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A High-Performing and Cost-Effective SNP Genotyping Method Using rhPCR and Universal Reporters  [PDF]
Kristin Beltz, Daniel Tsang, Junzhou Wang, Scott Rose, Yun Bao, Yu Wang, Katelyn Larkin, Susan Rupp, Daniela Schrepfer, Krishnalekha Datta, Keith Gunderson, Chris Sailor, Scott Hansen, Joseph Dobosy, Lynette Lewis, Aurita Menezes, Joseph Walder, Mark Behlke, Caifu Chen
Advances in Bioscience and Biotechnology (ABB) , 2018, DOI: 10.4236/abb.2018.99034
Abstract: We have developed a novel dual enzyme chemistry called rhAmp® SNP genotyping based on RNase H2-dependent PCR (rhPCR) that provides high signal and specificity for SNP analysis. rhAmp SNP genotyping combines a unique two-enzyme system with 3’ end blocked DNA-RNA hybrid primers to interrogate SNP loci. Activation of the blocked primers occurs upon hybridization to its perfectly matched target, which eliminates or greatly reduces primer dimers. A thermostable hot-start RNase H2 cleaves the primer immediately 5’ of the ribose sugar, releasing the blocking group and allowing primer extension. PCR specificity is further improved with the use of a mutant Taq DNA polymerase, resulting in improved allelic discrimination. Signal generation is obtained using a universal reporter system which requires only two reporter probes for any bi-allelic SNP. 1000 randomly selected SNPs were chosen to validate the 95% design rate of the design pipeline. A subsampling of 130 human SNP targets was tested and achieved a 98% call rate, and 99% call accuracy. rhAmp SNP genotyping assays are compatible with various qPCR instruments including QuantStudioTM 7 Flex, CFX384TM, IntelliQube®, and Biomark HDTM. In comparison to TaqMan®, rhAmp SNP genotyping assays show higher signal (Rn) and greater cluster separation, resulting in more reliable SNP genotyping performance. The rhAmp SNP genotyping solution is suited for high-throughput SNP genotyping applications in humans and plants.
Single-Walled Carbon Nanotube (SWCNT)-induced interstitial fibrosis in the lungs of rats is associated with increased levels of PDGF mRNA and the formation of unique intercellular carbon structures that bridge alveolar macrophages In Situ
James B Mangum, Elizabeth A Turpin, Aurita Antao-Menezes, Mark F Cesta, Edilberto Bermudez, James C Bonner
Particle and Fibre Toxicology , 2006, DOI: 10.1186/1743-8977-3-15
Abstract: SWCNT or CB caused no overt inflammatory response at 1 or 21 days post-exposure as determined by histopathology and evaluation of cells (>95% macrophages) in bronchoalveolar lavage (BAL) fluid. However, SWCNT induced the formation of small, focal interstitial fibrotic lesions within the alveolar region of the lung at 21 days. A small fraction of alveolar macrophages harvested by BAL from the lungs of SWCNT-exposed rats at 21 days were bridged by unique intercellular carbon structures that extended into the cytoplasm of each macrophage. These "carbon bridge" structures between macrophages were also observed in situ in the lungs of SWCNT-exposed rats. No carbon bridges were observed in CB-exposed rats. SWCNT caused cell proliferation only at sites of fibrotic lesion formation as measured by bromodeoxyuridine uptake into alveolar cells. SWCNT increased platelet-derived growth factor (PDGF)-A, PDGF-B, and PDGF-C mRNA levels significantly at 1 day as measured by Taqman quantitative real-time RT-PCR. At 21 days, SWCNT did not increase any mRNAs evaluated, while V2O5 significantly increased mRNAs encoding PDGF-A, -B, and -C chains, PDGF-Rα, osteopontin (OPN), connective tissue growth factor (CTGF), and transforming growth factor (TGF)-β1.Our findings indicate that SWCNT do not cause lung inflammation and yet induce the formation of small, focal interstital fibrotic lesioins in the alveolar region of the lungs of rats. Of greatest interest was the discovery of unique intercellular carbon structures composed of SWCNT that bridged lung macrophages. These "carbon bridges" offer a novel and easily identifiable biomarker of exposure.The commercial interest in single walled carbon nanotubes (SWCNT) is rapidly increasing due to their superior mechanical, electric and thermal properties [1]. With the development of mass production and handling facilities for SWCNT, it is critical to fully understand the risk associated with exposure since it is likely that increasing human exposure
Respiratory syncytial virus infection reduces lung inflammation and fibrosis in mice exposed to vanadium pentoxide
Elizabeth A Turpin, Aurita Antao-Menezes, Mark F Cesta, James B Mangum, Duncan G Wallace, Edilberto Bermudez, James C Bonner
Respiratory Research , 2010, DOI: 10.1186/1465-9921-11-20
