-01

    Full Text Available The role of broad host range IncP-1ε plasmids in the dissemination of antibiotic resistance in agricultural systems has not yet been investigated. These plasmids were detected in total DNA from all of 16 manure samples and in arable soil based on a novel 5’-nuclease assay for real time PCR. A correlation between IncP-1ε plasmid abundance and antibiotic usage was revealed. In a soil microcosm experiment the abundance of IncP-1ε plasmids was significantly increased even 127 days after application of manure containing the antibiotic compound sulfadiazine, compared to soil receiving only manure, only sulfadiazine, or water. Fifty IncP-1ε plasmids that were captured in E. coli CV601gfp from bacterial communities of manure and arable soil were characterized by PCR and hybridisation. All plasmids carried class 1 integrons with highly varying sizes of the gene cassette region and the sul1 gene. Three IncP-1ε plasmids captured from soil bacteria and one from manure were completely sequenced. The backbones were nearly identical to that of the previously described IncP-1ε plasmid pKJK5. The plasmids differed mainly in the composition of a Tn402-like transposon carrying a class 1 integron with varying gene cassettes, IS1326, and in three of the plasmids the tetracycline resistance transposon Tn1721 with various truncations. Diverse Beta- and Gammaproteobacteria were revealed as hosts of one of the IncP-1ε plasmids in soil microcosms. Our data suggest that IncP-1ε plasmids are important vectors for horizontal transfer of antibiotic resistance in agricultural systems.

  13. LES investigation of infinite staggered wind-turbine arrays

    International Nuclear Information System (INIS)

    The layouts of turbines affect the turbine wake interactions and thus the wind farm performance. The wake interactions in infinite staggered wind-turbine arrays are investigated and compared with infinite aligned turbine arrays in this paper. From the numerical results we identify three types of wake behaviours, which are significantly different from wakes in aligned wind-turbine arrays. For the first type, each turbine wake interferes with the pair of staggered downstream turbine wakes and the aligned downstream turbine. For the second type, each turbine wake interacts with the first two downstream turbine wakes but does not show significant interference with the second aligned downstream turbine. For the third type, each turbine wake recovers immediately after passing through the gap of the first two downstream turbines and has little interaction with the second downstream turbine wakes The extracted power density and power efficiency are also studied and compared with aligned wind-turbine arrays

  14. LES investigation of infinite staggered wind-turbine arrays

    Science.gov (United States)

    Yang, Xiaolei; Sotiropoulos, Fotis

    2014-12-01

    The layouts of turbines affect the turbine wake interactions and thus the wind farm performance. The wake interactions in infinite staggered wind-turbine arrays are investigated and compared with infinite aligned turbine arrays in this paper. From the numerical results we identify three types of wake behaviours, which are significantly different from wakes in aligned wind-turbine arrays. For the first type, each turbine wake interferes with the pair of staggered downstream turbine wakes and the aligned downstream turbine. For the second type, each turbine wake interacts with the first two downstream turbine wakes but does not show significant interference with the second aligned downstream turbine. For the third type, each turbine wake recovers immediately after passing through the gap of the first two downstream turbines and has little interaction with the second downstream turbine wakes The extracted power density and power efficiency are also studied and compared with aligned wind-turbine arrays.

  15. Developments in large gamma-ray detector arrays

    CERN Document Server

    Lee, I Y; Vetter, K

    2003-01-01

    Gamma-ray spectroscopy was revolutionized with the introduction of high energy-resolution semiconductor germanium (Ge) detectors in the early 1960s. This led to the large increase in sensitivity realized by today's arrays of Compton-suppressed Ge detectors. A still larger increase in sensitivity is expected by implementing the new concept of tracking. A tracking array consists of highly segmented Ge detectors (that can cover the full 4 pi solid-angle) in which gamma rays will be identified by measuring and tracking every gamma ray interaction. This article reviews the physics motivation for such detectors and the development of the new technologies involved. The concept of tracking is explained using the example of a proposed array called gamma-ray energy tracking array (GRETA).

  16. Cholesterol efflux via ATP-binding cassette transporter A1 (ABCA1) and cholesterol uptake via the LDL receptor influences cholesterol-induced impairment of beta cell function in mice

    NARCIS (Netherlands)

    Kruit, J. K.; Kremer, P. H. C.; Dai, L.; Tang, R.; Ruddle, P.; de Haan, W.; Brunham, L. R.; Verchere, C. B.; Hayden, M. R.

    2010-01-01

    Cellular cholesterol accumulation is an emerging mechanism for beta cell dysfunction in type 2 diabetes. Absence of the cholesterol transporter ATP-binding cassette transporter A1 (ABCA1) results in increased islet cholesterol and impaired insulin secretion, indicating that impaired cholesterol effl

  17. An innovative and integrated approach based on DNA walking to identify unauthorised GMOs.

    Science.gov (United States)

    Fraiture, Marie-Alice; Herman, Philippe; Taverniers, Isabel; De Loose, Marc; Deforce, Dieter; Roosens, Nancy H

    2014-03-15

    In the coming years, the frequency of unauthorised genetically modified organisms (GMOs) being present in the European food and feed chain will increase significantly. Therefore, we have developed a strategy to identify unauthorised GMOs containing a pCAMBIA family vector, frequently present in transgenic plants. This integrated approach is performed in two successive steps on Bt rice grains. First, the potential presence of unauthorised GMOs is assessed by the qPCR SYBR®Green technology targeting the terminator 35S pCAMBIA element. Second, its presence is confirmed via the characterisation of the junction between the transgenic cassette and the rice genome. To this end, a DNA walking strategy is applied using a first reverse primer followed by two semi-nested PCR rounds using primers that are each time nested to the previous reverse primer. This approach allows to rapidly identify the transgene flanking region and can easily be implemented by the enforcement laboratories. PMID:24206686

  18. The Cherenkov Telescope Array

    CERN Document Server

    Bigongiari, Ciro

    2016-01-01

    The Cherenkov Telescope Array (CTA) is planned to be the next generation ground based observatory for very high energy (VHE) gamma-ray astronomy. Gamma-rays provide a powerful insight into the non-thermal universe and hopefully a unique probe for new physics. Imaging Cherenkov telescopes have already discovered more than 170 VHE gamma-ray emitters providing plentiful of valuable data and clearly demonstrating the power of this technique. In spite of the impressive results there are indications that the known sources represent only the tip of the iceberg. A major step in sensitivity is needed to increase the number of detected sources, observe short time-scale variability and improve morphological studies of extended sources. An extended energy coverage is advisable to observe far-away extragalactic objects and improve spectral analysis. CTA aims to increase the sensitivity by an order of magnitude compared to current facilities, to extend the accessible gamma-ray energies from a few tens of GeV to a hundred o...

  19. VLSI array processor

    Science.gov (United States)

    Greenwood, E.

    1982-07-01

    The Arithmetic Processor Unit (APU) data base design check was completed. Minor design rule violations and design improvements were accomplished. The APU mask set has been fabricated and checked. Initial checking of all mask layers revealed a design rule problem in one layer. That layer was corrected, refabricated and checked out. The mask set has been delivered to the chip fabrication area. The fabrication process has been initiated. All work on the Array Processor Demonstration System (APDS) has been suspended at CHI until the additionally requested funding was received. That funding has been authorized and CHI will begin work on the APDS in July. The following activities are planned in the following quarter: 1) Complete fabrication of the first lot of VLSI APU devices. 2) Complete integration and check-out of the APDS simulator. 3) Complete integration and check-out of the APU breadboard. 4) Verify the VLSI APU wafer tests with the APU breadboard. 5) Complete check-out of the APDS using the APU breadboard.

  20. Freeform array projection

    Science.gov (United States)

    Michaelis, D.; Schreiber, P.; Li, C.; Bräuer, A.; Gross, H.

    2015-09-01

    The concept of multichannel array projection is generalized in order to realize an ultraslim, highly efficient optical system for structured illumination with high lumen output, where additionally the Köhler illumination principle is utilized and source light homogenization occurs. The optical system consists of a multitude of neighboring optical channels. In each channel two optical freeforms generate a real or a virtual spatial light pattern and furthermore, the ray directions are modified to enable Köhler illumination of a subsequent projection lens. The internal light pattern may be additionally influenced by absorbing apertures or slides. The projection lens transfers the resulting light pattern to a target, where the total target distribution is produced by superposition of all individual channel output pattern. The optical system without absorbing apertures can be regarded as a generalization of a fly's eye condenser for structured illumination. In this case light pattern is exclusively generated by freeform light redistribution. The commonly occurring blurring effect for freeform beamshaping is reduced due to the creation of a virtual object light structure by means of the two freeform surfaces and its imaging towards the target. But, the remaining blurring inhibits very high spatial frequencies at the target. In order to create target features with very high spatial resolution the absorbing apertures can be utilized. In this case the freeform beamshaping can be used for an enhanced light transmission through the absorbing apertures. The freeform surfaces are designed by a generalized approach of Cartesian oval representation.

  1. CLAES focal plane array. [Cryogenic Limb Array Etalon Spectrometer

    Science.gov (United States)

    Roche, A. E.; Sterritt, L. W.; Kumer, J. B.; Callary, P. C.; Nielsen, R. L.

    1989-01-01

    The Cryogenic Limb Array Etalon Spectrometer for the NASA Upper Atmospheric Research Satellite uses solid-state focal plane arrays to detect emission from the earth's atmosphere over the IR wavelength range 3.5 to 13 microns. This paper discusses the design of the focal plane detector assembly and compares calculated performance with measurements. Measurements were made of focal plane noise and responsivity as functions of frequency (2 to 500 Hz) and temperature (12 to 19 K), pixel-to-pixel and across-array crosstalk, and linearity over a dynamic range of 100,000. The measurements demonstrate that the arrays satisfy the science requirements, and that, in general, there is reasonable agreement between the measurements and the analytical model.

  2. Arrayed imaging reflectometry for inexpensive and label-free protein arrays

    Science.gov (United States)

    Striemer, Christopher C.; Mace, Charles R.; Carter, Jared A.; Mehta, Sourabh D.; Miller, Benjamin L.

    2009-02-01

    Highly sensitive optical techniques, capable of detecting very small quantities of specific proteins in a label-free format, offer great promise for pathogen detection because they avoid the complexity, expense, and process time associated with the use of secondary reporter elements. Arrayed Imaging Reflectometry (AIR) is one of the simplest label-free methodologies, combining laser reflectance imaging of a thermally oxidized silicon chip with standard microarray printing technology to create a platform with the potential to identify and quantify 100's of target proteins in a matter of minutes. This technique exploits a reflectance zero condition that is formed when s-polarized light strikes the surface of a silicon wafer with a single-layer oxide coating. In the vicinity of this deep reflectance minimum, picometer-scale variations in film thickness (surface relief) can be imaged directly in a reflected laser signal imaged with a CCD camera. By directly arraying probe molecules onto this substrate, minute changes in the optical thickness of each spot, corresponding to binding of the target of interest, can be measured. Array size is limited only by the resolution of the imaging system and the array printer, enabling complex protein signatures, indicative of specific pathogens or disease states to be measured in a biosample. The cost-effectiveness of a low-complexity substrate and reader, combined with the short assay times associated with label-free detection make AIR a promising new technology for pathogen and toxic exposure assessment.

  3. Large scale biomimetic membrane arrays

    DEFF Research Database (Denmark)

    Hansen, Jesper Søndergaard; Perry, Mark; Vogel, Jörg;

    2009-01-01

    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......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......, and furthermore demonstrate that the design can conveniently be scaled up to support planar lipid bilayers in large square-centimeter partition arrays....

  4. 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

  5. Antenna arrays a computational approach

    CERN Document Server

    Haupt, Randy L

    2010-01-01

    This book covers a wide range of antenna array topics that are becoming increasingly important in wireless applications, particularly in design and computer modeling. Signal processing and numerical modeling algorithms are explored, and MATLAB computer codes are provided for many of the design examples. Pictures of antenna arrays and components provided by industry and government sources are presented with explanations of how they work. Antenna Arrays is a valuable reference for practicing engineers and scientists in wireless communications, radar, and remote sensing, and an excellent textbook for advanced antenna courses.

  6. DFB Quantum Cascade Laser Arrays

    OpenAIRE

    Lee, Benjamin G.; Belkin, Mikhail A.; Pflügl, Christian; Diehl, Laurent; Zhang, Haifei; Audet, Ross M.; MacArthur, Jim B.; Bour, David P.; Corzine, Scott W.; Höfler, Gloria E.; Capasso, Federico

    2009-01-01

    DFB quantum cascade laser (DFB-QCL) arrays operating between 8.7 and 9.4 mum are investigated for their performance characteristics-single-mode selection of the DFB grating, and variability in threshold, slope efficiency, and output power of different lasers in the array. Single-mode selection refers to the ability to choose a desired mode/frequency of laser emission with a DFB grating. We apply a theoretical framework developed for general DFB gratings to analyze DFB-QCL arrays. We calculate...

  7. Silicon Heat Pipe Array

    Science.gov (United States)

    Yee, Karl Y.; Ganapathi, Gani B.; Sunada, Eric T.; Bae, Youngsam; Miller, Jennifer R.; Beinsford, Daniel F.

    2013-01-01

    Improved methods of heat dissipation are required for modern, high-power density electronic systems. As increased functionality is progressively compacted into decreasing volumes, this need will be exacerbated. High-performance chip power is predicted to increase monotonically and rapidly with time. Systems utilizing these chips are currently reliant upon decades of old cooling technology. Heat pipes offer a solution to this problem. Heat pipes are passive, self-contained, two-phase heat dissipation devices. Heat conducted into the device through a wick structure converts the working fluid into a vapor, which then releases the heat via condensation after being transported away from the heat source. Heat pipes have high thermal conductivities, are inexpensive, and have been utilized in previous space missions. However, the cylindrical geometry of commercial heat pipes is a poor fit to the planar geometries of microelectronic assemblies, the copper that commercial heat pipes are typically constructed of is a poor CTE (coefficient of thermal expansion) match to the semiconductor die utilized in these assemblies, and the functionality and reliability of heat pipes in general is strongly dependent on the orientation of the assembly with respect to the gravity vector. What is needed is a planar, semiconductor-based heat pipe array that can be used for cooling of generic MCM (multichip module) assemblies that can also function in all orientations. Such a structure would not only have applications in the cooling of space electronics, but would have commercial applications as well (e.g. cooling of microprocessors and high-power laser diodes). This technology is an improvement over existing heat pipe designs due to the finer porosity of the wick, which enhances capillary pumping pressure, resulting in greater effective thermal conductivity and performance in any orientation with respect to the gravity vector. In addition, it is constructed of silicon, and thus is better

  8. Internally readable identifying tag

    International Nuclear Information System (INIS)

    A method of identifying non-metallic objects by means of X-ray equipment is described in detail. A small metal pin with a number of grooves cut in a pre-determined equi-spaced pattern is implanted into the non-metallic object and by decoding the groove patterns using X-ray equipment, the object is uniquely identified. A specific example of such an application is in studying the migratory habits of fish. The pin inserted into the snout of the fish is 0.010 inch in diameter, 0.040 inch in length with 8 possible positions for grooves if spaced 0.005 inch apart. With 6 of the groove positions available for data, the capacity is 26 or 64 combinations; clearly longer pins would increase the data capacity. This method of identification is a major advance over previous techniques which necessitated destruction of the fish in order to recover the identification tag. (UK)

  9. Identifying Fiscal Inflation

    OpenAIRE

    De Graeve, Ferre; Queijo von Heideken, Virginia

    2013-01-01

    Fiscal theorists warn about the risk of future inflation as a consequence of current fiscal imbalances in the US. Because actual inflation remains historically low and data on inflation expectations do not corroborate such risks, warnings for fiscal inflation are often ignored in policy and academic circles. This paper shows that a canonical NK- DSGE model enables identifying an anticipated component of inflation expectations that is closely related to fiscal policy. Estimation results sugges...

  10. 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...

  11. The Murchison Widefield Array Correlator

    CERN Document Server

    Ord, S M; Emrich, D; Pallot, D; Wayth, R B; Clark, M A; Tremblay, S E; Arcus, W; Barnes, D; Bell, M; Bernardi, G; Bhat, N D R; Bowman, J D; Briggs, F; Bunton, J D; Cappallo, R J; Corey, B E; Deshpande, A A; deSouza, L; Ewell-Wice, A; Feng, L; Goeke, R; Greenhill, L J; Hazelton, B J; Herne, D; Hewitt, J N; Hindson, L; Hurley-Walker, H; Jacobs, D; Johnston-Hollitt, M; Kaplan, D L; Kasper, J C; Kincaid, B B; Koenig, R; Kratzenberg, E; Kudryavtseva, N; Lenc, E; Lonsdale, C J; Lynch, M J; McKinley, B; McWhirter, S R; Mitchell, D A; Morales, M F; Morgan, E; Oberoi, D; Offringa, A; Pathikulangara, J; Pindor, B; Prabu, T; Procopio, P; Remillard, R A; Riding, J; Rogers, A E E; Roshi, A; Salah, J E; Sault, R J; Shankar, N Udaya; Srivani, K S; Stevens, J; Subrahmanyan, R; Tingay, S J; Waterson, M; Webster, R L; Whitney, A R; Williams, A; Williams, C L; Wyithe, J S B

    2015-01-01

    The Murchison Widefield Array (MWA) is a Square Kilometre Array (SKA) Precursor. The telescope is located at the Murchison Radio--astronomy Observatory (MRO) in Western Australia (WA). The MWA consists of 4096 dipoles arranged into 128 dual polarisation aperture arrays forming a connected element interferometer that cross-correlates signals from all 256 inputs. A hybrid approach to the correlation task is employed, with some processing stages being performed by bespoke hardware, based on Field Programmable Gate Arrays (FPGAs), and others by Graphics Processing Units (GPUs) housed in general purpose rack mounted servers. The correlation capability required is approximately 8 TFLOPS (Tera FLoating point Operations Per Second). The MWA has commenced operations and the correlator is generating 8.3 TB/day of correlation products, that are subsequently transferred 700 km from the MRO to Perth (WA) in real-time for storage and offline processing. In this paper we outline the correlator design, signal path, and proce...

  12. Integrated Spatial Filter Array Project

    Data.gov (United States)

    National Aeronautics and Space Administration — To address the NASA Earth Science Division need for spatial filter arrays for amplitude and wavefront control, Luminit proposes to develop a novel Integrated...

  13. Light propagation in nanorod arrays

    CERN Document Server

    Rahachou, A I

    2006-01-01

    We study propagation of TM- and TE-polarized light in two-dimensional arrays of silver nanorods of various diameters in a gelatin background. We calculate the transmittance, reflectance and absorption of arranged and disordered nanorod arrays and compare the exact numerical results with the predictions of the Maxwell-Garnett effective-medium theory. We show that interactions between nanorods, multipole contributions and formations of photonic gaps affect strongly the transmittance spectra that cannot be accounted for in terms of the conventional effective-medium theory. We also demonstrate and explain the degradation of the transmittance in arrays with randomly located rods as well as weak influence of their fluctuating diameter. For TM modes we outline the importance of skin-effect, which causes the full reflection of the incoming light. We then illustrate the possibility of using periodic arrays of nanorods as high-quality polarizers.

  14. Thermopile Area Array Readout Project

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA/JPL thermopile detector linear arrays, wire bonded to Black Forest Engineering (BFE) CMOS readout integrated circuits (ROICs), have been utilized in NASA...

  15. 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...

  16. IRIS Arrays: Observing Wavefields at Multiple Scales and Frequencies

    Science.gov (United States)

    Sumy, D. F.; Woodward, R.; Frassetto, A.

    2014-12-01

    The Incorporated Research Institutions for Seismology (IRIS) provides instruments for creating and operating seismic arrays at a wide range of scales. As an example, for over thirty years the IRIS PASSCAL program has provided instruments to individual Principal Investigators to deploy arrays of all shapes and sizes on every continent. These arrays have ranged from just a few sensors to hundreds or even thousands of sensors, covering areas with dimensions of meters to thousands of kilometers. IRIS also operates arrays directly, such as the USArray Transportable Array (TA) as part of the EarthScope program. Since 2004, the TA has rolled across North America, at any given time spanning a swath of approximately 800 km by 2,500 km, and thus far sampling 2% of the Earth's surface. This achievement includes all of the lower-48 U.S., southernmost Canada, and now parts of Alaska. IRIS has also facilitated specialized arrays in polar environments and on the seafloor. In all cases, the data from these arrays are freely available to the scientific community. As the community of scientists who use IRIS facilities and data look to the future they have identified a clear need for new array capabilities. In particular, as part of its Wavefields Initiative, IRIS is exploring new technologies that can enable large, dense array deployments to record unaliased wavefields at a wide range of frequencies. Large-scale arrays might utilize multiple sensor technologies to best achieve observing objectives and optimize equipment and logistical costs. Improvements in packaging and power systems can provide equipment with reduced size, weight, and power that will reduce logistical constraints for large experiments, and can make a critical difference for deployments in harsh environments or other situations where rapid deployment is required. We will review the range of existing IRIS array capabilities with an overview of previous and current deployments and examples of data and results. We

  17. A calorimeter with array detectors

    International Nuclear Information System (INIS)

    A 5 x 25 = 125 detector array has been designed for a calorimeter. Each element is consisted of a graphite block and a chromel-alumel. A new '0'-point set up was designed by using the critical temperature of the liquid nitrogen as the '0'-point of the temperature. A FY-1 data acquisition system was used for the detector array. The energy distribution of the electron beam has been measured on large-area diode with the system

  18. Solar maximum: solar array degradation

    International Nuclear Information System (INIS)

    The 5-year in-orbit power degradation of the silicon solar array aboard the Solar Maximum Satellite was evaluated. This was the first spacecraft to use Teflon R FEP as a coverglass adhesive, thus avoiding the necessity of an ultraviolet filter. The peak power tracking mode of the power regulator unit was employed to ensure consistent maximum power comparisons. Telemetry was normalized to account for the effects of illumination intensity, charged particle irradiation dosage, and solar array temperature. Reference conditions of 1.0 solar constant at air mass zero and 301 K (28 C) were used as a basis for normalization. Beginning-of-life array power was 2230 watts. Currently, the array output is 1830 watts. This corresponds to a 16 percent loss in array performance over 5 years. Comparison of Solar Maximum Telemetry and predicted power levels indicate that array output is 2 percent less than predictions based on an annual 1.0 MeV equivalent election fluence of 2.34 x ten to the 13th power square centimeters space environment

  19. Protein kinase substrate identification on functional protein arrays

    Directory of Open Access Journals (Sweden)

    Zhou Fang

    2008-02-01

    Full Text Available Abstract Background Over the last decade, kinases have emerged as attractive therapeutic targets for a number of different diseases, and numerous high throughput screening efforts in the pharmaceutical community are directed towards discovery of compounds that regulate kinase function. The emerging utility of systems biology approaches has necessitated the development of multiplex tools suitable for proteomic-scale experiments to replace lower throughput technologies such as mass spectroscopy for the study of protein phosphorylation. Recently, a new approach for identifying substrates of protein kinases has applied the miniaturized format of functional protein arrays to characterize phosphorylation for thousands of candidate protein substrates in a single experiment. This method involves the addition of protein kinases in solution to arrays of immobilized proteins to identify substrates using highly sensitive radioactive detection and hit identification algorithms. Results To date, the factors required for optimal performance of protein array-based kinase substrate identification have not been described. In the current study, we have carried out a detailed characterization of the protein array-based method for kinase substrate identification, including an examination of the effects of time, buffer compositions, and protein concentration on the results. The protein array approach was compared to standard solution-based assays for assessing substrate phosphorylation, and a correlation of greater than 80% was observed. The results presented here demonstrate how novel substrates for protein kinases can be quickly identified from arrays containing thousands of human proteins to provide new clues to protein kinase function. In addition, a pooling-deconvolution strategy was developed and applied that enhances characterization of specific kinase-substrate relationships and decreases reagent consumption. Conclusion Functional protein microarrays are an

  20. On identified predictive control

    Science.gov (United States)

    Bialasiewicz, Jan T.

    1993-01-01

    Self-tuning control algorithms are potential successors to manually tuned PID controllers traditionally used in process control applications. A very attractive design method for self-tuning controllers, which has been developed over recent years, is the long-range predictive control (LRPC). The success of LRPC is due to its effectiveness with plants of unknown order and dead-time which may be simultaneously nonminimum phase and unstable or have multiple lightly damped poles (as in the case of flexible structures or flexible robot arms). LRPC is a receding horizon strategy and can be, in general terms, summarized as follows. Using assumed long-range (or multi-step) cost function the optimal control law is found in terms of unknown parameters of the predictor model of the process, current input-output sequence, and future reference signal sequence. The common approach is to assume that the input-output process model is known or separately identified and then to find the parameters of the predictor model. Once these are known, the optimal control law determines control signal at the current time t which is applied at the process input and the whole procedure is repeated at the next time instant. Most of the recent research in this field is apparently centered around the LRPC formulation developed by Clarke et al., known as generalized predictive control (GPC). GPC uses ARIMAX/CARIMA model of the process in its input-output formulation. In this paper, the GPC formulation is used but the process predictor model is derived from the state space formulation of the ARIMAX model and is directly identified over the receding horizon, i.e., using current input-output sequence. The underlying technique in the design of identified predictive control (IPC) algorithm is the identification algorithm of observer/Kalman filter Markov parameters developed by Juang et al. at NASA Langley Research Center and successfully applied to identification of flexible structures.

  1. The Applicability of Incoherent Array Processing to IMS Seismic Array Stations

    Science.gov (United States)

    Gibbons, S. J.

    2012-04-01

    The seismic arrays of the International Monitoring System for the CTBT differ greatly in size and geometry, with apertures ranging from below 1 km to over 60 km. Large and medium aperture arrays with large inter-site spacings complicate the detection and estimation of high frequency phases since signals are often incoherent between sensors. Many such phases, typically from events at regional distances, remain undetected since pipeline algorithms often consider only frequencies low enough to allow coherent array processing. High frequency phases that are detected are frequently attributed qualitatively incorrect backazimuth and slowness estimates and are consequently not associated with the correct event hypotheses. This can lead to missed events both due to a lack of contributing phase detections and by corruption of event hypotheses by spurious detections. Continuous spectral estimation can be used for phase detection and parameter estimation on the largest aperture arrays, with phase arrivals identified as local maxima on beams of transformed spectrograms. The estimation procedure in effect measures group velocity rather than phase velocity and the ability to estimate backazimuth and slowness requires that the spatial extent of the array is large enough to resolve time-delays between envelopes with a period of approximately 4 or 5 seconds. The NOA, AKASG, YKA, WRA, and KURK arrays have apertures in excess of 20 km and spectrogram beamforming on these stations provides high quality slowness estimates for regional phases without additional post-processing. Seven arrays with aperture between 10 and 20 km (MJAR, ESDC, ILAR, KSRS, CMAR, ASAR, and EKA) can provide robust parameter estimates subject to a smoothing of the resulting slowness grids, most effectively achieved by convolving the measured slowness grids with the array response function for a 4 or 5 second period signal. The MJAR array in Japan recorded high SNR Pn signals for both the 2006 and 2009 North Korea

  2. Locating noise sources with a microphone array

    International Nuclear Information System (INIS)

    Noise pollution is one of the contributors to the public opposition of wind farms. Most of the noise produced by turbines is caused by the aerodynamic interactions between the turbine blades and the surrounding air. This poster presentation discussed a series of aeroacoustic tests conducted to account for the different in vortical structures caused by the rotation of the blades. Microphone arrays were used measure and locate the source of noise. A beam forming technique was used to measure the noise using an algorithm that identified a scanning grid on a plane where the source was thought to be located. It delayed each microphone's signal by the length of time required for the sound to travel from the scan position to each microphone, and accounted for the amplitudes according to the distance from the scan position to each microphone. Demonstration test cases were conducted using piezo buzzers attached to aluminum bars and mounted to the shaft of a DC motor that produced a rotational diameter of 0.95 meter. The buzzers were placed 1 meter from the array. Multiple sound sources at the same frequency were identified, and the moving sources were accurately measured and located. tabs., figs.

  3. Instrumentation for multi-detector arrays

    Indian Academy of Sciences (India)

    R K Bhowmik

    2001-07-01

    The new generation of detector arrays require complex instrumentation and data acquisition system to ensure increased reliability of operation, high degree of integration, software control and faster data handling capability. The main features of some of the existing multi-detector arrays like MSU 4 array, Gammasphere and Eurogam are summarized. The instrumentation for the proposed INGA array in India is discussed.

  4. Evaluating Translocation Gene Fusions by SNP Array Data

    OpenAIRE

    Hong Liu; Asher Zilberstein; Pascal Pannier; Frederic Fleche; Christopher Arendt; Christoph Lengauer; Chang S Hahn

    2011-01-01

    Somatic cell genetic alterations are a hallmark of tumor development and progression. Although various technologies have been developed and utilized to identify genetic aberrations, identifying genetic translocations at the chromosomal level is still a challenging task. High density SNP microarrays are useful to measure DNA copy number variation (CNV) across the genome. Utilizing SNP array data of cancer cell lines and patient samples, we evaluated the CNV and copy number breakpoints for seve...

  5. Specificity of the Linear Array HPV Genotyping Test for detecting human papillomavirus genotype 52 (HPV-52):

    OpenAIRE

    Kocjan, Boštjan; Poljak, Mario; Oštrbenk, Anja

    2014-01-01

    Introduction: HPV-52 is one of the most frequent human papillomavirus (HPV) genotypes causing significant cervical pathology. The most widely used HPV genotyping assay, the Roche Linear Array HPV Genotyping Test (Linear Array), is unable to identify HPV- 52 status in samples containing HPV-33, HPV-35, and/or HPV-58. Methods: Linear Array HPV-52 analytical specificity was established by testing 100 specimens reactive with the Linear Array HPV- 33/35/52/58 cross-reactive probe, but not with the...

  6. 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.

  7. 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.

  8. Solid-state array cameras.

    Science.gov (United States)

    Strull, G; List, W F; Irwin, E L; Farnsworth, D L

    1972-05-01

    Over the past few years there has been growing interest shown in the rapidly maturing technology of totally solid-state imaging. This paper presents a synopsis of developments made in this field at the Westinghouse ATL facilities with emphasis on row-column organized monolithic arrays of diffused junction phototransistors. The complete processing sequence applicable to the fabrication of modern highdensity arrays is described from wafer ingot preparation to final sensor testing. Special steps found necessary for high yield processing, such as surface etching prior to both sawing and lapping, are discussed along with the rationale behind their adoption. Camera systems built around matrix array photosensors are presented in a historical time-wise progression beginning with the first 50 x 50 element converter developed in 1965 and running through the most recent 400 x 500 element system delivered in 1972. The freedom of mechanical architecture made available to system designers by solid-state array cameras is noted from the description of a bare-chip packaged cubic inch camera. Hybrid scan systems employing one-dimensional line arrays are cited, and the basic tradeoffs to their use are listed. PMID:20119094

  9. 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.