Abstract: In this study we investigated the effect of RSV pre- or post-exposure to V2O5 in male AKR mice. Mice were pre-exposed by intranasal aspiration to RSV or media vehicle prior to intranasal aspiration of V2O5 or saline vehicle at day 1 or day 7. A parallel group of mice were treated first with V2O5 or saline vehicle at day 1 and day 7 then post-exposed to RSV or media vehicle at day 8.V2O5-induced airway inflammation and fibrosis were decreased by RSV pre- or post-exposure. Real time quantitative RT-PCR showed that V2O5 significantly increased lung mRNAs encoding pro-fibrogenic growth factors (TGF-β1, CTGF, PDGF-C) and collagen (Col1A2), but also increased mRNAs encoding anti-fibrogenic type I interferons (IFN-α, -β) and IFN-inducible chemokines (CXCL9 and CXCL10). RSV pre- or post-exposure caused a significantly reduced mRNAs of pro-fibrogenic growth factors and collagen, yet reduced RNA levels of anti-fibrogenic interferons and CXC chemokines.Collectively these data suggest that RSV infection reduces the severity of V2O5-induced fibrosis by suppressing growth factors and collagen genes. However, RSV suppression of V2O5-induced IFNs and IFN-inducible chemokines suggests that viral infection also suppresses the innate immune response that normally serves to resolve V2O5-induced fibrosis.A variety of metal oxides cause occupational lung diseases referred to as pneumoconioses. Vanadium is a transition metal commonly found in various types of ores, coals, and oil [1]. Vanadium pentoxide (V2O5), the most common form of vanadium, is the primary form found in industrial exposure situations [2]. In addition, atmospheric emissions released from power plants that burn coal and oil contribute ~64,000 metric tons of vanadium into the atmosphere each year [2]. Occupational exposure to V2O5 dust is common in coal-burning power plants and individuals exposed to inhaled V2O5-containing fly ash suffer from chronic bronchitis and reduced lung function [3,4]. The consequences of environ
Genomic analysis of human lung fibroblasts exposed to vanadium pentoxide to identify candidate genes for occupational bronchitis
Jennifer L Ingram, Aurita Antao-Menezes, Elizabeth A Turpin, Duncan G Wallace, James B Mangum, Linda J Pluta, Russell S Thomas, James C Bonner
Respiratory Research , 2007, DOI: 10.1186/1465-9921-8-34
Abstract: Normal human lung fibroblasts were exposed to V2O5 in a time course experiment. Gene expression was measured at various time points over a 24 hr period using the Affymetrix Human Genome U133A 2.0 Array. Selected genes that were significantly changed in the microarray experiment were validated by RT-PCR.V2O5 altered more than 1,400 genes, of which ~300 were induced while >1,100 genes were suppressed. Gene ontology categories (GO) categories unique to induced genes included inflammatory response and immune response, while GO catogories unique to suppressed genes included ubiquitin cycle and cell cycle. A dozen genes were validated by RT-PCR, including growth factors (HBEGF, VEGF, CTGF), chemokines (IL8, CXCL9, CXCL10), oxidative stress response genes (SOD2, PIPOX, OXR1), and DNA-binding proteins (GAS1, STAT1).Our study identified a variety of genes that could play pivotal roles in inflammation, fibrosis and repair during V2O5-induced bronchitis. The induction of genes that mediate inflammation and immune responses, as well as suppression of genes involved in growth arrest appear to be important to the lung fibrotic reaction to V2O5.Occupational exposure to vanadium pentoxide (V2O5) has been associated with an increased incidence of chronic obstructive airway disease and a reduction in lung function [1]. V2O5 is the most common commercial form of vanadium and is the primary form found in industrial exposure situations [2]. Occupational exposure to V2O5 occurs during the cleaning of oil-fired boilers and furnaces, during handling of catalysts in chemical plants, and during the refining, processing, and burning of vanadium-rich fossil fuels [3].We previously reported that V2O5 causes airway disease in rats that is similar to the pathology of asthma and bronchitis in humans [4]. These pathologic changes include mucous cell hyperplasia, increased airway smooth muscle mass, and peribronchiolar fibrosis. Lung fibroblasts are thought to play a major role in V2O5-induced airwa
Second Language Acquisition: Reconciling Theories  [PDF]
Vera Menezes
Open Journal of Applied Sciences (OJAppS) , 2013, DOI: 10.4236/ojapps.2013.37050

This article argues that previous attempts to explain SLA should not be disregarded. Instead, when they are put together, they provide a broader and deeper view of the acquisition process. There is evidence to support the claim that second language acquisition (SLA) is a complex adaptive system due to its inherent ability to adapt to different conditions present in both internal and external environments. Based on this understanding, widely discussed second language theories, including behaviorism, will be treated as explanations of parts of a whole, since each captures a different aspect of SLA. In order to justify this assumption, excerpts from some English language learning histories are provided to exemplify how learners describe their learning processes. The final claim is that SLA should be seen as a chaotic/complex system.