  10. Wavenumber response of Shanghai Seismic Array

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@Seismic array can be traced back to 1950s when it mainly aimed at detecting and distinguishing the signals of nuclear explosion and seismic signals. The research on seismic array includes seismic array techniques and applications of array in geophysics. Array techniques involve array design and data processing methods (Anne, 1990). Nowadays, the continuous development of seismic array¢s theory could relate to many scientific issues in geophysical field (Tormod, 1989; Mykkeltveit, Bungum, 1984). Seismic array is mainly applied to detect weak events. The response characteristic of array is an important indication of array¢s detection ability. Therefore, when we study an array or construct an array, one of the neces-sary works is to calculate the response characteristics of the array (Harjes, 1990). The aperture and layout of array are two dominating geometrical features. The typical aperture of interna-tional array is generally from several to tens kilometers. For instance, arrays with aperture of dozens kilometers aperture are KSA, WRA, YKA, etc, while arrays with several kilometer aperture are ARC, FIN, GEE, etc. Moreo-ver, in the view of array¢s layout, NOR, GER, etc have circle layout, while WRA, YKA, etc have decussating layout. This paper mainly discusses the relation between deployment of array and wavenumber response. With the example of constructing Shanghai Seismic Array, this paper provides one practical solution to search the proper array deployment. In this paper, the simple delay beam technique is adopted to calculate the response characteris-tics of array. Certainly, the different processing methods have different result, but the result from the simple delay beam processing could be enough to reflect the feature of an array.

  11. Distributed Phased Arrays and Wireless Beamforming Networks

    OpenAIRE

    David Jenn; Yong Loke; Tong Chin Hong Matthew; Yeo Eng Choon; Ong Chin Siang; Yeo Siew Yam

    2009-01-01

    Distributed phased arrays have advantages over conventional arrays in many radar and communication applications. Additional advantages are realized by replacing the microwave beamforming circuit by a wireless network, thus forming a wirelessly networked distributed sensor array. This article examines various aspects of a distributed phased array that incorporates wireless beamforming. First, the fundamental array theory and digital signal processing are reviewed. Basic equations are presented...

  12. Parallelism and array processing

    International Nuclear Information System (INIS)

    Modern computing, as well as the historical development of computing, has been dominated by sequential monoprocessing. Yet there is the alternative of parallelism, where several processes may be in concurrent execution. This alternative is discussed in a series of lectures, in which the main developments involving parallelism are considered, both from the standpoint of computing systems and that of applications that can exploit such systems. The lectures seek to discuss parallelism in a historical context, and to identify all the main aspects of concurrency in computation right up to the present time. Included will be consideration of the important question as to what use parallelism might be in the field of data processing. (orig.)

  13. Mathematical Simulating Model of Phased-Array Antenna in Multifunction Array Radar

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    A mathematical simulating model of phased-array antenna in multifunction array radar has been approached in this paper, including the mathematical simulating model of plane phased-array pattern, the mathematical simulating model of directionality factor, the mathematical simulating model of array factor, the mathematical simulating model of array element factor and the mathematical simulating model of beam steering.

  14. Identifying Phronotypes in Psychiatry

    Directory of Open Access Journals (Sweden)

    F. AndrewKozel

    2010-10-01

    Full Text Available Refinements in the methods of diagnosis for psychiatric disorders are critically needed. These new methods should be based on objectively measured brain characteristics that provide clinically useful information. Studying the brain with respect to psychiatric disorders, however, faces numerous challenges. Utilizing techniques learned in other areas of medicine to deal with symptoms that lead to complex disorders can provide insight into improving diagnostic models in psychiatry. Specifically, many areas of medicine use objective measures of an organ’s function or characteristic to guide clinical management of particular subjective complaints. In psychiatry, an objectively measured brain characteristic that provides clinically useful information is proposed to be that person’s “phronotype.” Important requirements to developing phronotypes are discussed. Identifying phronotypes in psychiatry will require a specific investigative approach that must be grounded in rigorous scientific methodology. Successfully developing such markers will have a profound impact on clinical care, clinical research, basic science research, and most importantly the lives of those suffering from these illnesses.

  15. HYTAR : a Hybrid Telescope Array for Reaction dynamics

    International Nuclear Information System (INIS)

    HYTAR is an array of Hybrid detector telescopes developed at IUAC for the study of reaction mechanisms around coulomb barrier. The hybrid detector module is a combination of gas (ΔE) and silicon detector (stopping). They have been developed for heavy ion detection and particle identification in nuclear physics experiments in GPSC/NAND facility at IUAC. Currently the array has 13 such telescopes. The detector telescopes have been earlier used for studying the angular distribution of fission fragments. The detector system can also be used to identify projectile like fragments and thus can be used for studying quasi-elastic scattering, transfer and breakup reactions

  16. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis

    DEFF Research Database (Denmark)

    Beecham, Ashley H; Patsopoulos, Nikolaos A; Xifara, Dionysia K;

    2013-01-01

    Using the ImmunoChip custom genotyping array, we analyzed 14,498 subjects with multiple sclerosis and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (P...

  17. 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.

  18. Thin, Flexible IMM Solar Array

    Science.gov (United States)

    Walmsley, Nicholas

    2015-01-01

    NASA needs solar arrays that are thin, flexible, and highly efficient; package compactly for launch; and deploy into large, structurally stable high-power generators. Inverted metamorphic multijunction (IMM) solar cells can enable these arrays, but integration of this thin crystalline cell technology presents certain challenges. The Thin Hybrid Interconnected Solar Array (THINS) technology allows robust and reliable integration of IMM cells into a flexible blanket comprising standardized modules engineered for easy production. The modules support the IMM cell by using multifunctional materials for structural stability, shielding, coefficient of thermal expansion (CTE) stress relief, and integrated thermal and electrical functions. The design approach includes total encapsulation, which benefits high voltage as well as electrostatic performance.

  19. Coherent magnetic semiconductor nanodot arrays

    Directory of Open Access Journals (Sweden)

    Xiu Faxian

    2011-01-01

    Full Text Available Abstract In searching appropriate candidates of magnetic semiconductors compatible with mainstream Si technology for future spintronic devices, extensive attention has been focused on Mn-doped Ge magnetic semiconductors. Up to now, lack of reliable methods to obtain high-quality MnGe nanostructures with a desired shape and a good controllability has been a barrier to make these materials practically applicable for spintronic devices. Here, we report, for the first time, an innovative growth approach to produce self-assembled and coherent magnetic MnGe nanodot arrays with an excellent reproducibility. Magnetotransport experiments reveal that the nanodot arrays possess giant magneto-resistance associated with geometrical effects. The discovery of the MnGe nanodot arrays paves the way towards next-generation high-density magnetic memories and spintronic devices with low-power dissipation.

  20. Thermal comfort and indoor air quality in the lecture room with 4-way cassette air-conditioner and mixing ventilation system

    International Nuclear Information System (INIS)

    We performed the experimental and the numerical studies on thermal comfort (TC) and indoor air quality (IAQ) in the lecture room with cooling loads when the operating conditions are changed. Predicted mean vote (PMV) value and CO2 concentration of the lecture room were measured and compared to the numerical results. Both of them showed a reasonable agreement with each other and then we applied the numerical model to analyze TC and IAQ for a couple of different operating conditions. From the results we found that the increment of the discharge angle of 4-way cassette air-conditioner makes uniformity of TC worse, but rarely affects IAQ. It turned out that TC and IAQ are hardly affected by the variation of the discharge airflow. Finally TC was merely affected by the increment of the ventilation rate, but when the ventilation rate is more than 800m3/h, the average CO2 concentration can be satisfied with the standard limits of Japanese in our case studies. (author)

  1. On the Use of Molecular Weight Cutoff Cassettes to Measure Dynamic Relaxivity of Novel Gadolinium Contrast Agents: Example Using Hyaluronic Acid Polymer Complexes in Phosphate-Buffered Saline

    Directory of Open Access Journals (Sweden)

    Nima Kasraie

    2011-01-01

    Full Text Available The aims of this study were to determine whether standard extracellular contrast agents of Gd(III ions in combination with a polymeric entity susceptible to hydrolytic degradation over a finite period of time, such as Hyaluronic Acid (HA, have sufficient vascular residence time to obtain comparable vascular imaging to current conventional compounds and to obtain sufficient data to show proof of concept that HA with Gd-DTPA ligands could be useful as vascular imaging agents. We assessed the dynamic relaxivity of the HA bound DTPA compounds using a custom-made phantom, as well as relaxation rates at 10.72 MHz with concentrations ranging between 0.09 and 7.96 mM in phosphate-buffered saline. Linear dependences of static longitudinal relaxation rate (R1 on concentration were found for most measured samples, and the HA samples continued to produce high signal strength after 24 hours after injection into a dialysis cassette at 3T, showing superior dynamic relaxivity values compared to conventional contrast media such as Gd-DTPA-BMA.

  2. On the Use of Molecular Weight Cutoff Cassettes to Measure Dynamic Relaxivity of Novel Gadolinium Contrast Agents: Example Using Hyaluronic Acid Polymer Complexes in Phosphate-Buffered Saline

    International Nuclear Information System (INIS)

    The aims of this study were to determine whether standard extracellular contrast agents of Gd(III) ions in combination with a polymeric entity susceptible to hydrolytic degradation over a finite period of time, such as Hyaluronic Acid (HA), have sufficient vascular residence time to obtain comparable vascular imaging to current conventional compounds and to obtain sufficient data to show proof of concept that HA with Gd-DTPA ligands could be useful as vascular imaging agents. We assessed the dynamic relaxivity of the HA bound DTPA compounds using a custom-made phantom, as well as relaxation rates at 10.72 MHz with concentrations ranging between 0.09 and 7.96 mM in phosphate-buffered saline. Linear dependences of static longitudinal relaxation rate (R1) on concentration were found for most measured samples, and the HA samples continued to produce high signal strength after 24 hours after injection into a dialysis cassette at 3T, showing superior dynamic relaxivity values compared to conventional contrast media such as Gd-DTPA-BMA

  3. Large genomic fragment deletion and functional gene cassette knock-in via Cas9 protein mediated genome editing in one-cell rodent embryos.

    Science.gov (United States)

    Wang, Liren; Shao, Yanjiao; Guan, Yuting; Li, Liang; Wu, Lijuan; Chen, Fangrui; Liu, Meizhen; Chen, Huaqing; Ma, Yanlin; Ma, Xueyun; Liu, Mingyao; Li, Dali

    2015-01-01

    The CRISPR-Cas RNA-guided system has versatile uses in many organisms and allows modification of multiple target sites simultaneously. Generating novel genetically modified mouse and rat models is one valuable application of this system. Through the injection of Cas9 protein instead of mRNA into embryos, we observed fewer off-target effects of Cas9 and increased point mutation knock-in efficiency. Large genomic DNA fragment (up to 95 kb) deletion mice were generated for in vivo study of lncRNAs and gene clusters. Site-specific insertion of a 2.7 kb CreERT2 cassette into the mouse Nfatc1 locus allowed labeling and tracing of hair follicle stem cells. In addition, we combined the Cre-Loxp system with a gene-trap strategy to insert a GFP reporter in the reverse orientation into the rat Lgr5 locus, which was later inverted by Cre-mediated recombination, yielding a conditional knockout/reporter strategy suitable for mosaic mutation analysis. PMID:26620761

  4. Corticotropin-Releasing Hormone (CRH Promotes Macrophage Foam Cell Formation via Reduced Expression of ATP Binding Cassette Transporter-1 (ABCA1.

    Directory of Open Access Journals (Sweden)

    Wonkyoung Cho

    Full Text Available Atherosclerosis, the major pathology of cardiovascular disease, is caused by multiple factors involving psychological stress. Corticotropin-releasing hormone (CRH, which is released by neurosecretory cells in the hypothalamus, peripheral nerve terminals and epithelial cells, regulates various stress-related responses. Our current study aimed to verify the role of CRH in macrophage foam cell formation, the initial critical stage of atherosclerosis. Our quantitative real-time reverse transcriptase PCR (qRT-PCR, semi-quantitative reverse transcriptase PCR, and Western blot results indicate that CRH down-regulates ATP-binding cassette transporter-1 (ABCA1 and liver X receptor (LXR-α, a transcription factor for ABCA1, in murine peritoneal macrophages and human monocyte-derived macrophages. Oil-red O (ORO staining and intracellular cholesterol measurement of macrophages treated with or without oxidized LDL (oxLDL and with or without CRH (10 nM in the presence of apolipoprotein A1 (apoA1 revealed that CRH treatment promotes macrophage foam cell formation. The boron-dipyrromethene (BODIPY-conjugated cholesterol efflux assay showed that CRH treatment reduces macrophage cholesterol efflux. Western blot analysis showed that CRH-induced down-regulation of ABCA1 is dependent on phosphorylation of Akt (Ser473 induced by interaction between CRH and CRH receptor 1(CRHR1. We conclude that activation of this pathway by CRH accelerates macrophage foam cell formation and may promote stress-related atherosclerosis.

  5. Homologous Recombination-Independent Large Gene Cassette Knock-in in CHO Cells Using TALEN and MMEJ-Directed Donor Plasmids

    Directory of Open Access Journals (Sweden)

    Tetsushi Sakuma

    2015-10-01

    Full Text Available Gene knock-in techniques have rapidly evolved in recent years, along with the development and maturation of genome editing technology using programmable nucleases. We recently reported a novel strategy for microhomology-mediated end-joining-dependent integration of donor DNA by using TALEN or CRISPR/Cas9 and optimized targeting vectors, named PITCh (Precise Integration into Target Chromosome vectors. Here we describe TALEN and PITCh vector-mediated integration of long gene cassettes, including a single-chain Fv-Fc (scFv-Fc gene, in Chinese hamster ovary (CHO cells, with comparison of targeting and cloning efficiency among several donor design and culture conditions. We achieved 9.6-kb whole plasmid integration and 7.6-kb backbone-free integration into a defined genomic locus in CHO cells. Furthermore, we confirmed the reasonable productivity of recombinant scFv-Fc protein of the knock-in cells. Using our protocol, the knock-in cell clones could be obtained by a single transfection and a single limiting dilution using a 96-well plate, without constructing targeting vectors containing long homology arms. Thus, the study described herein provides a highly practical strategy for gene knock-in of large DNA in CHO cells, which accelerates high-throughput generation of cell lines stably producing any desired biopharmaceuticals, including huge antibody proteins.

  6. MicroRNA 28-5p regulates ATP-binding cassette transporter A1 via inhibiting extracellular signal-regulated kinase 2.

    Science.gov (United States)

    Liu, Jia; Liu, Xue-Qing; Liu, Ying; Sun, Ya-Nan; Li, Si; Li, Chun-Mei; Li, Jie; Tian, Wei; Shang, Xiao-Ming; Zhou, Yun-Tao

    2016-01-01

    The biological function of the intronic microRNA-28 (miR-28) may be associated with the biological roles of its host gene, LIM domain lipoma‑preferred partner (LPP). LPP has been reported to promote smooth muscle cell migration in arterial injury and atherosclerosis. However, the mechanism of miR‑28 in atherosclerosis remains unclear. In the current study, the aim was to validate the inhibitory effect of miR‑28‑5p on extracellular signal‑regulated kinase 2 (ERK2), to investigate its biological role in atherosclerosis and its association with cardiovascular disease. Western blotting and stem‑loop reverse transcription‑quantitative polymerase chain reaction combined with TaqMAN microRNA analysis was conducted. The current study demonstrated that miR‑28‑5p upregulated the expression of ATP‑binding cassette transporter A1 (ABCA1) via the inhibition of ERK2 in HepG2 cells. In addition, increased levels of plasma miR‑28‑5p were positively correlated with the levels of high‑density lipoprotein cholesterol in patients with unstable angina. This suggests that miR-28-5p participates in atherosclerosis via ERK2-mediated upregulation of the ABCA1 pathway. PMID:26718613

  7. Homologous Recombination-Independent Large Gene Cassette Knock-in in CHO Cells Using TALEN and MMEJ-Directed Donor Plasmids.

    Science.gov (United States)

    Sakuma, Tetsushi; Takenaga, Mitsumasa; Kawabe, Yoshinori; Nakamura, Takahiro; Kamihira, Masamichi; Yamamoto, Takashi

    2015-01-01

    Gene knock-in techniques have rapidly evolved in recent years, along with the development and maturation of genome editing technology using programmable nucleases. We recently reported a novel strategy for microhomology-mediated end-joining-dependent integration of donor DNA by using TALEN or CRISPR/Cas9 and optimized targeting vectors, named PITCh (Precise Integration into Target Chromosome) vectors. Here we describe TALEN and PITCh vector-mediated integration of long gene cassettes, including a single-chain Fv-Fc (scFv-Fc) gene, in Chinese hamster ovary (CHO) cells, with comparison of targeting and cloning efficiency among several donor design and culture conditions. We achieved 9.6-kb whole plasmid integration and 7.6-kb backbone-free integration into a defined genomic locus in CHO cells. Furthermore, we confirmed the reasonable productivity of recombinant scFv-Fc protein of the knock-in cells. Using our protocol, the knock-in cell clones could be obtained by a single transfection and a single limiting dilution using a 96-well plate, without constructing targeting vectors containing long homology arms. Thus, the study described herein provides a highly practical strategy for gene knock-in of large DNA in CHO cells, which accelerates high-throughput generation of cell lines stably producing any desired biopharmaceuticals, including huge antibody proteins. PMID:26473830

  8. Functional expressions of adenosine triphosphate-binding cassette transporters during the development of zebrafish embryos and their effects on the detoxification of cadmium chloride and β-naphthoflavone.

    Science.gov (United States)

    Yin, Huancai; Bai, Pengli; Miao, Peng; Chen, Mingli; Hu, Jun; Deng, Xudong; Yin, Jian

    2016-07-01

    Adenosine triphosphate-binding cassette (ABC) transporters, including ABCB, ABCC and ABCG families represent general biological defenses against environmental toxicants in varieties of marine and freshwater organisms, but their physiological functions at differential developmental stages of zebrafish embryos remain undefined. In this work, functional expressions of typical ABC transporters including P-glycoprotein (Pgp), multiresistance associated protein 1 (Mrp1) and Mrp2 were studied in zebrafish embryos at 4, 24, 48 and 72 h post-fertilization (hpf). As a result, both the gene expressions and activities of Pgp and Mrps increased with the development of embryos. Correspondingly, 4-72 hpf embryos exhibited an increased tolerance to the toxicity caused by cadmium chloride (CdCl2 ) and β-naphthoflavone (BNF) with time. Such a correlation was assumed caused by the involvement of ABC transporters in the detoxification of chemicals. In addition, the assumption was supported by the fact that model efflux inhibitors of Pgp and Mrps such as reversine 205 and MK571 significantly inhibited the efflux of toxicants and increased the toxicity of Cd and BNF in zebrafish embryos. Moreover, exposure to CdCl2 and BNF induced the gene expressions of Pgp and Mrp1 in 72 hpf embryos. Thus, functional expressions of Pgp and Mrps increased with the development of zebrafish embryos, which could cause an increasing tolerance of zebrafish embryos to CdCl2 and BNF. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26387481

  9. Efficient Recombinase-Mediated Cassette Exchange in hPSCs to Study the Hepatocyte Lineage Reveals AAVS1 Locus-Mediated Transgene Inhibition

    Directory of Open Access Journals (Sweden)

    Laura Ordovás

    2015-11-01

    Full Text Available Tools for rapid and efficient transgenesis in “safe harbor” loci in an isogenic context remain important to exploit the possibilities of human pluripotent stem cells (hPSCs. We created hPSC master cell lines suitable for FLPe recombinase-mediated cassette exchange (RMCE in the AAVS1 locus that allow generation of transgenic lines within 15 days with 100% efficiency and without random integrations. Using RMCE, we successfully incorporated several transgenes useful for lineage identification, cell toxicity studies, and gene overexpression to study the hepatocyte lineage. However, we observed unexpected and variable transgene expression inhibition in vitro, due to DNA methylation and other unknown mechanisms, both in undifferentiated hESC and differentiating hepatocytes. Therefore, the AAVS1 locus cannot be considered a universally safe harbor locus for reliable transgene expression in vitro, and using it for transgenesis in hPSC will require careful assessment of the function of individual transgenes.

  10. The Klebsiella pneumoniae O12 ATP-binding Cassette (ABC) Transporter Recognizes the Terminal Residue of Its O-antigen Polysaccharide Substrate.

    Science.gov (United States)

    Mann, Evan; Mallette, Evan; Clarke, Bradley R; Kimber, Matthew S; Whitfield, Chris

    2016-04-29

    Export of the Escherichia coli serotype O9a O-antigenic polysaccharides (O-PS) involves an ATP-binding cassette (ABC) transporter. The process requires a non-reducing terminal residue, which is recognized by a carbohydrate-binding module (CBM) appended to the C terminus of the nucleotide-binding domain of the transporter. Here, we investigate the process in Klebsiella pneumoniae serotype O12 (and Raoultella terrigena ATCC 33257). The O12 polysaccharide is terminated at the non-reducing end by a β-linked 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) residue. The O12 ABC transporter also binds its cognate O-PS via a CBM, and export is dependent on the presence of the terminal β-Kdo residue. The overall structural architecture of the O12 CBM resembles the O9a prototype, but they share only weak sequence similarity, and the putative binding pocket for the O12 glycan is different. Removal of the CBM abrogated O-PS transport, but export was restored when the CBM was expressed in trans with the mutant CBM-deficient ABC transporter. These results demonstrate that the CBM-mediated substrate-recognition mechanism is evolutionarily conserved and can operate with glycans of widely differing structures. PMID:26934919

  11. Coexistence of heavy metal and antibiotic resistance within a novel composite staphylococcal cassette chromosome in a Staphylococcus haemolyticus isolate from bovine mastitis milk.

    Science.gov (United States)

    Xue, Huping; Wu, Zhaowei; Li, Longping; Li, Fan; Wang, Yiqing; Zhao, Xin

    2015-09-01

    The structure of a composite staphylococcal cassette chromosome (SCC) carried by a methicillin-resistant Staphylococcus haemolyticus (NW19A) isolated from a bovine milk sample was analyzed. The formation of the circular forms of both single SCC elements and composite SCC elements was detected in NW19A. Twenty heavy metal and antibiotic resistance-related genes coexisted in this composite SCC, suggesting that these genes might be coselected under environmental pressure. The mec gene complex in NW19A, designated type C3, is different from classic C1 or C2 gene complexes structurally and likely evolves differently. Furthermore, results from alignment of the SCC composite island of NW19A with 50 related sequences from different staphylococcal strains provided additional evidence to support the notion that coagulase-negative staphylococci (CoNS) are the original host of heavy metal resistance genes among staphylococci. Given that a SCC composite island could transfer freely among different staphylococcal species from different hosts, more attention should be paid to contamination with heavy metals and antibiotics in dairy farming environments, including wastewater, soil, feces, and feed. PMID:26169408

  12. Studies with an immobilized metal affinity chromatography cassette system involving binuclear triazacyclononane-derived ligands: automation of batch adsorption measurements with tagged recombinant proteins.

    Science.gov (United States)

    Petzold, Martin; Coghlan, Campbell J; Hearn, Milton T W

    2014-07-18

    This study describes the determination of the adsorption isotherms and binding kinetics of tagged recombinant proteins using a recently developed IMAC cassette system and employing automated robotic liquid handling procedures for IMAC resin screening. These results confirm that these new IMAC resins, generated from a variety of different metal-charged binuclear 1,4,7-triaza-cyclononane (tacn) ligands, interact with recombinant proteins containing a novel N-terminal metal binding tag, NT1A, with static binding capacities similar to those obtained with conventional hexa-His tagged proteins, but with significantly increased association constants. In addition, higher kinetic binding rates were observed with these new IMAC systems, an attribute that can be positively exploited to increase process productivity. The results from this investigation demonstrate that enhancements in binding capacities and affinities were achieved with these new IMAC resins and chosen NT1A tagged protein. Further, differences in the binding performances of the bis(tacn) xylenyl-bridged ligands were consistent with the distance between the metal binding centres of the two tacn moieties, the flexibility of the ligand and the potential contribution from the aromatic ring of the xylenyl group to undergo π/π stacking interactions with the tagged proteins. PMID:24891160

  13. Pro Isomerization in MLL1 PHD3-Bromo Cassette Connects H3K4me Readout to CyP33 and HDAC-Mediated Repression

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhanxin; Song, Jikui; Milne, Thomas A.; Wang, Gang G.; Li, Haitao; Allis, C. David; Patel, Dinshaw J. (MSKCC); (Rockefeller)

    2010-09-13

    The MLL1 gene is a frequent target for recurrent chromosomal translocations, resulting in transformation of hematopoietic precursors into leukemia stem cells. Here, we report on structure-function studies that elucidate molecular events in MLL1 binding of histone H3K4me3/2 marks and recruitment of the cyclophilin CyP33. CyP33 contains a PPIase and a RRM domain and regulates MLL1 function through HDAC recruitment. We find that the PPIase domain of CyP33 regulates the conformation of MLL1 through proline isomerization within the PHD3-Bromo linker, thereby disrupting the PHD3-Bromo interface and facilitating binding of the MLL1-PHD3 domain to the CyP33-RRM domain. H3K4me3/2 and CyP33-RRM target different surfaces of MLL1-PHD3 and can bind simultaneously to form a ternary complex. Furthermore, the MLL1-CyP33 interaction is required for repression of HOXA9 and HOXC8 genes in vivo. Our results highlight the role of PHD3-Bromo cassette as a regulatory platform, orchestrating MLL1 binding of H3K4me3/2 marks and cyclophilin-mediated repression through HDAC recruitment.

  14. Rescuing Trafficking Mutants of the ATP-binding Cassette Protein, ABCA4, with Small Molecule Correctors as a Treatment for Stargardt Eye Disease.

    Science.gov (United States)

    Sabirzhanova, Inna; Lopes Pacheco, Miquéias; Rapino, Daniele; Grover, Rahul; Handa, James T; Guggino, William B; Cebotaru, Liudmila

    2015-08-01

    Stargardt disease is the most common form of early onset macular degeneration. Mutations in ABCA4, a member of the ATP-binding cassette (ABC) family, are associated with Stargardt disease. Here, we have examined two disease-causing mutations in the NBD1 region of ABCA4, R1108C, and R1129C, which occur within regions of high similarity with CFTR, another ABC transporter gene, which is associated with cystic fibrosis. We show that R1108C and R1129C are both temperature-sensitive processing mutants that engage the cellular quality control mechanism and show a strong interaction with the chaperone Hsp 27. Both mutant proteins also interact with HDCAC6 and are degraded in the aggresome. We also demonstrate that novel corrector compounds that are being tested as treatment for cystic fibrosis, such as VX-809, can rescue the processing of the ABCA4 mutants, particularly their expression at the cell surface, and can reduce their binding to HDAC6. Thus, our data suggest that VX-809 can potentially be developed as a new therapy for Stargardt disease, for which there is currently no treatment. PMID:26092729

  15. Plasmodium falciparum erythrocyte membrane protein 1 domain cassettes 8 and 13 are associated with severe malaria in children

    DEFF Research Database (Denmark)

    Lavstsen, Thomas; Turner, Louise; Saguti, Fredy;

    2012-01-01

    The clinical outcome of Plasmodium falciparum infections ranges from asymptomatic parasitemia to severe malaria syndromes associated with high mortality. The virulence of P. falciparum infections is associated with the type of P. falciparum erythrocyte membrane protein 1 (PfEMP1) expressed on the...... surface of infected erythrocytes to anchor these to the vascular lining. Although var2csa, the var gene encoding the PfEMP1 associated with placental malaria, was discovered in 2003, the identification of the var/PfEMP1 variants associated with severe malaria in children has remained elusive. To identify...... var/PfEMP1 variants associated with severe disease outcome, we compared var transcript levels in parasites from 88 children with severe malaria and 40 children admitted to the hospital with uncomplicated malaria. Transcript analysis was performed by RT-quantitative PCR using a set of 42 primer pairs...

  16. Enhancing resolution properties of array antennas via field extrapolation: application to MIMO systems

    Science.gov (United States)

    Reggiannini, Ruggero

    2015-12-01

    This paper is concerned with spatial properties of linear arrays of antennas spaced less than half wavelength. Possible applications are in multiple-input multiple-output (MIMO) wireless links for the purpose of increasing the spatial multiplexing gain in a scattering environment, as well as in other areas such as sonar and radar. With reference to a receiving array, we show that knowledge of the received field can be extrapolated beyond the actual array size by exploiting the finiteness of the interval of real directions from which the field components impinge on the array. This property permits to increase the performance of the array in terms of angular resolution. A simple signal processing technique is proposed allowing formation of a set of beams capable to cover uniformly the entire horizon with an angular resolution better than that achievable by a classical uniform-weighing half-wavelength-spaced linear array. Results are also applicable to active arrays. As the above approach leads to arrays operating in super-directive regime, we discuss all related critical aspects, such as sensitivity to external and internal noises and to array imperfections, and bandwidth, so as to identify the basic design criteria ensuring the array feasibility.

  17. Design and application of locking hydraulic cylinder for roll cassette in straightener for heavy plate%中厚板矫直机辊盒锁紧液压缸的设计应用

    Institute of Scientific and Technical Information of China (English)

    曹一兵

    2013-01-01

    A security and reliable auto-locking device for the roll cassette of heavy plate straightener was designed to overcome the disadvantage that the locking device for roll cassette needs manual manipulation.The locking device works well in the straightener.It improved the operating reliability and security of straighteners.%针对中厚板矫直机上辊盒锁紧装置存在手动操作的问题,设计了一种安全可高的自动锁紧液压缸装置,该设装置在中厚板矫直机上的应用效果较好,提高了矫直机操作的可靠性及安全性.

  18. Analysis of the effect of the bovine adenosine triphosphate-binding cassette transporter G2 single nucleotide polymorphism Y581S on transcellular transport of veterinary drugs using new cell culture models.