Contribui??o ao conhecimento dos algas do gênero Euglena (Euglenophyceae) no município do Rio de Janeiro e arredores, Brasil
Menezes, Mariangela;
Acta Botanica Brasilica , 1989, DOI: 10.1590/S0102-33061989000100003
Abstract: a taxonomical survey was first carried out at a floristic inventory of the pigmented euglena ehr. (euglenophyceae), based on the analisys of near 150 samples, collected from august 1980 to november 1982 at accessible bodies of water of the municipality of rio de janeiro and surroundings, brazil. of the samples collected, 68 contained specimens of pigmented euglenoids, of these 36 showed repiesentatives of euglena. seventeen taxa were identified and distributed in 14 species and 3 varieties, of which 8 have already been identified for the state of rio de janeiro, being the others for the first time recorded in the area. euglena agilis h. j. cart, was the best represented taxon in number of samples studied, which occured in 22% of the 36 samples analized. each taxon was described in detail, measured, illustrated and commented on the bases of vegetative morphology in living material and whenever possible studied from population samples. information on geographic distribution of the 17 taxa in the state of rio de janeiro was provided, as well a indented artificial key for the recognition of species and varieties identified. forty eight illustrations, a map of the state and another of the municipality to show the collecting sites, complement the text.
A pra?a do Martim Moniz: etnografando lógicas socioculturais de inscri??o da pra?a no mapa social de Lisboa
Menezes, Marluci;
Horizontes Antropológicos , 2009, DOI: 10.1590/S0104-71832009000200013
Abstract: departing from the ethnography of use/appropriation episodes of martim moniz plaza, this paper discuss about the importance of the ethnographical practice in the apprehension and understanding of the everyday circumstances. some social/cultural aspects are discussed which contributed to the invention of a geography of resistance in this specific area of the city and also to the inscription of this plaza in the social and urban map of lisbon. four motives have oriented this reasoning: 1) the geographic situation of that plaza (at lisbon's centre); 2) it's building configuration as a result of a set of controversial social and urban policies; 3) the representativeness of this specific plaza - namely, of two shopping malls that arise, at the plaza, as symbolic meeting points - in an attempt to construct a multi-ethnic and a multi-cultural image of the city; 4) the role of this plaza regarding the definition of a set of political manifestations.
Major Reis e a constitui??o visual do Brasil enquanto na??o
Menezes, Paulo;
Horizontes Antropológicos , 2008, DOI: 10.1590/S0104-71832008000100010
Abstract: this article analyses the movie ao redor do brasil, from thomaz reis, taking as theoretical main references paulo arantes's, 'o sentido da forma??o', and foucault's 'a ordem do discurso'. in this direction, it interprets the movie as a speech immersed in the debates of its time related to the constitution of brazil as a nation, which was frequent in everyday life and an important intellectual issue in the 20's ans 30's last century. in parallel do what was being discussed in literature and plastic arts, the movie is carefully assembled, using several scenes from reis's previous movies to visually denote a nation, not in its way to consolidate itself, but with a countryside already pacified, which would give it a label of civility, therefore inserting it in the civilizing process and, at the same time, with definitive frontiers secured by the presence of a institutions characteristic of the modern state: schools, policy, army and others (an image very different from what could be effectively verified at that time).
Do espa?o ao lugar: do lugar às remodela??es sócio-espaciais
Menezes, Marluci;
Horizontes Antropológicos , 2000, DOI: 10.1590/S0104-71832000000100008
Abstract: considering the undertaken that the objectivity and visibility of the space are possible through the study of the "place", boarding some perspectives of theoretical and empirical scope that, in the continuation of the inquiry in urban contexts, have allowed me to reflect on the processes of maintenance and transformation. i use as parameter maker of this reflection the idea of "remodeling", for understanding that this allows to understand the social and spatial dynamics as processes of (re)creation or constant invention of the space-habitat, of the forms to inhabit and of the forms to think the habitat.
Vaccination of Callithrix jacchus (Linné, 1758) marmosets with the PF strain of Trypanosoma cruzi
Menezes, Humberto;
Memórias do Instituto Oswaldo Cruz , 1981, DOI: 10.1590/S0074-02761981000200004
Abstract: callithrix jacchus marmosets, vaccinated more than once with high doses of the pf strain of trypanosoma cruzi, showed a certain degree of parasitemia related to the number of parasites injected. thirty days after vaccination, all animals were alive and showed no apparent morbid symptoms. the relationship between the dose of injected trypanosomes and the observed parasitemias is discussed and analysed as well as the immunologic incompetence of the experimental animals used.
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