    Science.gov (United States)

    Real, R; González-Lobato, L; Baro, M F; Valbuena, S; de la Fuente, A; Prieto, J G; Alvarez, A I; Marques, M M; Merino, G

    2011-12-01

    In commercial dairy production, the risk of drug residues and environmental pollutants in milk from ruminants has become an outstanding problem. One of the main determinants of active drug secretion into milk is the ATP-binding cassette transporter G2/breast cancer resistance protein (ABCG2/BCRP). It is located in several organs associated with drug absorption, metabolism, and excretion, and its expression is highly induced during lactation in the mammary gland of ruminants, mice, and humans. As a consequence, potential contamination of milk could expose suckling infants to xenotoxins. In cows, a SNP for this protein affecting quality and quantity of milk production has been described previously (Y581S). In this study, our main purpose was to determine whether this polymorphism has an effect on transcellular transport of veterinary drugs because this could alter substrate pharmacokinetics and milk residues. We stably expressed the wild-type bovine ABCG2 and the Y581S variant in Madin-Darby canine kidney epithelial cells (MDCKII) and MEF3.8 cell lines generating cell models in which the functionality of the bovine transporter could be addressed. Functional studies confirmed the greater functional activity in mitoxantrone accumulation assays for the Y581S variant with a greater relative V(MAX) value (P = 0.040) and showed for the first time that the Y581S variant presents greater transcellular transport of the model ABCG2 substrate nitrofurantoin (P = 0.024) and of 3 veterinary antibiotics, the fluoroquinolone agents enrofloxacin (P = 0.035), danofloxacin (P = 0.001), and difloxacin (P = 0.008), identified as new substrates of the bovine ABCG2. In addition, the inhibitory effect of the macrocyclic lactone ivermectin on the activity of wild-type bovine ABCG2 and the Y581S variant was also confirmed, showing a greater inhibitory potency on the wild-type protein at all the concentrations tested (5 μM, P = 0.017; 10 μM, P = 0.001; 25 μM, P = 0.008; and 50 μM, P = 0

  19. Small satellite solar array substrate

    Science.gov (United States)

    Fiore, John N.; Rosanova, Giulio

    1994-01-01

    The SMall EXplorer (SMEX) Fast Auroral SnapshoT (FAST) spacecraft was developed to investigate plasma physics of auroral phenomena at high orbital altitude. The FAST satellite comprises a variety of deployable booms with sensors on the ends, and instruments that protrude from the main body of the spacecraft to obtain the plasma and electromagnetic fields data. This required the plasma disturbance around the satellite to be kept to a minimum. A non deployable, body mounted solar array was implemented. This led to the design of a light weight solar array substrate with a high degree of structural integrity.

  20. TV-SAT solar array

    Energy Technology Data Exchange (ETDEWEB)

    Urbain, G.; Rinn, C.; Bastard, J.L.

    1982-06-01

    The electrical and mechanical performance of the TV-SAT direct television broadcasting satellite is described. The 4.5 kW end of life 7.5yr array contains 43,200 back surface reflector solar cells. The first, 3.1 kW, array consists of two identical wings, providing power during transfer and geostationary orbit. Each wing is made up of four carbon fiber panels. The outboard panel of each wing is deployed at 90 deg in transfer orbit, during which the satellite is three axis stabilized.

  1. Future Plans of Telescope Array

    International Nuclear Information System (INIS)

    The Telescope Array (TA) experiment is the only ultra high energy cosmic ray observatory in the northern hemisphere. In addition, it will be the world's first air shower detector to be directly calibrated by an on-site accelerator beam. For wider and deeper understanding of cosmic rays by via high precision measurements, we have undertaken the study of extension plans for TA. One extension plan will extend the sensitive energy range of TA down to 1017 eV. A second plan would extend of the aperture area of the SD array. These plans are described in this note.

  2. Substrate integrated antennas and arrays

    CERN Document Server

    Cheng, Yu Jian

    2015-01-01

    Substrate Integrated Antennas and Arrays provides a single source for cutting-edge information on substrate integrated circuits (SICs), substrate integrated waveguide (SIW) feeding networks, SIW slot array antennas, SIC traveling-wave antennas, SIW feeding antennas, SIW monopulse antennas, and SIW multibeam antennas. Inspired by the author's extensive research, this comprehensive book:Describes a revolutionary SIC-based antenna technique with the potential to replace existing antenna technologiesExamines theoretical and experimental results connected to electrical and mechanical performanceExp

  3. Phased arrays: inline flow line hub inspection using phased arrays

    NARCIS (Netherlands)

    Bloom, J.G.P.; Chougrani, K.; Rundberg, H.; Oldenziel, G.; Deleye, X.; Martina, Q.

    2011-01-01

    The feasibility of the inspection of flow line hubs using the phased array technique was investigated to determine the surface area of the seal area degraded by corrosion. A clean model of the hub was simulated to gain insight into the geometrical echoes and to determine the area covered by the ultr

  4. Digital Identifier Systems: Comparative Evaluation

    OpenAIRE

    Hamid Reza Khedmatgozar; Mehdi Alipour-Hafezi; Payam Hanafizadeh

    2015-01-01

    Identifier is one of the main elements in identifying an object in digital environment. Digital identifier systems were developed followed by a lot of problems such as violation of persistency and uniqueness of physical identifiers and URL in digital environment. These identifiers try to guarantee uniqueness and persistency of hostnames by using indirect names for Domain Name System (DNS). The main objective of this research is to identify qualified digital identifier system among other syste...

  5. Directional field enhancement of dielectric nano optical disc antenna arrays

    Science.gov (United States)

    Wang, Ivan; Du, Y.

    2011-11-01

    This paper presents a discussion on the directive field enhancement of dielectric disc antenna arrays in optical band. The property of dielectric material is addressed, and field modes in a cylindrical resonator are discussed. It is identified that the fundamental mode of HE 11δ generates the far field with a higher directivity than other modes. More effective field enhancement in the radiation direction could be achieved by using multiple-disc antenna arrays. Simulation examples indicate that the directivity of a disc antenna array varies with the disc spacing. The maximum directivity is observed when the disc spacing is approximately equal to the half of the vacuum wavelength. The maximum directivity can be improved significantly when the disc number is increased.

  6. Large SNP arrays for genotyping in crop plants

    Indian Academy of Sciences (India)

    Martin W Ganal; Andreas Polley; Eva-Maria Graner; Joerg Plieske; Ralf Wieseke; Hartmut Luerssen; Gregor Durstewitz

    2012-11-01

    Genotyping with large numbers of molecular markers is now an indispensable tool within plant genetics and breeding. Especially through the identification of large numbers of single nucleotide polymorphism (SNP) markers using the novel high-throughput sequencing technologies, it is now possible to reliably identify many thousands of SNPs at many different loci in a given plant genome. For a number of important crop plants, SNP markers are now being used to design genotyping arrays containing thousands of markers spread over the entire genome and to analyse large numbers of samples. In this article, we discuss aspects that should be considered during the design of such large genotyping arrays and the analysis of individuals. The fact that crop plants are also often autopolyploid or allopolyploid is given due consideration. Furthermore, we outline some potential applications of large genotyping arrays including high-density genetic mapping, characterization (fingerprinting) of genetic material and breeding-related aspects such as association studies and genomic selection.

  7. A rev1-vpu polymorphism unique to HIV-1 subtype A and C strains impairs envelope glycoprotein expression from rev-vpu-env cassettes and reduces virion infectivity in pseudotyping assays

    International Nuclear Information System (INIS)

    Functional studies of HIV-1 envelope glycoproteins (Envs) commonly include the generation of pseudoviruses, which are produced by co-transfection of rev-vpu-env cassettes with an env-deficient provirus. Here, we describe six Env constructs from transmitted/founder HIV-1 that were defective in the pseudotyping assay, although two produced infectious virions when expressed from their cognate proviruses. All of these constructs exhibited an unusual gene arrangement in which the first exon of rev (rev1) and vpu were in the same reading frame without an intervening stop codon. Disruption of the rev1-vpu fusion gene by frameshift mutation, stop codon, or abrogation of the rev initiation codon restored pseudovirion infectivity. Introduction of the fusion gene into wildtype Env cassettes severely compromised their function. The defect was not due to altered env and rev transcription or a dominant negative effect of the expressed fusion protein, but seemed to be caused by inefficient translation at the env initiation codon. Although the rev1-vpu polymorphism affects Env expression only in vitro, it can cause problems in studies requiring Env complementation, such as analyses of co-receptor usage and neutralization properties, since 3% of subtype A, 20% of subtype C and 5% of CRF01A/E viruses encode the fusion gene. A solution is to eliminate the rev initiation codon when amplifying rev-vpu-env cassettes since this increases Env expression irrespective of the presence of the polymorphism.

  8. Modifying the emission of light from a semiconductor nanowire array

    Science.gov (United States)

    Anttu, Nicklas

    2016-07-01

    Semiconductor nanowire arrays have been identified as a promising platform for future light emitting diodes (LEDs), for example, due to the materials science freedom of combining lattice-mismatched materials in them. Furthermore, the emission of light from nanowires can be tailored by designing their geometry. Such tailoring could optimize the emission of light to the top side as well as enhance the emission rate through the Purcell effect. However, the possibility for enhanced light extraction from III-V nanowire arrays over a conventional bulk-like LED has not been investigated systematically. Here, we use electromagnetic modeling to study the emission of light from nanowire arrays. We vary both the diameter of the nanowires and the array period to show the benefit of moving from a bulk-like LED to a nanowire array LED. We study the fraction of light emitted to the top air side and to the substrate at wavelength λ. We find several diameter-dependent resonant peaks for which the emission to the top side is maximized. For the strongest such peak, by increasing the array period, the fraction of emitted light that is extracted at the top air side can be enhanced by a factor of 30 compared to that in a planar bulk LED. By modeling a single nanowire, we confirm that it is beneficial to place the nanowires further apart to enhance the emission to the top side. Furthermore, we predict that for a nanowire diameter D > λ/2, a majority of the emitted power ends up in the substrate. Our results offer direction for the design and optimization of nanowire-array based light emitting diodes.

  9. An Array of Optical Receivers for Deep-Space Communications

    Science.gov (United States)

    Vilnrotter, Chi-Wung; Srinivasan, Meera; Andrews, Kenneth

    2007-01-01

    An array of small optical receivers is proposed as an alternative to a single large optical receiver for high-data-rate communications in NASA s Deep Space Network (DSN). Because the telescope for a single receiver capable of satisfying DSN requirements must be greater than 10 m in diameter, the design, building, and testing of the telescope would be very difficult and expensive. The proposed array would utilize commercially available telescopes of 1-m or smaller diameter and, therefore, could be developed and verified with considerably less difficulty and expense. The essential difference between a single-aperture optical-communications receiver and an optical-array receiver is that a single-aperture receiver focuses all of the light energy it collects onto the surface of an optical detector, whereas an array receiver focuses portions of the total collected energy onto separate detectors, optically detects each fractional energy component, then combines the electrical signal from the array of detector outputs to form the observable, or "decision statistic," used to decode the transmitted data. A conceptual block diagram identifying the key components of the optical-array receiver suitable for deep-space telemetry reception is shown in the figure. The most conspicuous feature of the receiver is the large number of small- to medium-size telescopes, with individual apertures and number of telescopes selected to make up the desired total collecting area. This array of telescopes is envisioned to be fully computer- controlled via the user interface and prediction-driven to achieve rough pointing and tracking of the desired spacecraft. Fine-pointing and tracking functions then take over to keep each telescope pointed toward the source, despite imperfect pointing predictions, telescope-drive errors, and vibration caused by wind.

  10. A Novel Domain Cassette Identifies Plasmodium falciparum PfEMP1 Proteins Binding ICAM-1 and Is a Target of Cross-Reactive, Adhesion-Inhibitory Antibodies

    DEFF Research Database (Denmark)

    Bengtsson, Anja; Jørgensen, Louise; Rask, Thomas Salhøj;

    2013-01-01

    Cerebral Plasmodium falciparum malaria is characterized by adhesion of infected erythrocytes (IEs) to the cerebral microvasculature. This has been linked to parasites expressing the structurally related group A subset of the P. falciparum erythrocyte membrane protein 1 (PfEMP1) family of IE adhes...

  11. 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...

  12. Radar techniques using array antennas

    CERN Document Server

    Wirth, Wulf-Dieter

    2001-01-01

    This book gives an introduction to the possibilities of radar technology based on active array antennas, giving examples of modern practical systems. There are many valuable lessons presented for designers of future high standard multifunction radar systems for military and civil applications. The book will appeal to graduate level engineers, researchers, and managers in the field of radar, aviation and space technology.

  13. Photoelectrochemistry of Semiconductor Nanowire Arrays

    Energy Technology Data Exchange (ETDEWEB)

    Mallouk, Thomas E; Redwing, Joan M

    2009-11-10

    This project supported research on the growth and photoelectrochemical characterization of semiconductor nanowire arrays, and on the development of catalytic materials for visible light water splitting to produce hydrogen and oxygen. Silicon nanowires were grown in the pores of anodic aluminum oxide films by the vapor-liquid-solid technique and were characterized electrochemically. Because adventitious doping from the membrane led to high dark currents, silicon nanowire arrays were then grown on silicon substrates. The dependence of the dark current and photovoltage on preparation techniques, wire diameter, and defect density was studied for both p-silicon and p-indium phosphide nanowire arrays. The open circuit photovoltage of liquid junction cells increased with increasing wire diameter, reaching 350 mV for micron-diameter silicon wires. Liquid junction and radial p-n junction solar cells were fabricated from silicon nano- and microwire arrays and tested. Iridium oxide cluster catalysts stabilized by bidentate malonate and succinate ligands were also made and studied for the water oxidation reaction. Highlights of this project included the first papers on silicon and indium phosphide nanowire solar cells, and a new procedure for making ligand-stabilized water oxidation catalysts that can be covalently linked to molecular photosensitizers or electrode surfaces.

  14. Quantum Entanglement in Nanocavity Arrays

    OpenAIRE

    Liew, T.C.H.; Savona, V

    2011-01-01

    We show theoretically how quantum interference between linearly coupled modes with weak local nonlinearity allows the generation of continuous variable entanglement. By solving the quantum master equation for the density matrix, we show how the entanglement survives realistic levels of pure dephasing. The generation mechanism forms a new paradigm for entanglement generation in arrays of coupled quantum modes.

  15. BOLOMETRIC ARRAYS FOR MILLIMETER WAVELENGTHS

    Directory of Open Access Journals (Sweden)

    E. Castillo

    2009-01-01

    Full Text Available During last years, semiconductor bolometers using thin lms have been developed at INAOE, speci cally boron-doped hydrogenated amorphous silicon lms. The characteristics shown by these devices made them attractive to be used in astronomical instrumentation, mainly in two-dimentional arrays. These detector arrays used at the Large Millimeter Telescope will make possible to obtain astronomical images in millimeter and submillimeter wavelengths. With this in mind, we are developing a method to produce, with enough reliability, bolometer arrays at INAOE. Until now, silicon nitride diaphragm arrays, useful as radiation absorbers, have succesfully been obtained. Sizes going from one to four millimeter by element in a consistent way; however we have not tested thermometers and metallic contact deposition yet. At the same time, we are working on two possible con gurations for the readout electronics; one of them using commercial components while the other will be an integrated circuit speci cally designed for this application. Both versions will work below 77K.

  16. Phased array antennas with optimized element patterns

    CERN Document Server

    Skobelev, Sergei P

    2011-01-01

    This authoritative resource provides you with a detailed description of ideal array element characteristics that help you estimate the quality of development of real-world phased array antennas. You find several approaches to optimum phased array design, allowing you to provide specified array gain in a specific region of scan, using a minimum number of expensive, controlled devices. Moreover, this practical book presents important numerical methods that you can use to model and optimize phased array structure to obtain the best array characteristics that the chosen structure can provide.From

  17. The interaction field in arrays of ferromagnetic barcode nanowires

    International Nuclear Information System (INIS)

    A theoretical model and an experimental approach to the identification of the interaction field in ferromagnetic barcode nanowires are described and applied to electrodeposited Ni/Au cylindrical barcode arrays. Elementary hysteresis loops of individual magnetic segments in these barcode nanowires are considered as superpositions of fully irreversible and locally reversible magnetization processes, whose distributions of switching fields are experimentally identified by first order reversal curve measurements. Non-interacting major hysteresis loops of the arrays are computed as superpositions of several elementary loops by considering the distributions of switching fields as probability density functions. The interaction field is then computed from the condition that the geometric transformation of the experimental major hysteresis loop into the Preisach operative plane be well approximated by this non-interacting hysteresis loop. Experimental interaction field values are compared with those obtained by numerical micromagnetic computations and a very good agreement is obtained on extended Ni/Au barcode arrays. The simple and accurate phenomenological model for the interaction field in multisegmented ferromagnetic nanowire arrays proposed here provides an insight into the morphology of these magnetic nanomaterials, as quantitative information about individual nano-objects may be extracted from macroscopic measurements of their arrays

  18. The interaction field in arrays of ferromagnetic barcode nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Clime, L [NRC, Industrial Materials Institute, 75 de Mortagne Boulevard, Boucherville, J4B 6Y4 (Canada); Zhao, S Y [NRC, Industrial Materials Institute, 75 de Mortagne Boulevard, Boucherville, J4B 6Y4 (Canada); Chen, P [Research Center for Applied Sciences, Academia Sinica 128 Section 2, Academia Rd, Nankang, Taipei 11529, Taiwan (China); Normandin, F [NRC, Industrial Materials Institute, 75 de Mortagne Boulevard, Boucherville, J4B 6Y4 (Canada); Roberge, H [NRC, Industrial Materials Institute, 75 de Mortagne Boulevard, Boucherville, J4B 6Y4 (Canada); Veres, T [NRC, Industrial Materials Institute, 75 de Mortagne Boulevard, Boucherville, J4B 6Y4 (Canada)

    2007-10-31

    A theoretical model and an experimental approach to the identification of the interaction field in ferromagnetic barcode nanowires are described and applied to electrodeposited Ni/Au cylindrical barcode arrays. Elementary hysteresis loops of individual magnetic segments in these barcode nanowires are considered as superpositions of fully irreversible and locally reversible magnetization processes, whose distributions of switching fields are experimentally identified by first order reversal curve measurements. Non-interacting major hysteresis loops of the arrays are computed as superpositions of several elementary loops by considering the distributions of switching fields as probability density functions. The interaction field is then computed from the condition that the geometric transformation of the experimental major hysteresis loop into the Preisach operative plane be well approximated by this non-interacting hysteresis loop. Experimental interaction field values are compared with those obtained by numerical micromagnetic computations and a very good agreement is obtained on extended Ni/Au barcode arrays. The simple and accurate phenomenological model for the interaction field in multisegmented ferromagnetic nanowire arrays proposed here provides an insight into the morphology of these magnetic nanomaterials, as quantitative information about individual nano-objects may be extracted from macroscopic measurements of their arrays.

  19. Could the IMS Infrasound Stations Support a Global Network of Small Aperture Seismic Arrays?

    Science.gov (United States)

    J, Gibbons, Steven; Kværna, Tormod; Mykkeltveit, Svein

    2015-04-01

    The infrasound stations of the International Monitoring System are arrays consisting of up to 15 sites and with apertures of up to 3 km. The arrays are distributed remarkably uniformly over the globe and provide excellent coverage of South America, Africa, and Antarctica. This is to say that there are many infrasound arrays in regions many thousands of kilometers from the closest seismic array. Several infrasound arrays are in the immediate vicinity of existing 3-component seismic stations and these provide us with examples of how typical seismic signals look at these locations. We can make idealized estimates of the predicted performance of seismic arrays, consisting of seismometers at each site of the infrasound arrays, by duplicating the signals from the 3-C stations at all sites of the array. However, the true performance of seismic arrays at these sites will depend both upon Signal-to-Noise Ratios of seismic signals and the coherence of both signal and noise between sensors. These properties can only be determined experimentally. Recording seismic data of sufficient quality at many of these arrays may require borehole deployments since the microbarometers in the infrasound arrays are often situated in vaults placed in soft sediments. The geometries of all the current IMS infrasound arrays are examined and compared and we demonstrate that, from a purely geometrical perspective, essentially all the array configurations would provide seismic arrays with acceptable slowness resolution for both regional and teleseismic phase arrivals. Seismic arrays co-located with the infrasound arrays in many regions would likely enhance significantly the seismic monitoring capability in parts of the world where only 3-component stations are currently available. Co-locating seismic and infrasound sensors would facilitate the development of seismic arrays that share the infrastructure of the infrasound arrays, reducing the development and operational costs. Hosting countries might

  20. Mapping binding sites for the PDE4D5 cAMP-specific phosphodiesterase to the N- and C-domains of beta-arrestin using spot-immobilized peptide arrays.

    Science.gov (United States)

    Baillie, George S; Adams, David R; Bhari, Narinder; Houslay, Thomas M; Vadrevu, Suryakiran; Meng, Dong; Li, Xiang; Dunlop, Allan; Milligan, Graeme; Bolger, Graeme B; Klussmann, Enno; Houslay, Miles D

    2007-05-15

    Beta2-ARs (beta2-adrenoceptors) become desensitized rapidly upon recruitment of cytosolic beta-arrestin. PDE4D5 (family 4 cAMP-specific phosphodiesterase, subfamily D, isoform 5) can be recruited in complex with beta-arrestin, whereupon it regulates PKA (cAMP-dependent protein kinase) phosphorylation of the beta2-AR. In the present study, we have used novel technology, employing a library of overlapping peptides (25-mers) immobilized on cellulose membranes that scan the entire sequence of beta-arrestin 2, to define the interaction sites on beta-arrestin 2 for binding of PDE4D5 and the cognate long isoform, PDE4D3. We have identified a binding site in the beta-arrestin 2 N-domain for the common PDE4D catalytic unit and two regions in the beta-arrestin 2 C-domain that confer specificity for PDE4D5 binding. Alanine-scanning peptide array analysis of the N-domain binding region identified severely reduced interaction with PDE4D5 upon R26A substitution, and reduced interaction upon either K18A or T20A substitution. Similar analysis of the beta-arrestin 2 C-domain identified Arg286 and Asp291, together with the Leu215-His220 region, as being important for binding PDE4D5, but not PDE4D3. Transfection with wild-type beta-arrestin 2 profoundly decreased isoprenaline-stimulated PKA phosphorylation of the beta2-AR in MEFs (mouse embryo fibroblasts) lacking both beta-arrestin 1 and beta-arrestin 2. This effect was negated using either the R26A or the R286A mutant form of beta-arrestin 2 or a mutant with substitution of an alanine cassette for Leu215-His220, which showed little or no PDE4D5 binding, but was still recruited to the beta2-AR upon isoprenaline challenge. These data show that the interaction of PDE4D5 with both the N- and C-domains of beta-arrestin 2 are essential for beta2-AR regulation. PMID:17288540

  1. The development of a mini-array for estimating the disease state of gastric adenocarcinoma by array CGH

    International Nuclear Information System (INIS)

    The treatment strategy usually depends on the disease state in the individual patient. However, it is difficult to estimate the disease state before treatment in many patients. The purpose of this study was to develop a BAC (bacterial artificial chromosome) mini-array allowing for the estimation of node metastasis, liver metastasis, peritoneal dissemination and the depth of tumor invasion in gastric cancers. Initially, the DNA copy number aberrations (DCNAs) were analyzed by array-based comparative genomic hybridization (aCGH) in 83 gastric adenocarcinomas as a training-sample set. Next, two independent analytical methods were applied to the aCGH data to identify the BAC clones with DNA copy number aberrations that were linked with the disease states. One of the methods, a decision-tree model classifier, identified 6, 4, 4, 4, and 7 clones for estimating lymph node metastasis, liver metastasis, peritoneal dissemination, depth of tumor invasion, and histological type, respectively. In the other method, a clone-by-clone comparison of the frequency of the DNA copy number aberrations selected 26 clones to estimate the disease states. By spotting these 50 clones together with 26 frequently or rarely involved clones and 62 reference clones, a mini-array was made to estimate the above parameters, and the diagnostic performance of the mini-array was evaluated for an independent set of 30 gastric cancers (blinded – sample set). In comparison to the clinicopathological features, the overall accuracy was 66.7% for node metastasis, 86.7% for liver metastasis, 86.7% for peritoneal dissemination, and 96.7% for depth of tumor invasion. The intratumoral heterogeneity barely affected the diagnostic performance of the mini-array. These results suggest that the mini-array makes it possible to determine an optimal treatment for each of the patients with gastric adenocarcinoma

  2. The development of a mini-array for estimating the disease state of gastric adenocarcinoma by array CGH

    Directory of Open Access Journals (Sweden)

    Oga Atsunori

    2008-12-01

    Full Text Available Abstract Background The treatment strategy usually depends on the disease state in the individual patient. However, it is difficult to estimate the disease state before treatment in many patients. The purpose of this study was to develop a BAC (bacterial artificial chromosome mini-array allowing for the estimation of node metastasis, liver metastasis, peritoneal dissemination and the depth of tumor invasion in gastric cancers. Methods Initially, the DNA copy number aberrations (DCNAs were analyzed by array-based comparative genomic hybridization (aCGH in 83 gastric adenocarcinomas as a training-sample set. Next, two independent analytical methods were applied to the aCGH data to identify the BAC clones with DNA copy number aberrations that were linked with the disease states. One of the methods, a decision-tree model classifier, identified 6, 4, 4, 4, and 7 clones for estimating lymph node metastasis, liver metastasis, peritoneal dissemination, depth of tumor invasion, and histological type, respectively. In the other method, a clone-by-clone comparison of the frequency of the DNA copy number aberrations selected 26 clones to estimate the disease states. Results By spotting these 50 clones together with 26 frequently or rarely involved clones and 62 reference clones, a mini-array was made to estimate the above parameters, and the diagnostic performance of the mini-array was evaluated for an independent set of 30 gastric cancers (blinded – sample set. In comparison to the clinicopathological features, the overall accuracy was 66.7% for node metastasis, 86.7% for liver metastasis, 86.7% for peritoneal dissemination, and 96.7% for depth of tumor invasion. The intratumoral heterogeneity barely affected the diagnostic performance of the mini-array. Conclusion These results suggest that the mini-array makes it possible to determine an optimal treatment for each of the patients with gastric adenocarcinoma.

  3. Smart trigger logic for focal plane arrays

    Science.gov (United States)

    Levy, James E; Campbell, David V; Holmes, Michael L; Lovejoy, Robert; Wojciechowski, Kenneth; Kay, Randolph R; Cavanaugh, William S; Gurrieri, Thomas M

    2014-03-25

    An electronic device includes a memory configured to receive data representing light intensity values from pixels in a focal plane array and a processor that analyzes the received data to determine which light values correspond to triggered pixels, where the triggered pixels are those pixels that meet a predefined set of criteria, and determines, for each triggered pixel, a set of neighbor pixels for which light intensity values are to be stored. The electronic device also includes a buffer that temporarily stores light intensity values for at least one previously processed row of pixels, so that when a triggered pixel is identified in a current row, light intensity values for the neighbor pixels in the previously processed row and for the triggered pixel are persistently stored, as well as a data transmitter that transmits the persistently stored light intensity values for the triggered and neighbor pixels to a data receiver.

  4. Space Station Solar Array Joint Repair

    Science.gov (United States)

    Loewenthal, Stuart; Allmon, Curtis; Reznik, Carter; McFatter, Justin; Davis, Robert E.

    2015-01-01

    In Oct 2007 the International Space Station (ISS) crew noticed a vibrating camera in the vicinity of Starboard Solar Alpha Rotary Joint (SARJ). It had less than 5 months of run time when the anomaly was observed. This approximately 3.2 meter diameter bearing joint supports solar arrays that power the station critical to its operation. The crew performed an EVA to identify what was causing the vibration. It was discovered that one of the 3 bearing tracks of this unconventional bearing had significant spalling damage. This paper discusses the SARJ's unique bearing design and the vulnerability in its design leading to the observed anomaly. The design of a SARJ vacuum test rig is also described along with the results of a life test that validated the proposed repair should extend the life of the SARJ a minimum of 18 years on-orbit.

  5. Arrayed primer extension in the "array of arrays" format: a rational approach for microarray-based SNP genotyping

    DEFF Research Database (Denmark)

    Klitø, Niels G F; Tan, Qihua; Nyegaard, Mette;

    2007-01-01

    This study provides a new version of the arrayed primer extension (APEX) protocol adapted to the 'array of arrays' platform using an instrumental setup for microarray processing not previously described. The primary aim of the study is to implement a system for rational cost-efficient genotyping...

  6. Optical networks for wideband sensor array

    Science.gov (United States)

    Sheng, Lin Horng

    2011-12-01

    This thesis presents the realization of novel systems for optical sensing networks with an array of long-period grating (LPG) sensors. As a launching point of the thesis, the motivation to implement optical sensing network in precisely catering LPG sensors is presented. It highlights the flexibility of the sensing network to act as the foundation in order to boost the application of the various LPG sensor design in biological and chemical sensing. After the thorough study on the various optical sensing networks, sub-carrier multiplexing (SCM) and optical time division multiplexing (OTDM) schemes are adopted in conjunction with tunable laser source (TLS) to facilitate simultaneous interrogation of the LPG sensors array. In fact, these systems are distinct to have the capability to accommodate wideband optical sensors. Specifically, the LPG sensors which is in 20nm bandwidth are identified to operate in these systems. The working principles of the systems are comprehensively elucidated in this thesis. It highlights the mathematical approach to quantify the experimental setup of the optical sensing network. Additionally, the system components of the designs are identified and methodically characterized so that the components well operate in the designed environment. A mockup has been setup to demonstrate the application in sensing of various liquid indices and analyse the response of the LPG sensors in order to evaluate the performance of the systems. Eventually, the resemblance of the demultiplexed spectral response to the pristine spectral response are quantified to have excellent agreement. Finally, the promising result consistency of the systems is verified through repeatability test.

  7. Large Format Uncooled Focal Plane Array Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Uncooled focal plane arrays have improved dramatically and array sizes of 320x240 elements in a 50-?m pitch are commercially available at affordable cost. Black...

  8. Low Cost Phased Array Antenna System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — JEM Engineering proved the technical feasibility of the FlexScan array?a very low-cost, highly-efficient, wideband phased array antenna?in Phase I, and stands ready...

  9. The capacity of Listeria monocytogenes mutants with in-frame deletions in putative ATP-binding cassette transporters to form biofilms and comparison with the wild type

    Directory of Open Access Journals (Sweden)

    Marina Ceruso

    2014-02-01

    Full Text Available Listeria monocytogenes (Lm is a food-borne pathogen responsible for human listeriosis, an invasive infection with high mortality rates. Lm has developed efficient strategies for survival under stress conditions such as starvation and wide variations in temperature, pH, and osmolarity. Therefore, Lm can survive in food under multiple stress conditions. Detailed studies to determine the mode of action of this pathogen for survival under stress conditions are important to control Lm in food. It has been shown that genes encoding for ATP-binding cassette (ABC transporters are induced in Lm in food, in particular under stress conditions. Previous studies showed that these genes are involved in sensitivity to nisin, acids, and salt. The aim of this study was to determine the involvement of some ABC transporters in biofilm formation. Therefore, deletion mutants of ABC transporter genes (LMOf2365_1875 and LMOf2365_1877 were created in Lm F2365, and then were compared to the wild type for their capacity to form biofilms. Lm strain F2365 was chosen as reference since the genome is fully sequenced and furthermore this strain is particularly involved in food-borne outbreaks of listeriosis. Our results showed that DLMOf2365_1875 had an increased capacity to form biofilms compared to the wild type, indicating that LMOf2365_1875 negatively regulates biofilm formation. A deeper knowledge on the ability to form biofilms in these mutants may help in the development of intervention strategies to control Lm in food and in the environment.

  10. Galectin-3 silencing inhibits epirubicin-induced ATP binding cassette transporters and activates the mitochondrial apoptosis pathway via β-catenin/GSK-3β modulation in colorectal carcinoma.

    Directory of Open Access Journals (Sweden)

    Yung-Kuo Lee

    Full Text Available Multidrug resistance (MDR, an unfavorable factor compromising the treatment efficacy of anticancer drugs, involves the upregulation of ATP binding cassette (ABC transporters and induction of galectin-3 signaling. Galectin-3 plays an anti-apoptotic role in many cancer cells and regulates various pathways to activate MDR. Thus, the inhibition of galectin-3 has the potential to enhance the efficacy of the anticancer drug epirubicin. In this study, we examined the effects and mechanisms of silencing galectin-3 via RNA interference (RNAi on the β-catenin/GSK-3β pathway in human colon adenocarcinoma Caco-2 cells. Galectin-3 knockdown increased the intracellular accumulation of epirubicin in Caco-2 cells; suppressed the mRNA expression of galectin-3, β-catenin, cyclin D1, c-myc, P-glycoprotein (P-gp, MDR-associated protein (MRP 1, and MRP2; and downregulated the protein expression of P-gp, cyclin D1, galectin-3, β-catenin, c-Myc, and Bcl-2. Moreover, galectin-3 RNAi treatment significantly increased the mRNA level of GSK-3β, Bax, caspase-3, and caspase-9; remarkably increased the Bax-to-Bcl-2 ratio; and upregulated the GSK-3β and Bax protein expressions. Apoptosis was induced by galectin-3 RNAi and/or epirubicin as demonstrated by chromatin condensation, a higher sub-G1 phase proportion, and increased caspase-3 and caspase-9 activity, indicating an intrinsic/mitochondrial apoptosis pathway. Epirubicin-mediated resistance was effectively inhibited via galectin-3 RNAi treatment. However, these phenomena could be rescued after galectin-3 overexpression. We show for the first time that the silencing of galectin-3 sensitizes MDR cells to epirubicin by inhibiting ABC transporters and activating the mitochondrial pathway of apoptosis through modulation of the β-catenin/GSK-3β pathway in human colon cancer cells.

  11. Transferring a Gene Expression Cassette Lacking the Vector Backbone Sequences of the 1Ax1 High Molecular Weight Glutenin Subunit into Two Chinese Hexaploid Wheat Genotypes

    Institute of Scientific and Technical Information of China (English)

    SHI Nong-nong; HE Guang-yuan; LI Ke-xiu; WANG Hui-zhong; CHEN Guan-ping; XU Ying

    2007-01-01

    1Ax1 high molecular weight glutenin subunit (HMW-GS) gene expression cassette (GEC) lacking vector backbone sequences together with selectable marker Bar GEC were co-transformed into Chinese hexaploid cultivars Een 1 and Emai 12 to test the feasibility and the efficiency of explant regeneration, transformation frequency and transgene expression comparing with whole vector transformation by the approaches of plasmid extraction and excision, immature embryo isolation, particle co-bombardment, tissue culture, DNA extraction, PCR amplification, southern hybridization, leaf-painting test and SDS-PAGE etc. No significant difference was shown in tissue culture response of the proportion of embryogenic calli, somatic embryogenesis and regeneration frequency between GEC and whole plasmid bombarded embryos, but both regenerated less well than non-bombarded control. Total 56 plantlets that survived PPT selection had insertion of at least the Bar gene, 18 were from the GEC treatment and 38 from the whole plasmid treatment, the escape ratio averaged 0.23. Six independent transplants f230 - f235 with GEC transformation from genotype Emai 12 presented clear PCR amplification bands of Bar and 1Ax1 gene. The transformation and co-transformation frequency were 3.51 and 100% respectively. PCR amplification using a primer-pair specific for ampicillin resistant gene indicated the existence of AmpR gene in whole vectors but the removal in GECs and transplants. Southern blot of total DNA and PCR products from transgenic plants of 1Ax1 GEC confirmed the integration of the transgene 1Ax1 and the absence of the EcoR Ⅰ recognition site at both ends of the 1Ax1 GEC when integrated. SDS-PAGE showed the expression of 1Ax1 GEC and un-expression of whole plasmid. The length of integrated fragment, the proportion of the gene of interest (GOI) and the selectable marker (MG), bombardment pressure and genotypes are vital for the expression of a transformed GEC.

  12. Automatic synthesis of 16{alpha}-[{sup 18}F]fluoro-17{beta}-estradiol using a cassette-type [{sup 18}F]fluorodeoxyglucose synthesizer

    Energy Technology Data Exchange (ETDEWEB)

    Mori, Tetsuya [Biomedical Imaging Research Center, University of Fukui, Matsuoka, Fukui 910-1193 (Japan)]. E-mail: morit@fmsrsa.fukui-med.ac.jp; Kasamatsu, Shingo [JFE P and S Fukui Branch, University of Fukui, Matsuoka, Fukui 910-1193 (Japan); Mosdzianowski, Christoph [GE Healthcare Technologies, Parc Scientifique du Sart Tilman Av. Pre-Aliy (c/o Socran) B-4031 Liege (Belgium); Welch, Michael J. [Mallinckrodt Institute of Radiology, Washington University Medical Center, St. Louis, MO 63110 (United States); Yonekura, Yoshiharu [Biomedical Imaging Research Center, University of Fukui, Matsuoka, Fukui 910-1193 (Japan); Fujibayashi, Yasuhisa [Biomedical Imaging Research Center, University of Fukui, Matsuoka, Fukui 910-1193 (Japan)

    2006-02-15

    16{alpha}-[{sup 18}F]fluoro-17{beta}-estradiol ([{sup 18}F]FES) is a radiotracer for imaging estrogen receptors by positron emission tomography. We developed a clinically applicable automatic preparation system for [{sup 18}F]FES by modifying a cassette-type [{sup 18}F]fluorodeoxyglucose synthesizer. Two milligrams of 3-O-methoxymethyl-16,17-O-sulfuryl-16-epiestriol in acetonitrile was heated at 105{sup o}C for 10 min with dried [{sup 18}F]fluoride. The resultant solution was evaporated and hydrolyzed with 0.2 N HCl in 90% acetonitrile/water at 95{sup o}C for 10 min under pressurized condition. The neutralization was carried out with 2.8% NaHCO{sub 3}, and then the high-performance liquid chromatography (HPLC) purification was performed. The desired radioactive fraction was collected and the solvent was replaced by 10 ml of saline, and then passed through a 0.22-{mu}m filter into a pyrogen-free vial as the final product. The HPLC purification data demonstrated that [{sup 18}F]FES was synthesized with a yield of 76.4{+-}1.9% (n=5). The yield as the final product for clinical use was 42.4{+-}3.2% (n=5, decay corrected). The total preparation time was 88.2{+-}6.4 min, including the HPLC purification and the solvent replacement process. The radiochemical purity of the final product was >99%, and the specific activity was more than 111 GBq/{mu}mol. The final product was stable for more than 6 h in saline containing sodium ascorbate. This new preparation system enables us to produce [{sup 18}F]FES safe for clinical use with high and reproducible yield.

  13. Cholera in Vietnam: changes in genotypes and emergence of class I integrons containing aminoglycoside resistance gene cassettes in vibrio cholerae O1 strains isolated from 1979 to 1996.

    Science.gov (United States)

    Dalsgaard, A; Forslund, A; Tam, N V; Vinh, D X; Cam, P D

    1999-03-01

    The number of cholera cases and the mortality rates reported from different regions of Vietnam varied considerably in the period from 1979 to 1996, with between 2,500 and 6,000 cases reported annually from 1992 to 1995. Annual mortality rates ranged from 2.0 to 9.6% from 1979 to 1983 to less than 1.8% after 1983. Major cholera outbreaks were reported from the High Plateau region for the first time in 1994 and 1995; this is an area with limited access to health services and safe drinking-water supplies. All cases were associated with Vibrio cholerae O1. Using ribotyping, cholera toxin (CT) genotyping, and characterization of antibiotic susceptibility patterns and antibiotic resistance genes by PCR, we show that strains isolated after 1990 were clearly different from strains isolated before 1991. In contrast to strains isolated before 1991, 94% of 104 strains isolated after 1990 showed an identical ribotype R1, were resistant to sulfamethoxazole and streptomycin, and showed a different CT genotype. Furthermore, PCR analysis revealed that sulfamethoxazole-resistant strains harbored class I integrons containing a gene cassette ant(3")-1a encoding resistance to streptomycin and spectinomycin. This is, to our knowledge, the first report of class I integrons in V. cholerae. The development of cholera and the changes in the phenotypic and genotypic properties of V. cholerae O1 shown in the present study highlight the importance of monitoring V. cholerae O1 in Vietnam as in other parts of the world. In particular, the emergence of the new ribotype R1 strain containing class I integrons should be further studied. PMID:9986842

  14. Evaluation of solar cells and arrays for potential solar power satellite applications

    Science.gov (United States)

    Almgren, D. W.; Csigi, K.; Gaudet, A. D.

    1978-01-01

    Proposed solar array designs and manufacturing methods are evaluated to identify options which show the greatest promise of leading up to the develpment of a cost-effective SPS solar cell array design. The key program elements which have to be accomplished as part of an SPS solar cell array development program are defined. The issues focussed on are: (1) definition of one or more designs of a candidate SPS solar array module, using results from current system studies; (2) development of the necessary manufacturing requirements for the candidate SPS solar cell arrays and an assessment of the market size, timing, and industry infrastructure needed to produce the arrays for the SPS program; (3) evaluation of current DOE, NASA and DOD photovoltaic programs to determine the impacts of recent advances in solar cell materials, array designs and manufacturing technology on the candidate SPS solar cell arrays; and (4) definition of key program elements for the development of the most promising solar cell arrays for the SPS program.

  15. Exergetic Optimization of a Solar Photovoltaic Array

    OpenAIRE

    Amin Behzadmehr; Hossein Ajam; Said Farahat; Faramarz Sarhaddi

    2009-01-01

    An exergetic optimization is developed to determine the optimal performance and design parameters of a solar photovoltaic (PV) array. A detailed energy and exergy analysis is carried out to evaluate the electrical performance, exergy destruction components, and exergy efficiency of a typical PV array. The exergy efficiency of a PV array obtained in this paper is a function of climatic, operating, and design parameters such as ambient temperature, solar radiation intensity, PV array temperatur...

  16. 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.

  17. CAPweb: a bioinformatics CGH array Analysis Platform

    OpenAIRE

    Liva, Stéphane; Hupé, Philippe; Neuvial, Pierre; Brito, Isabel; Viara, Eric; La Rosa, Philippe; Barillot, Emmanuel

    2006-01-01

    Assessing variations in DNA copy number is crucial for understanding constitutional or somatic diseases, particularly cancers. The recently developed array-CGH (comparative genomic hybridization) technology allows this to be investigated at the genomic level. We report the availability of a web tool for analysing array-CGH data. CAPweb (CGH array Analysis Platform on the Web) is intended as a user-friendly tool enabling biologists to completely analyse CGH arrays from the raw data to the visu...

  18. Far-infrared imaging antenna arrays

    OpenAIRE

    Neikirk, Dean P.; Rutledge, David B.; Muha, Michael S.; Park, Hyeon; Yu, Chang-Xuan

    1982-01-01

    A far-infrared imaging antenna array has been demonstrated for the first time. The array is a line of evaporated silver bow-tie antennas on a fused-quartz substrate with bismuth-microbolometer detectors. The measured optical transfer function shows that the system is diffraction limited. This imaging array should find direct application in fusion plasma diagnostics. If the microbolometers can be replaced by more sensitive diode detectors, the array should also find application in radiometry a...

  19. Application of Seismic Array Processing to Earthquake Early Warning

    Science.gov (United States)

    Meng, L.; Allen, R. M.; Ampuero, J. P.

    2013-12-01

    Earthquake early warning (EEW) systems that can issue warnings prior to the arrival of strong ground shaking during an earthquake are essential in mitigating seismic hazard. Many of the currently operating EEW systems work on the basis of empirical magnitude-amplitude/frequency scaling relations for a point source. This approach is of limited effectiveness for large events, such as the 2011 Tohoku-Oki earthquake, for which ignoring finite source effects may result in underestimation of the magnitude. Here, we explore the concept of characterizing rupture dimensions in real time for EEW using clusters of dense low-cost accelerometers located near active faults. Back tracing the waveforms recorded by such arrays allows the estimation of the earthquake rupture size, duration and directivity in real-time, which enables the EEW of M > 7 earthquakes. The concept is demonstrated with the 2004 Parkfield earthquake, one of the few big events (M>6) that have been recorded by a local small-scale seismic array (UPSAR array, Fletcher et al, 2006). We first test the approach against synthetic rupture scenarios constructed by superposition of empirical Green's functions. We find it important to correct for the bias in back azimuth induced by dipping structures beneath the array. We implemented the proposed methodology to the mainshock in a simulated real-time environment. After calibrating the dipping-layer effect with data from smaller events, we obtained an estimated rupture length of 9 km, consistent with the distance between the two main high frequency subevents identified by back-projection using all local stations (Allman and Shearer, 2007). We proposed to deploy small-scale arrays every 30 km along the San Andreas Fault. The array processing is performed in local processing centers at each array. The output is compared with finite fault solutions based on real-time GPS system and then incorporated into the standard ElarmS system. The optimal aperture and array geometry is

  20. Microneedle array electrode for human EEG recording

    NARCIS (Netherlands)

    Luttge, Regina; Bystrova, S.N.; Putten, van M.J.A.M; Vander Sloten, Jos; Verdonck, Pascal; Nyssen, Marc; Haueisen, Jens

    2009-01-01

    Microneedle array electrodes for EEG significantly reduce the mounting time, particularly by circumvention of the need for skin preparation by scrubbing. We designed a new replication process for numerous types of microneedle arrays. Here, polymer microneedle array electrodes with 64 microneedles, i

  1. Laser diode array and transmission optics

    Science.gov (United States)

    Kwon, Jin H.

    1989-01-01

    Information on laser diode array and transmission optics is given in viewgraph form. Information is given on coherent combining of laser diode arrays, amplification through a laser diode array, the far field pattern of a laser diode transmitter, and beam diameter at receiver vs. transmission distance.

  2. Ferroelectric transistor memory arrays on flexible foils

    NARCIS (Netherlands)

    Breemen, A. van; Kam, B.; Cobb, B.; Rodriguez, F.G.; Heck, G. van; Myny, K.; Marrani, A.; Vinciguerra, V.; Gelinck, G.H.

    2013-01-01

    In this paper, we successfully fabricated and operated passive matrix P(VDF-TrFE) transistor arrays, i.e. memory arrays in which no pass-transistors or other additional electronic components are used. Because of the smaller cell, a higher integration density is possible. We demonstrate arrays up to

  3. A Brassica exon array for whole-transcript gene expression profiling.

    Directory of Open Access Journals (Sweden)

    Christopher G Love

    Full Text Available Affymetrix GeneChip® arrays are used widely to study transcriptional changes in response to developmental and environmental stimuli. GeneChip® arrays comprise multiple 25-mer oligonucleotide probes per gene and retain certain advantages over direct sequencing. For plants, there are several public GeneChip® arrays whose probes are localised primarily in 3' exons. Plant whole-transcript (WT GeneChip® arrays are not yet publicly available, although WT resolution is needed to study complex crop genomes such as Brassica, which are typified by segmental duplications containing paralogous genes and/or allopolyploidy. Available sequence data were sampled from the Brassica A and C genomes, and 142,997 gene models identified. The assembled gene models were then used to establish a comprehensive public WT exon array for transcriptomics studies. The Affymetrix GeneChip® Brassica Exon 1.0 ST Array is a 5 µM feature size array, containing 2.4 million 25-base oligonucleotide probes representing 135,201 gene models, with 15 probes per gene distributed among exons. Discrimination of the gene models was based on an E-value cut-off of 1E(-5, with ≤98% sequence identity. The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18, and categorisation by Gene Ontologies (GO based on gene orthology with Arabidopsis thaliana. Technical validation involved comparison of the exon array with a 60-mer array platform using the same starting RNA samples. The 135 k Brassica Exon Array is a robust platform. All data relating to the array design and probe identities are available in the public domain and are curated within the BrassEnsembl genome viewer at http://www.brassica.info/BrassEnsembl/index.html.

  4. Successive normalization of rectangular arrays

    CERN Document Server

    Olshen, Richard A; 10.1214/09-AOS743

    2010-01-01

    Standard statistical techniques often require transforming data to have mean 0 and standard deviation 1. Typically, this process of "standardization" or "normalization" is applied across subjects when each subject produces a single number. High throughput genomic and financial data often come as rectangular arrays where each coordinate in one direction concerns subjects who might have different status (case or control, say), and each coordinate in the other designates "outcome" for a specific feature, for example, "gene," "polymorphic site" or some aspect of financial profile. It may happen, when analyzing data that arrive as a rectangular array, that one requires BOTH the subjects and the features to be "on the same footing." Thus there may be a need to standardize across rows and columns of the rectangular matrix. There arises the question as to how to achieve this double normalization. We propose and investigate the convergence of what seems to us a natural approach to successive normalization which we lea...

  5. 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 ...

  6. 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...

  7. Recent Results from Telescope Array

    CERN Document Server

    Fukushima, M

    2015-01-01

    The Telescope Array (TA) is an experiment to observe Ultra-High Energy Cosmic Rays (UHECRs). TA's recent results, the energy spectrum and anisotropy based on the 6-year surface array data, and the primary composition obtained from the shower maximum Xmax are reported. The spectrum demonstrates a clear dip and cutoff. The shape of the spectrum is well described by the energy loss of extra-galactic protons interacting with the cosmic microwave background (CMB). Above the cutoff, a medium-scale (20 degrees radius) flux enhancement was observed near the Ursa-Major. A chance probability of creating this hotspot from the isotropic flux is 4.0 sigma. The measured Xmax is consistent with the primary being proton or light nuclei for energies 10^18.2 eV - 10^19.2 eV.

  8. Automated Camera Array Fine Calibration

    Science.gov (United States)

    Clouse, Daniel; Padgett, Curtis; Ansar, Adnan; Cheng, Yang

    2008-01-01

    Using aerial imagery, the JPL FineCalibration (JPL FineCal) software automatically tunes a set of existing CAHVOR camera models for an array of cameras. The software finds matching features in the overlap region between images from adjacent cameras, and uses these features to refine the camera models. It is not necessary to take special imagery of a known target and no surveying is required. JPL FineCal was developed for use with an aerial, persistent surveillance platform.

  9. Optical MEMS-based arrays

    Science.gov (United States)

    Ruffin, Paul B.

    2003-07-01

    Industrial Micro Electro Mechanical Systems (MEMS) developers are rapidly bringing to demonstration inertial radio frequency, and optical MEMS devices and components. The Army has a requirement for compact, highly reliable, and inexpensive laser beam steering components for missile seekers and unmanned aerial vehicles remote sensing components to provide a fast scanning capability for pointing, acquisition, tracking, and data communication. The coupling of this requirement with recent developments in the micro-optics area, has led scientists and engineers at the Army Aviation and Missile Command (AMCOM) to consider optical MEMS-based phased arrays, which have potential applications in the commercial industry as well as in the military, as a replacement for gimbals. Laser beam steering in commercial applications such as free space communicataion, scanning display, bar-code reading, and gimbaled seekers; require relatively large monolithic micro-mirrors to accomplish the required optical resolution. The Army will benefit from phased arrays composed of relatively small micro-mirrors that can be actuated through large deflection angles with substantially reduced volume times. The AMCOM Aviation and Missile Research, Development, and Engineering Center (AMRDEC) has initiated a research project to develop MEMS-based phased arrays for use in a small volume, inexpensive Laser Detection and Ranging (LADAR) seeker that is particularly attractive because of its ability to provide large field-of-regard and autonomous target acquisition for reconnaissance mission applications. The primary objective of the collaborative project with the Defence Advanced Research Projects Agency (DARPA) is to develop a rugged, MEMS-based phased arrays for incorporation into the 2-D scanner of a LADAR seeker. Design challenges and approach to achieving performance requirements will be discussed.

  10. Digital Identifier Systems: Comparative Evaluation

    Directory of Open Access Journals (Sweden)

    Hamid Reza Khedmatgozar

    2015-02-01

    Full Text Available Identifier is one of the main elements in identifying an object in digital environment. Digital identifier systems were developed followed by a lot of problems such as violation of persistency and uniqueness of physical identifiers and URL in digital environment. These identifiers try to guarantee uniqueness and persistency of hostnames by using indirect names for Domain Name System (DNS. The main objective of this research is to identify qualified digital identifier system among other systems. To achieve the research objective, researchers have considered two major steps: first, identifying main criteria for distinguishing digital identifier based on literature review and focus group interview; and second, performing a comparative evaluation on common identifier systems in the world. Findings of first step demonstrated seven main criteria in three domains for distinguishing digital identifier systems: identifier uniqueness and persistency in the identifier features domain, digital identification, digital uniqueness, digital persistency and digital actionability in the digital coverage domain, and globality in the comprehensiveness of scope domain. In the second step, results of the comparative evaluation on common identifier systems indicated that six identifier systems, included, DOI, Handle, UCI, URN, ARK and PURL, are appropriate choices for using as a digital identifier system. Also, according to these results, three identification systems Including NBN, MARIAM and ISNI were identified as suitable choices for digital identification in certain specialized fields. According to many benefits of using these identifiers in important applied fields, such as, digital content chains and networks integration, digital right management, cross referencing, digital libraries and citation analysis, results of this study can help digital environment experts to diagnose digital identifier and their effective use in applied fields.

  11. Molecular Occupancy of Nanodot Arrays.

    Science.gov (United States)

    Cai, Haogang; Wolfenson, Haguy; Depoil, David; Dustin, Michael L; Sheetz, Michael P; Wind, Shalom J

    2016-04-26

    Single-molecule nanodot arrays, in which a biomolecule of choice (protein, nucleic acid, etc.) is bound to a metallic nanoparticle on a solid substrate, are becoming an increasingly important tool in the study of biomolecular and cellular interactions. We have developed an on-chip measurement protocol to monitor and control the molecular occupancy of nanodots. Arrays of widely spaced nanodots and nanodot clusters were fabricated on glass surfaces by nanolithography and functionalized with fluorescently labeled proteins. The molecular occupancy was determined by monitoring individual fluorophore bleaching events, while accounting for fluorescence quenching effects. We found that the occupancy can be interpreted as a packing problem, and depends on nanodot size and binding ligand concentration, where the latter is easily adjusted to compensate the flexibility of dimension control in nanofabrication. The results are scalable with nanodot cluster size, extending to large area close packed arrays. As an example, the nanoarray platform was used to probe the geometric requirement of T-cell activation at the single-molecule level. PMID:26966946

  12. High resolution SNP array profiling identifies variability in retinoblastoma genome stability

    NARCIS (Netherlands)

    Mol, Berber M.; Massink, Maarten P. G.; van der Hout, Annemarie H.; Dommering, Charlotte J.; Zaman, Johannes M. A.; Bosscha, Machteld I.; Kors, Wijnanda A.; Meijers-Heijboer, Hanne E.; Kaspers, Gertjan J. L.; te Riele, Hein; Moll, Annette C.; Cloos, Jacqueline; Dorsman, Josephine C.

    2014-01-01

    Both hereditary and nonhereditary retinoblastoma (Rb) are commonly initiated by loss of both copies of the retinoblastoma tumor suppressor gene (RB1), while additional genomic changes are required for tumor initiation and progression. Our aim was to determine whether there is genomic heterogeneity b

  13. An in vivo platform for identifying inhibitors of protein aggregation

    OpenAIRE

    Saunders, JC; Young, LM; Mahood, RA; Jackson, MP; Revill, CH; Foster, RJ; Smith, DA; Ashcroft, AE; Brockwell, DJ; Radford, SE

    2016-01-01

    Protein aggregation underlies an array of human diseases, yet only one small molecule therapeutic has been successfully developed to date. Here, we introduce an in vivo system, based on a β-lactamase tripartite fusion construct, capable of identifying aggregation-prone sequences in the periplasm of Escherichia coli and inhibitors that prevent their aberrant self-assembly. We demonstrate the power of the system using a range of proteins, from small unstructured peptides (islet amyloid polypept...

  14. Measured Aperture-Array Noise Temperature of the Mark II Phased Array Feed for ASKAP

    CERN Document Server

    Chippendale, A P; Beresford, R J; Hampson, G A; Shaw, R D; Hayman, D B; Macleod, A; Forsyth, A R; Hay, S G; Leach, M; Cantrall, C; Brothers, M L; Hotan, A W

    2015-01-01

    We have measured the aperture-array noise temperature of the first Mk. II phased array feed that CSIRO has built for the Australian Square Kilometre Array Pathfinder telescope. As an aperture array, the Mk. II phased array feed achieves a beam equivalent noise temperature less than 40 K from 0.78 GHz to 1.7 GHz and less than 50 K from 0.7 GHz to 1.8 GHz for a boresight beam directed at the zenith. We believe these are the lowest reported noise temperatures over these frequency ranges for ambient-temperature phased arrays. The measured noise temperature includes receiver electronics noise, ohmic losses in the array, and stray radiation from sidelobes illuminating the sky and ground away from the desired field of view. This phased array feed was designed for the Australian Square Kilometre Array Pathfinder to demonstrate fast astronomical surveys with a wide field of view for the Square Kilometre Array.

  15. A novel algorithm for automatic arrays detection in a layout

    Science.gov (United States)

    Shafee, Marwah; Park, Jea-Woo; Aslyan, Ara; Torres, Andres; Madkour, Kareem; ElManhawy, Wael

    2013-03-01

    Integrated circuits suffer from serious layout printability issues associated to the lithography manufacturing process. Regular layout designs are emerging as alternative solutions to help reducing these systematic sub-wavelength lithography variations. From CAD point of view, regular layouts can be treated as repeated patterns that are arranged in arrays. In most modern mask synthesis and verification tools, cell based hierarchical processing has been able to identify repeating cells by analyzing the design's cell placement; however, there are some routing levels which are not inside the cell and yet they create an array-like structure because of the underlying topologies which could be exploited by detecting repeated patterns in layout thus reducing simulation run-time by simulating only the representing cells and then restore all the simulation results in their corresponding arrays. The challenge is to make the array detection and restoration of the results a very lightweight operation to fully realize the benefits of the approach. A novel methodology for detecting repeated patterns in a layout is proposed. The main idea is based on translating the layout patterns into string of symbols and construct a "Symbolic Layout". By finding repetitions in the symbolic layout, repeated patterns in the drawn layout are detected. A flow for layout reduction based on arrays-detection followed by pattern-matching is discussed. Run time saving comes from doing all litho simulations on the base-patterns only. The pattern matching is then used to restore all the simulation results over the arrays. The proposed flow shows 1.4x to 2x run time enhancement over the regular litho simulation flow. An evaluation for the proposed flow in terms of coverage and run-time is drafted.

  16. Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

    Energy Technology Data Exchange (ETDEWEB)

    Apel, William A.; Thompson, Vicki S; Lacey, Jeffrey A.; Gentillon, Cynthia A.

    2016-08-09

    A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

  17. The Colorado Lightning Mapping Array

    Science.gov (United States)

    Rison, W.; Krehbiel, P. R.; Thomas, R. J.; Rodeheffer, D.; Fuchs, B.

    2012-12-01

    A fifteen station Lightning Mapping Array (LMA) was installed in northern Colorado in the spring of 2012. While the driving force for the array was to produce 3-dimensional lightning data to support the Deep Convective Clouds and Chemistry (DC3) Experiment (Barth, this conference), data from the array are being used for several other projects. These include: electrification studies in conjunction with the CSU CHILL radar (Lang et al, this conference); observations of the parent lightning discharges of sprites (Lyons et al, this conference); trying to detect upward discharges triggered by wind turbines, characterizing conditions in which aircraft flying through clouds produce discharges which can be detected by the LMA, and other opportunities, such as observations of lightning in pyrocumulus clouds produced by the High Park Fire west of Fort Collins, CO. All the COLMA stations are solar-powered, and use broadband cellular modems for data communications. This makes the stations completely self-contained and autonomous, allowing a station to be installed anywhere a cellular signal is available. Because most of the stations were installed well away from anthropogenic noise sources, the COLMA is very sensitive. This is evidenced by the numerous plane tracks detected in its the vicinity. The diameter, D, of the COLMA is about 100 km, significantly larger than other LMAs. Because the error in the radial distance r is proportional to (r/D)2, and the error in the altitude z is proportional to (z/D)2, the larger array diameter greatly expands the usable range of the COLMA. The COLMA is able to detect and characterize lighting flashes to a distance of about 350 km from the array center. In addition to a web-based display (lightning.nmt.edu/colma), geo-referenced images are produced and updated at one-minute intervals. These geo-referenced images can be used to overlay the real-time lightning data on Google Earth and other mapping software. These displays were used by the DC3

  18. Acoustic array systems theory, implementation, and application

    CERN Document Server

    Bai, Mingsian R; Benesty, Jacob

    2013-01-01

    Presents a unified framework of far-field and near-field array techniques for noise source identification and sound field visualization, from theory to application. Acoustic Array Systems: Theory, Implementation, and Application provides an overview of microphone array technology with applications in noise source identification and sound field visualization. In the comprehensive treatment of microphone arrays, the topics covered include an introduction to the theory, far-field and near-field array signal processing algorithms, practical implementations, and common applic

  19. Precise annealing of focal plane arrays for optical detection

    Science.gov (United States)

    Bender, Daniel A.

    2015-09-22

    Precise annealing of identified defective regions of a Focal Plane Array ("FPA") (e.g., exclusive of non-defective regions of the FPA) facilitates removal of defects from an FPA that has been hybridized and/or packaged with readout electronics. Radiation is optionally applied under operating conditions, such as under cryogenic temperatures, such that performance of an FPA can be evaluated before, during, and after annealing without requiring thermal cycling.

  20. Iso-array rewriting P systems with context-free iso-array rules

    OpenAIRE

    Bhuvaneswari, K; Kalyani, T.; Thomas, D G; Nagar, A. K.; Thamburaj, R.

    2014-01-01

    A new computing model called P system is a highly distributed and parallel theoretical model, which is proposed in the area of membrane computing. Ceterchi et al. initially proposed array rewriting P systems by extending the notion of string rewriting P systems to arrays (2003). A theoretical model for picture generation using context-free iso-array grammar rules and puzzle iso-array grammar rules are introduced by Kalyani et al. (2004, 2006). Also iso-array rewriting P...